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Conserved domains on  [gi|552953687|ref|NP_001272802|]
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tripartite motif-containing protein 3 isoform b [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NHL_TRIM2_like cd14960
NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; ...
 471-695 1.87e-168

NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L levels in axons and subsequent axonopathy. TRIM2 is also involved in regulating axon outgrowth during development; it contains RING and BBOX domains, the NHL repeat domain is located at its C-terminus. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


:

Pssm-ID: 271330 [Multi-domain]  Cd Length: 274  Bit Score: 484.16  E-value: 1.87e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 471 ELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVA 550
Cdd:cd14960    1 DLIFRIGTKGRNKGEFTNLQGVAASSSGRLVIADSNNQCVQVFSNDGQFKLRFGVRGRSPGQLQRPTGVAVTLNGDIIIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 551 DYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAV 630
Cdd:cd14960   81 DYDNKWVSIFSPDGKFKSKIGAGKLMGPKGVAVDRNGHIIVVDNKACCVFIFQPNGKLVTRFGSRGNGDRQFAGPHFAAV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 552953687 631 NNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14960  161 NNNNEIIVTDFHNHSVKVFNAEGEFLFKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 225
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
 158-284 7.18e-38

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


:

Pssm-ID: 128778  Cd Length: 127  Bit Score: 137.01  E-value: 7.18e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   158 HKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKVLQTQ 237
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 552953687   238 LDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRERLAALAAQ 284
Cdd:smart00502  81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
 16-63 9.50e-31

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


:

Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 114.33  E-value: 9.50e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  16 DKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16768    1 DKQFLVCSICLDRYHNPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 48
Bbox_SF super family cl00034
B-box-type zinc finger superfamily; The B-box-type zinc finger is a short zinc binding domain ...
 107-153 1.75e-28

B-box-type zinc finger superfamily; The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2).


The actual alignment was detected with superfamily member cd19825:

Pssm-ID: 469587 [Multi-domain]  Cd Length: 47  Bit Score: 107.79  E-value: 1.75e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687 107 AVAGRPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRD 153
Cdd:cd19825    1 AVAGKPLSCPNHEGKTMEFYCESCETAMCRECTEGEHREHVTVPLRD 47
IG_FLMN smart00557
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 322-419 2.37e-25

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


:

Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 100.37  E-value: 2.37e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   322 AHETVATGEGLRQALVGQPASLTVTTKDKdgrlvrtGSAELCAEITGPDGVRLAVPVVDHKNGTYELVYTARTEGDLLLS 401
Cdd:smart00557   1 ASKVKASGPGLEKGVVGEPAEFTVDTRDA-------GGGELEVEVTGPSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVT 73

                           90
                   ....*....|....*...
gi 552953687   402 VLLYGQPVRGSPFRVRAL 419
Cdd:smart00557  74 VKFGGEHIPGSPFTVKVG 91
 
Name Accession Description Interval E-value
NHL_TRIM2_like cd14960
NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; ...
 471-695 1.87e-168

NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L levels in axons and subsequent axonopathy. TRIM2 is also involved in regulating axon outgrowth during development; it contains RING and BBOX domains, the NHL repeat domain is located at its C-terminus. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271330 [Multi-domain]  Cd Length: 274  Bit Score: 484.16  E-value: 1.87e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 471 ELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVA 550
Cdd:cd14960    1 DLIFRIGTKGRNKGEFTNLQGVAASSSGRLVIADSNNQCVQVFSNDGQFKLRFGVRGRSPGQLQRPTGVAVTLNGDIIIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 551 DYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAV 630
Cdd:cd14960   81 DYDNKWVSIFSPDGKFKSKIGAGKLMGPKGVAVDRNGHIIVVDNKACCVFIFQPNGKLVTRFGSRGNGDRQFAGPHFAAV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 552953687 631 NNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14960  161 NNNNEIIVTDFHNHSVKVFNAEGEFLFKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 225
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
 158-284 7.18e-38

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 137.01  E-value: 7.18e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   158 HKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKVLQTQ 237
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 552953687   238 LDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRERLAALAAQ 284
Cdd:smart00502  81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
CC_brat-like cd20482
coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...
 158-278 3.23e-37

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.


Pssm-ID: 467844 [Multi-domain]  Cd Length: 122  Bit Score: 134.97  E-value: 3.23e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 158 HKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKVLQTQ 237
Cdd:cd20482    1 HKESLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLNEQ 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 552953687 238 LDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRERL 278
Cdd:cd20482   81 QQKLQETIEKIQQGCEFTERLLKHGSETEVLLFKKLLEARL 121
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
 16-63 9.50e-31

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 114.33  E-value: 9.50e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  16 DKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16768    1 DKQFLVCSICLDRYHNPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 48
Bbox2_TRIM3_C-VII cd19825
B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
 107-153 1.75e-28

B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in neuroblastoma. It binds to the ck inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclins D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It corresponds to gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of presynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendrite spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380883 [Multi-domain]  Cd Length: 47  Bit Score: 107.79  E-value: 1.75e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687 107 AVAGRPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRD 153
Cdd:cd19825    1 AVAGKPLSCPNHEGKTMEFYCESCETAMCRECTEGEHREHVTVPLRD 47
IG_FLMN smart00557
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 322-419 2.37e-25

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 100.37  E-value: 2.37e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   322 AHETVATGEGLRQALVGQPASLTVTTKDKdgrlvrtGSAELCAEITGPDGVRLAVPVVDHKNGTYELVYTARTEGDLLLS 401
Cdd:smart00557   1 ASKVKASGPGLEKGVVGEPAEFTVDTRDA-------GGGELEVEVTGPSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVT 73

                           90
                   ....*....|....*...
gi 552953687   402 VLLYGQPVRGSPFRVRAL 419
Cdd:smart00557  74 VKFGGEHIPGSPFTVKVG 91
Filamin pfam00630
Filamin/ABP280 repeat;
322-415 3.31e-23

Filamin/ABP280 repeat;


Pssm-ID: 395505  Cd Length: 89  Bit Score: 94.28  E-value: 3.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  322 AHETVATGEGLRQALVGQPASLTVTTKDKDGrlvrtgsaELCAEITGPDGVRLAVPVVDHKNGTYELVYTARTEGDLLLS 401
Cdd:pfam00630   4 ASKVKASGPGLEPGVVGKPAEFTVDTRDAGG--------EGEVEVTGPDGSPVPVEVTDNGDGTYTVSYTPTEPGDYTVS 75

                          90
                  ....*....|....
gi 552953687  402 VLLYGQPVRGSPFR 415
Cdd:pfam00630  76 VKFNGQHIPGSPFK 89
Vgb COG4257
Streptogramin lyase [Defense mechanisms];
484-693 7.50e-23

Streptogramin lyase [Defense mechanisms];


Pssm-ID: 443399 [Multi-domain]  Cd Length: 270  Bit Score: 98.94  E-value: 7.50e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 484 GEFTNLQGVSAASSGRIVVADSNNQCIQVFS-NEGQFKfrfgvrGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSP 562
Cdd:COG4257   14 APGSGPRDVAVDPDGAVWFTDQGGGRIGRLDpATGEFT------EYPLGGGSGPHGIAVDPDGNLWFTDNGNNRIGRIDP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 563 -EGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNksccvftfqpNGKLVGRF-GGRGATDRHF-----AGPHFVAVNNKNE 635
Cdd:COG4257   88 kTGEITTFALPGGGSNPHGIAFDPDGNLWFTDQ----------GGNRIGRLdPATGEVTEFPlptggAGPYGIAVDPDGN 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 636 IVVTDFHNHSVKVYSADGEFLFKFgshgEGNGQFNAPTGVAVDSNGNIIVADWGNSRI 693
Cdd:COG4257  158 LWVTDFGANAIGRIDPDTGTLTEY----ALPTPGAGPRGLAVDPDGNLWVADTGSGRI 211
BBOX smart00336
B-Box-type zinc finger;
110-151 7.33e-13

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 63.13  E-value: 7.33e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 552953687   110 GRPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLL 151
Cdd:smart00336   1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 22-62 3.47e-10

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 55.59  E-value: 3.47e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 552953687    22 CSICLDRY-RCPKVLPCLHTFCERCLQNYIppQSLTLSCPVC 62
Cdd:smart00184   1 CPICLEEYlKDPVILPCGHTFCRSCIRKWL--ESGNNTCPIC 40
zf-B_box pfam00643
B-box zinc finger;
115-151 8.30e-10

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 54.40  E-value: 8.30e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 552953687  115 CPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLL 151
Cdd:pfam00643   6 CPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
 22-60 4.99e-09

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 52.02  E-value: 4.99e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 552953687   22 CSICLDRYRCPkVLPCLHTFCERCLQNYIPPQSLTLSCP 60
Cdd:pfam13445   1 CPICLELFTDP-VLPCGHTFCRECLEEMSQKKGGKFKCP 38
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
 6-88 5.26e-09

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 58.86  E-value: 5.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687    6 DSPGPEVQPMDkQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRqtsiLPEQGvSALQNNFFISSL 85
Cdd:TIGR00599  14 TTPIPSLYPLD-TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP---KCPLCR----AEDQE-SKLRSNWLVSEI 84


                  ...
gi 552953687   86 MEA 88
Cdd:TIGR00599  85 VES 87
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
10-88 5.97e-07

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 52.40  E-value: 5.97e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552953687  10 PEVQPMDkQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLtlsCPVCRQtsilPEQgVSALQNNFFISSLMEA 88
Cdd:COG5432   17 PSLKGLD-SMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF---CPVCRE----DPC-ESRLRGSSGSREINES 86
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
157-320 8.59e-07

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 52.46  E-value: 8.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 157 QHKAALQRQLEAVRGRLPQLSAAIALVggisQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKvLQT 236
Cdd:COG4717  132 QELEALEAELAELPERLEELEERLEEL----RELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEE-LQQ 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 237 QLDTLRQGQEHIGSSCSFAEQALRlgsAPEVLLVRKHMRERLAALAAQAFPerphENAQLELVLEVDGLRRSVLNLGALL 316
Cdd:COG4717  207 RLAELEEELEEAQEELEELEEELE---QLENELEAAALEERLKEARLLLLI----AAALLALLGLGGSLLSLILTIAGVL 279


                 ....
gi 552953687 317 TTSA 320
Cdd:COG4717  280 FLVL 283
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 669-696 1.04e-06

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 45.47  E-value: 1.04e-06
                          10        20
                  ....*....|....*....|....*...
gi 552953687  669 FNAPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 153-312 4.03e-05

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 47.09  E-value: 4.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   153 DVVEQHkAALQRQLEAVRGRLPQ----LSAAIALV---GGISQQLQERKAEALAQISAAFEDLEQALQQRKQA------L 219
Cdd:pfam01576  219 DLQEQI-AELQAQIAELRAQLAKkeeeLQAALARLeeeTAQKNNALKKIRELEAQISELQEDLESERAARNKAekqrrdL 297

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   220 VSDLESicgakqkvLQTQL-DTLrqgqehigsSCSFAEQALRLGSAPEVLLVRKHMRERLAALAAQAFPERPHENAQL-E 297
Cdd:pfam01576  298 GEELEA--------LKTELeDTL---------DTTAAQQELRSKREQEVTELKKALEEETRSHEAQLQEMRQKHTQALeE 360

                          170
                   ....*....|....*
gi 552953687   298 LVLEVDGLRRSVLNL 312
Cdd:pfam01576  361 LTEQLEQAKRNKANL 375
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 142-261 4.99e-04

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 43.42  E-value: 4.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   142 EHREHGTVLLRD----VVEQHKAALQRQLEAVRGRLPQLSAAIAlvggisQQLQERKAEALAQISAAfedleQALQQRKQ 217
Cdd:TIGR00618  405 LQREQATIDTRTsafrDLQGQLAHAKKQQELQQRYAELCAAAIT------CTAQCEKLEKIHLQESA-----QSLKEREQ 473

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 552953687   218 ALvSDLESICgakQKVLQTQLDTLRQGQEHIGSSCSFAEQALRL 261
Cdd:TIGR00618  474 QL-QTKEQIH---LQETRKKAVVLARLLELQEEPCPLCGSCIHP 513
PLN02919 PLN02919
haloacid dehalogenase-like hydrolase family protein
 611-690 7.07e-04

haloacid dehalogenase-like hydrolase family protein


Pssm-ID: 215497 [Multi-domain]  Cd Length: 1057  Bit Score: 42.92  E-value: 7.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  611 RFGGRGATDRhFAGPHFVAVNNKNEIVVTDFhnhsvkvysaDGEFLFKFGSHGE--------GNGQFNAPTGVAVDSNGN 682
Cdd:PLN02919  568 KFPGKLAIDL-LNNRLFISDSNHNRIVVTDL----------DGNFIVQIGSTGEeglrdgsfEDATFNRPQGLAYNAKKN 636


                  ....*....
gi 552953687  683 II-VADWGN 690
Cdd:PLN02919  637 LLyVADTEN 645
PRK08268 PRK08268
3-hydroxy-acyl-CoA dehydrogenase; Validated
 148-229 4.44e-03

3-hydroxy-acyl-CoA dehydrogenase; Validated


Pssm-ID: 236211 [Multi-domain]  Cd Length: 507  Bit Score: 40.22  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 148 TVLLRDV----VEQHKAALQRQLE--AVRGRLPQlSAAIALVGGIS--QQLQERKAEALAqISAAFEDLEQalqqrKQAL 219
Cdd:PRK08268  32 TVLLYDAragaAAAARDGIAARLAklVEKGKLTA-EQADAALARLRpvEALADLADCDLV-VEAIVERLDV-----KQAL 104

                         90
                 ....*....|
gi 552953687 220 VSDLESICGA 229
Cdd:PRK08268 105 FAQLEAIVSP 114
 
Name Accession Description Interval E-value
NHL_TRIM2_like cd14960
NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; ...
 471-695 1.87e-168

NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L levels in axons and subsequent axonopathy. TRIM2 is also involved in regulating axon outgrowth during development; it contains RING and BBOX domains, the NHL repeat domain is located at its C-terminus. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271330 [Multi-domain]  Cd Length: 274  Bit Score: 484.16  E-value: 1.87e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 471 ELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVA 550
Cdd:cd14960    1 DLIFRIGTKGRNKGEFTNLQGVAASSSGRLVIADSNNQCVQVFSNDGQFKLRFGVRGRSPGQLQRPTGVAVTLNGDIIIA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 551 DYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAV 630
Cdd:cd14960   81 DYDNKWVSIFSPDGKFKSKIGAGKLMGPKGVAVDRNGHIIVVDNKACCVFIFQPNGKLVTRFGSRGNGDRQFAGPHFAAV 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 552953687 631 NNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14960  161 NNNNEIIVTDFHNHSVKVFNAEGEFLFKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 225
NHL cd05819
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ...
 480-696 4.32e-86

NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats.


Pssm-ID: 271320 [Multi-domain]  Cd Length: 269  Bit Score: 272.27  E-value: 4.32e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 480 GREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSI 559
Cdd:cd05819    1 GTGPGELNNPQGIAVDSSGNIYVADTGNNRIQVFDPDGNFITSFGSFGSGDGQFNEPAGVAVDSDGNLYVADTGNHRIQK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 560 FSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKN 634
Cdd:cd05819   81 FDPDGNFLASFGgsgdgDGEFNGPRGIAVDSSGNIYVADTGNHRIQKFDPDGEFLTTFGSGGSGPGQFNGPTGVAVDSDG 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 552953687 635 EIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:cd05819  161 NIYVADTGNHRIQVFDPDGNFLTTFGSTGTGPGQFNYPTGIAVDSDGNIYVADSGNNRVQVF 222
NHL_TRIM71_like cd14954
NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; ...
 472-708 1.73e-82

NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271324 [Multi-domain]  Cd Length: 285  Bit Score: 263.25  E-value: 1.73e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 LVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVAD 551
Cdd:cd14954    9 PLLSFGKEGSKDGELCRPWGVAVDKDGRIIVADRSNNRVQVFDPDGKFLRKFGSYGSRDGQFDRPAGVAVNSRGRIIVAD 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 552 YDNRWVSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPH 626
Cdd:cd14954   89 KDNHRIQVFDLNGRFLLKFGergtkNGQFNYPWGVAVDSEGRIYVSDTRNHRVQVFDSDGQFIRKFGFEGAGPGQLDSPR 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 627 FVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVWRMESprSRCW 706
Cdd:cd14954  169 GVAVNPDGNIVVSDFNNHRLQVFDPDGQFLRFFGSEGSGNGQFKRPRGVAVDDEGNIIVADSGNHRVQVFSPDG--EFLC 246


                 ..
gi 552953687 707 CF 708
Cdd:cd14954  247 SF 248
NHL_like_4 cd14955
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 477-694 5.65e-69

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271325 [Multi-domain]  Cd Length: 279  Bit Score: 227.46  E-value: 5.65e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14955    6 GSYGSGDGQFNSPSGIAVDSAGNVYVADTGNNRIQKFDSTGTFLTKWGSSGSGDGQFYSPTGIAVDSDGNVYVADTGNHR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 557 VSIFSPEGKFKTK-----IGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVN 631
Cdd:cd14955   86 IQKFDSTGTFLTKwgssgSGDGQFNSPSGIAVDSAGNVYVTDSGNNRIQKFDSSGTFITKWGSFGSGDGQFNSPTGIAVD 165

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 552953687 632 NKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQ 694
Cdd:cd14955  166 SAGNVYVADTGNNRIQKFTSTGTFLTKWGSEGSGDGQFNAPYGIAVDSAGNVYVADTGNNRIQ 228
NHL_like_2 cd14957
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 474-696 1.38e-66

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271327 [Multi-domain]  Cd Length: 280  Bit Score: 220.99  E-value: 1.38e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 474 FRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYD 553
Cdd:cd14957    5 YAFGSNGSGNGQFNTPRGIAVDSAGNIYVADTGNNRIQVFTSSGVYSYSIGSGGTGSGQFNSPYGIAVDSNGNIYVADTD 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 554 NRWVSIFSPEGKFKTKIGA-----GRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFV 628
Cdd:cd14957   85 NNRIQVFNSSGVYQYSIGTggsgdGQFNGPYGIAVDSNGNIYVADTGNHRIQVFTSSGTFSYSIGSGGTGPGQFNGPQGI 164

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 629 AVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:cd14957  165 AVDSDGNIYVADTGNHRIQVFTSSGTFQYTFGSSGSGPGQFSDPYGIAVDSDGNIYVADTGNHRIQVF 232
NHL_like_2 cd14957
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 476-697 7.87e-64

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271327 [Multi-domain]  Cd Length: 280  Bit Score: 213.67  E-value: 7.87e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 476 VGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNR 555
Cdd:cd14957   54 IGSGGTGSGQFNSPYGIAVDSNGNIYVADTDNNRIQVFNSSGVYQYSIGTGGSGDGQFNGPYGIAVDSNGNIYVADTGNH 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 556 WVSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAV 630
Cdd:cd14957  134 RIQVFTSSGTFSYSIGsggtgPGQFNGPQGIAVDSDGNIYVADTGNHRIQVFTSSGTFQYTFGSSGSGPGQFSDPYGIAV 213

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687 631 NNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVWR 697
Cdd:cd14957  214 DSDGNIYVADTGNHRIQVFTSSGAYQYSIGTSGSGNGQFNYPYGIAVDNDGKIYVADSNNNRIQVFN 280
NHL_like_3 cd14956
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 477-699 1.03e-61

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271326 [Multi-domain]  Cd Length: 274  Bit Score: 207.91  E-value: 1.03e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14956    3 GGRGSGPGQFKDPRGIAVDADDNVYVADARNGRIQVFDKDGTFLRRFGTTGDGPGQFGRPRGLAVDKDGWLYVADYWGDR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 557 VSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVN 631
Cdd:cd14956   83 IQVFTLTGELQTIGGssgsgPGQFNAPRGVAVDADGNLYVADFGNQRIQKFDPDGSFLRQWGGTGIEPGSFNYPRGVAVD 162

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 632 NKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVWRME 699
Cdd:cd14956  163 PDGTLYVADTYNDRIQVFDNDGAFLRKWGGRGTGPGQFNYPYGIAIDPDGNVFVADFGNNRIQKFTAD 230
NHL_like_3 cd14956
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 475-696 4.48e-58

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271326 [Multi-domain]  Cd Length: 274  Bit Score: 197.89  E-value: 4.48e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 475 RVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDN 554
Cdd:cd14956   48 RFGTTGDGPGQFGRPRGLAVDKDGWLYVADYWGDRIQVFTLTGELQTIGGSSGSGPGQFNAPRGVAVDADGNLYVADFGN 127

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 555 RWVSIFSPEGKF-----KTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVA 629
Cdd:cd14956  128 QRIQKFDPDGSFlrqwgGTGIEPGSFNYPRGVAVDPDGTLYVADTYNDRIQVFDNDGAFLRKWGGRGTGPGQFNYPYGIA 207

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687 630 VNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:cd14956  208 IDPDGNVFVADFGNNRIQKFTADGTFLTSWGSPGTGPGQFKNPWGVVVDADGTVYVADSNNNRVQRF 274
NHL_like_5 cd14963
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 494-696 8.70e-56

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271333 [Multi-domain]  Cd Length: 268  Bit Score: 191.74  E-value: 8.70e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 494 AASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAG 573
Cdd:cd14963   16 AVSDGRIYVADTNNHRVQVFDYEGKFKKSFGGPGTGPGEFKYPYGIAVDSDGNIYVADLYNGRIQVFDPDGKFLKYFPEK 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 574 R----LMGPKGVAVDRnGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVY 649
Cdd:cd14963   96 KdrvkLISPAGLAIDD-GKLYVSDVKKHKVIVFDLEGKLLLEFGKPGSEPGELSYPNGIAVDEDGNIYVADSGNGRIQVF 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 650 SADGEFL-----------------------------------------------FKFGSHGEGNGQFNAPTGVAVDSNGN 682
Cdd:cd14963  175 DKNGKFIkelngspdgksgfvnprgiavdpdgnlyvvdnlshrvyvfdeqgkelFTFGGRGKDDGQFNLPNGLFIDDDGR 254

                        250
                 ....*....|....
gi 552953687 683 IIVADWGNSRIQVW 696
Cdd:cd14963  255 LYVTDRENNRVAVY 268
NHL cd05819
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ...
 468-695 6.05e-52

NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats.


Pssm-ID: 271320 [Multi-domain]  Cd Length: 269  Bit Score: 181.36  E-value: 6.05e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 468 IEDELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDI 547
Cdd:cd05819   83 PDGNFLASFGGSGDGDGEFNGPRGIAVDSSGNIYVADTGNHRIQKFDPDGEFLTTFGSGGSGPGQFNGPTGVAVDSDGNI 162

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 548 IVADYDNRWVSIFSPEGKFktkigagrlmgpkgvavdrnghiivvdnksccvftfqpngklVGRFGGRGATDRHFAGPHF 627
Cdd:cd05819  163 YVADTGNHRIQVFDPDGNF------------------------------------------LTTFGSTGTGPGQFNYPTG 200

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 628 VAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd05819  201 IAVDSDGNIYVADSGNNRVQVFDPDGAGFGGNGNFLGSDGQFNRPSGLAVDSDGNLYVADTGNNRIQV 268
NHL_like_4 cd14955
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 523-694 1.64e-48

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271325 [Multi-domain]  Cd Length: 279  Bit Score: 171.99  E-value: 1.64e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 523 FGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSC 597
Cdd:cd14955    5 WGSYGSGDGQFNSPSGIAVDSAGNVYVADTGNNRIQKFDSTGTFLTKWGssgsgDGQFYSPTGIAVDSDGNVYVADTGNH 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 598 CVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAV 677
Cdd:cd14955   85 RIQKFDSTGTFLTKWGSSGSGDGQFNSPSGIAVDSAGNVYVTDSGNNRIQKFDSSGTFITKWGSFGSGDGQFNSPTGIAV 164

                        170
                 ....*....|....*..
gi 552953687 678 DSNGNIIVADWGNSRIQ 694
Cdd:cd14955  165 DSAGNVYVADTGNNRIQ 181
NHL_like_2 cd14957
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 519-696 2.60e-48

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271327 [Multi-domain]  Cd Length: 280  Bit Score: 171.68  E-value: 2.60e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 519 FKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAGrLMG------PKGVAVDRNGHIIVV 592
Cdd:cd14957    3 FSYAFGSNGSGNGQFNTPRGIAVDSAGNIYVADTGNNRIQVFTSSGVYSYSIGSG-GTGsgqfnsPYGIAVDSNGNIYVA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 593 DNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAP 672
Cdd:cd14957   82 DTDNNRIQVFNSSGVYQYSIGTGGSGDGQFNGPYGIAVDSNGNIYVADTGNHRIQVFTSSGTFSYSIGSGGTGPGQFNGP 161

                        170       180
                 ....*....|....*....|....
gi 552953687 673 TGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:cd14957  162 QGIAVDSDGNIYVADTGNHRIQVF 185
NHL_brat_like cd14959
NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins; ...
 471-695 6.06e-48

NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins; Drosophila brain-tumor (brat) has been identified as a tumor suppressor that negatively regulates cell proliferation during development of the Drosophila larval brain. It appears to be recruited to the 3'-untranslated region of hunchback RNA and regulates its translation by forming a complex with Pumilio (Pum) and Nanos (Nos). The NHL domain of brat appears to be involved by interacting with the RNA-binding Puf repeats of Pumilio, a sequence-specific RNA binding protein. This family also contains the Caenorhabditis elegans homolog NCL-1. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271329 [Multi-domain]  Cd Length: 274  Bit Score: 170.53  E-value: 6.06e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 471 ELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAV-DTNGDIIV 549
Cdd:cd14959    6 IIHCKFGESGSGEGQFNSPSGFCLGEDEDILVADTNNHRIQVFDKEGEFKFQFGIPGKRDGQLWYPNKVAVcRVTGRYVV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 550 ADYDN--RWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGgrgaTDRHFAGPHF 627
Cdd:cd14959   86 TDRGNprHRMQIFTKRGQFVRKFGARYLQHVRGLTVDAAGHIIVVESKVMRVFIFDESGNVLKWFD----CSKYLEEPSD 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 628 VAVNNkNEIVVTDFHNHSVKVYSADGEFLFKFGshgeGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14959  162 VAVND-NEIYICDNKGHCVVVFNYDGQFLRRIG----GEGITNYPIGVDISSAGDVLVADNHGNHFHV 224
NHL_TRIM32_like cd14961
NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins; ...
 477-693 4.08e-47

NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins; The E3 ubiquitin-protein ligase TRIM32 (HT2A) is widely expressed and is responsible for ubiquinating a large variety of targets, including dysbindin (DTNBP1), NPHP7/Glis2, TAp73, and others. TRIM32 promotes disassociation of the plakoglobin-PI3K complex and reduces PI3K-Akt-FoxO signaling. Mutations in TRIM32 have been implemented in the two diverse diseases limb-girdle muscular dystrophy type 2H (LGMD2H) or sarcotubular myopathy (STM) and Bardet-Biedl syndrome type 11 (BBS11). The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271331 [Multi-domain]  Cd Length: 273  Bit Score: 168.22  E-value: 4.08e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14961    1 GSFGGWPGTLNNPTGVAVTPTGRVVVADDGNKRIQVFDSDGNCLQQFGPKGDAGQDIRYPLDVAVTPDGHIVVTDAGDRS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 557 VSIFSPEGKFKTKIGaGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLvGRFGGRGATDRHFAGPHFVAVNNKNEI 636
Cdd:cd14961   81 VKVFSFDGRLKLFVR-KSFSLPWGVAVNPSGEILVTDSEAGKLFVLTVDFKL-GILKKGQKLCSQLCRPRFVAVSRLGAV 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687 637 VVTD--------FHNHSVKVYSADGEFLFKFGS--HGEGNGQFNAPTGVAVDSNGNIIVADWGNSRI 693
Cdd:cd14961  159 AVTEhlfangtrSSSTRVKVFSSGGQLLGQIDSfgLNLVFPSLICASGVAFDSEGNVIVADTGSGAI 225
NHL_like_6 cd14962
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 481-695 5.59e-45

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271332 [Multi-domain]  Cd Length: 271  Bit Score: 161.99  E-value: 5.59e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 481 REKGEFTNLQGVSAASSGRIVVADSNNQCIQVFsNEGQFKFRFgVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIF 560
Cdd:cd14962    6 RPKEALTRPYGVAADGRGRIYVADTGRGAVFVF-DLPNGKVFV-IGNAGPNRFVSPIGVAIDANGNLYVSDAELGKVFVF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 561 SPEGKFKTKIGAGRLMG-PKGVAVD-RNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVV 638
Cdd:cd14962   84 DRDGKFLRAIGAGALFKrPTGIAVDpAGKRLYVVDTLAHKVKVFDLDGRLLFDIGKRGSGPGEFNLPTDLAVDRDGNLYV 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687 639 TDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14962  164 TDTMNFRVQIFDADGKFLRSFGERGDGPGSFARPKGIAVDSEGNIYVVDAAFDNVQI 220
NHL_TRIM71_like cd14954
NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; ...
 473-649 8.16e-45

NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271324 [Multi-domain]  Cd Length: 285  Bit Score: 161.95  E-value: 8.16e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 473 VFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADY 552
Cdd:cd14954  104 LLKFGERGTKNGQFNYPWGVAVDSEGRIYVSDTRNHRVQVFDSDGQFIRKFGFEGAGPGQLDSPRGVAVNPDGNIVVSDF 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 553 DNRWVSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHF 627
Cdd:cd14954  184 NNHRLQVFDPDGQFLRFFGsegsgNGQFKRPRGVAVDDEGNIIVADSGNHRVQVFSPDGEFLCSFGTEGNGEGQFDRPSG 263

                        170       180
                 ....*....|....*....|..
gi 552953687 628 VAVNNKNEIVVTDFHNHSVKVY 649
Cdd:cd14954  264 VAVTPDGRIVVVDRGNHRIQVF 285
NHL_like_3 cd14956
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 523-695 1.93e-42

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271326 [Multi-domain]  Cd Length: 274  Bit Score: 155.13  E-value: 1.93e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 523 FGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGA-----GRLMGPKGVAVDRNGHIIVVDNKSC 597
Cdd:cd14956    2 WGGRGSGPGQFKDPRGIAVDADDNVYVADARNGRIQVFDKDGTFLRRFGTtgdgpGQFGRPRGLAVDKDGWLYVADYWGD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 598 CVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAV 677
Cdd:cd14956   82 RIQVFTLTGELQTIGGSSGSGPGQFNAPRGVAVDADGNLYVADFGNQRIQKFDPDGSFLRQWGGTGIEPGSFNYPRGVAV 161

                        170
                 ....*....|....*...
gi 552953687 678 DSNGNIIVADWGNSRIQV 695
Cdd:cd14956  162 DPDGTLYVADTYNDRIQV 179
NHL_like_6 cd14962
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 473-697 2.90e-41

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271332 [Multi-domain]  Cd Length: 271  Bit Score: 151.59  E-value: 2.90e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 473 VFRVGSRGREKgeFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGvrgrSPGQLQRPTGVAVD-TNGDIIVAD 551
Cdd:cd14962   45 VFVIGNAGPNR--FVSPIGVAIDANGNLYVSDAELGKVFVFDRDGKFLRAIG----AGALFKRPTGIAVDpAGKRLYVVD 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 552 YDNRWVSIFSPEGKFKTKIG-----AGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPH 626
Cdd:cd14962  119 TLAHKVKVFDLDGRLLFDIGkrgsgPGEFNLPTDLAVDRDGNLYVTDTMNFRVQIFDADGKFLRSFGERGDGPGSFARPK 198

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 552953687 627 FVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVWR 697
Cdd:cd14962  199 GIAVDSEGNIYVVDAAFDNVQIFNPEGELLLTVGGPGSGPGEFYLPSGIAIDKDDRIYVVDQFNRRIQVFQ 269
BBC smart00502
B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
 158-284 7.18e-38

B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains


Pssm-ID: 128778  Cd Length: 127  Bit Score: 137.01  E-value: 7.18e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   158 HKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKVLQTQ 237
Cdd:smart00502   1 QREALEELLTKLRKKAAELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 552953687   238 LDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRERLAALAAQ 284
Cdd:smart00502  81 LESLTQKQEKLSHAINFTEEALNSGDPTELLLSKKLIIERLQNLLKQ 127
CC_brat-like cd20482
coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family ...
 158-278 3.23e-37

coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins; This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs.


Pssm-ID: 467844 [Multi-domain]  Cd Length: 122  Bit Score: 134.97  E-value: 3.23e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 158 HKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKVLQTQ 237
Cdd:cd20482    1 HKESLQQLLEEARAKIPELRDALKNVEHALSRLQMQYHKAQNEINETFQFYRSMLEERKDELLKELESIYNAKQLSLNEQ 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 552953687 238 LDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRERL 278
Cdd:cd20482   81 QQKLQETIEKIQQGCEFTERLLKHGSETEVLLFKKLLEARL 121
NHL_like_4 cd14955
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 477-650 3.53e-35

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271325 [Multi-domain]  Cd Length: 279  Bit Score: 134.63  E-value: 3.53e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14955  100 GSSGSGDGQFNSPSGIAVDSAGNVYVTDSGNNRIQKFDSSGTFITKWGSFGSGDGQFNSPTGIAVDSAGNVYVADTGNNR 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 557 VSIFSPEGKFKTK-----IGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVN 631
Cdd:cd14955  180 IQKFTSTGTFLTKwgsegSGDGQFNAPYGIAVDSAGNVYVADTGNNRIQKFDSSGTFITKWGSEGSGDGQFNSPSGIAVD 259

                        170
                 ....*....|....*....
gi 552953687 632 NKNEIVVTDFHNHSVKVYS 650
Cdd:cd14955  260 SAGNVYVADSGNNRIQKFA 278
NHL_PAL_like cd14958
Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the ...
 530-695 1.01e-32

Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the N-dealkylation of peptidyl-alpha-hydroxyglycine, which results in an alpha-amidated peptide and glyoxylate. Amidation of the C-terminus is required for the activity of many peptide hormones and neuropeptides. The catalytic residues of PAL are located on several NHL-repeats. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271328 [Multi-domain]  Cd Length: 300  Bit Score: 128.15  E-value: 1.01e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 530 PGQLQRPTGVAVDTNGD-IIVADYDNRWVS--------------------IFSPEGKFKTKIGAGRLMGPKGVAVDRNGH 588
Cdd:cd14958    9 SLKLGQVSGVAVDSLGNgVVFHRGGRVWDAnsfdanvyvfkgpieedtilVFDPDGGFLRSWGAGLFYMPHGLTIDPDGN 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 589 IIVVDNKSCCVFTFQPNGKLV-----GRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFH-NHSVKVYSADGEFLFKFGSH 662
Cdd:cd14958   89 IWVTDVGLHQVFKFDPEGKLLplltlGERGEPGSDQTHFCKPTDVAVAPDGDIFVADGYcNSRIVKFSPDGKLLKSWGEP 168

                        170       180       190
                 ....*....|....*....|....*....|...
gi 552953687 663 GEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14958  169 GSGPGQFNLPHSIALDEDGRVYVADRENGRIQV 201
NHL_TRIM2_like cd14960
NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; ...
 404-598 2.32e-32

NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins; The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L levels in axons and subsequent axonopathy. TRIM2 is also involved in regulating axon outgrowth during development; it contains RING and BBOX domains, the NHL repeat domain is located at its C-terminus. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271330 [Multi-domain]  Cd Length: 274  Bit Score: 126.69  E-value: 2.32e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 404 LYGQPVRGSPFRVRALRpGDLPpSPDDVKRRVKSP-GGPGSHVRQkaVRRPSSMYSTGgKRKDNPIEDE----------- 471
Cdd:cd14960   30 LVIADSNNQCVQVFSND-GQFK-LRFGVRGRSPGQlQRPTGVAVT--LNGDIIIADYD-NKWVSIFSPDgkfkskigagk 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 ---------------------------------LVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQ 518
Cdd:cd14960  105 lmgpkgvavdrnghiivvdnkaccvfifqpngkLVTRFGSRGNGDRQFAGPHFAAVNNNNEIIVTDFHNHSVKVFNAEGE 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 519 FKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIG--AGRLMGPKGVAVDRNGHIIVVDNKS 596
Cdd:cd14960  185 FLFKFGSNGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVFDSSGSFLSYINtsADPLYGPQGLALTSDGHVVVADSGN 264


                 ..
gi 552953687 597 CC 598
Cdd:cd14960  265 HC 266
NHL_like_1 cd14953
Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat ...
 486-693 4.05e-31

Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271323 [Multi-domain]  Cd Length: 323  Bit Score: 124.18  E-value: 4.05e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 486 FTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQ---FKFRfGVRGRSPG-----QLQRPTGVAVDTNGDIIVADYDNRWV 557
Cdd:cd14953   22 FNSPSGVAVDAAGNLYVADRGNHRIRKITPDGVvttVAGT-GTAGFADGggaaaQFNTPSGVAVDAAGNLYVADTGNHRI 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 558 SIFSPEGKFKTKIGAG-------------RLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLV--------GRFGGRG 616
Cdd:cd14953  101 RKITPDGVVSTLAGTGtagfsddggataaQFNYPTGVAVDAAGNLYVADTGNHRIRKITPDGVVTtvagtggaGYAGDGP 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 617 ATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEG--------NGQFNAPTGVAVDSNGNIIVADW 688
Cdd:cd14953  181 ATAAQFNNPTGVAVDAAGNLYVADRGNHRIRKITPDGVVTTVAGTGTAGfsgdggatAAQLNNPTGVAVDAAGNLYVADS 260


                 ....*
gi 552953687 689 GNSRI 693
Cdd:cd14953  261 GNHRI 265
RING-HC_TRIM3 cd16768
RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
 16-63 9.50e-31

RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438424 [Multi-domain]  Cd Length: 48  Bit Score: 114.33  E-value: 9.50e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  16 DKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16768    1 DKQFLVCSICLDRYHNPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 48
NHL_like_4 cd14955
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 477-604 1.07e-29

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271325 [Multi-domain]  Cd Length: 279  Bit Score: 118.83  E-value: 1.07e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14955  147 GSFGSGDGQFNSPTGIAVDSAGNVYVADTGNNRIQKFTSTGTFLTKWGSEGSGDGQFNAPYGIAVDSAGNVYVADTGNNR 226

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687 557 VSIFSPEGKFKTKIGA-----GRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQP 604
Cdd:cd14955  227 IQKFDSSGTFITKWGSegsgdGQFNSPSGIAVDSAGNVYVADSGNNRIQKFAP 279
NHL_TRIM71_like cd14954
NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; ...
 602-695 5.63e-29

NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271324 [Multi-domain]  Cd Length: 285  Bit Score: 116.88  E-value: 5.63e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 602 FQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNG 681
Cdd:cd14954    3 YRAKGRPLLSFGKEGSKDGELCRPWGVAVDKDGRIIVADRSNNRVQVFDPDGKFLRKFGSYGSRDGQFDRPAGVAVNSRG 82

                         90
                 ....*....|....
gi 552953687 682 NIIVADWGNSRIQV 695
Cdd:cd14954   83 RIIVADKDNHRIQV 96
NHL_like_6 cd14962
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 472-593 7.05e-29

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271332 [Multi-domain]  Cd Length: 271  Bit Score: 116.53  E-value: 7.05e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 LVFRVGSRGREKGEF---TNlqgVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDII 548
Cdd:cd14962  133 LLFDIGKRGSGPGEFnlpTD---LAVDRDGNLYVTDTMNFRVQIFDADGKFLRSFGERGDGPGSFARPKGIAVDSEGNIY 209

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 552953687 549 VAD--YDNrwVSIFSPEGKF-----KTKIGAGRLMGPKGVAVDRNGHIIVVD 593
Cdd:cd14962  210 VVDaaFDN--VQIFNPEGELlltvgGPGSGPGEFYLPSGIAIDKDDRIYVVD 259
NHL_like_1 cd14953
Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat ...
 532-693 1.49e-28

Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271323 [Multi-domain]  Cd Length: 323  Bit Score: 116.86  E-value: 1.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 532 QLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAG------------RLMGPKGVAVDRNGHIIVVDNKSCC- 598
Cdd:cd14953   21 RFNSPSGVAVDAAGNLYVADRGNHRIRKITPDGVVTTVAGTGtagfadgggaaaQFNTPSGVAVDAAGNLYVADTGNHRi 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 599 --------VFTFQPNGKlVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEF-----LFKFGSHGEG 665
Cdd:cd14953  101 rkitpdgvVSTLAGTGT-AGFSDDGGATAAQFNYPTGVAVDAAGNLYVADTGNHRIRKITPDGVVttvagTGGAGYAGDG 179

                        170       180       190
                 ....*....|....*....|....*....|.
gi 552953687 666 NG---QFNAPTGVAVDSNGNIIVADWGNSRI 693
Cdd:cd14953  180 PAtaaQFNNPTGVAVDAAGNLYVADRGNHRI 210
Bbox2_TRIM3_C-VII cd19825
B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also ...
 107-153 1.75e-28

B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3); TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in neuroblastoma. It binds to the ck inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclins D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It corresponds to gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of presynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendrite spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380883 [Multi-domain]  Cd Length: 47  Bit Score: 107.79  E-value: 1.75e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687 107 AVAGRPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRD 153
Cdd:cd19825    1 AVAGKPLSCPNHEGKTMEFYCESCETAMCRECTEGEHREHVTVPLRD 47
NHL_like_1 cd14953
Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat ...
 490-693 2.66e-28

Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271323 [Multi-domain]  Cd Length: 323  Bit Score: 116.09  E-value: 2.66e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 490 QGVSAASSGRIVVADSNNQCIQVFSNEGQF---------KFRFGVrGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIF 560
Cdd:cd14953   80 SGVAVDAAGNLYVADTGNHRIRKITPDGVVstlagtgtaGFSDDG-GATAAQFNYPTGVAVDAAGNLYVADTGNHRIRKI 158

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 561 SPEGKFKTKIGAG-------------RLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKL--------VGRFGGRGATD 619
Cdd:cd14953  159 TPDGVVTTVAGTGgagyagdgpataaQFNNPTGVAVDAAGNLYVADRGNHRIRKITPDGVVttvagtgtAGFSGDGGATA 238

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 620 RHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGE----FLFKFGSHGEGNG----QFNAPTGVAVDSNGNIIVADWGNS 691
Cdd:cd14953  239 AQLNNPTGVAVDAAGNLYVADSGNHRIRKITPAGVvttvAGGGAGFSGDGGPatsaQFNNPTGVAVDAAGNLYVADTGNN 318


                 ..
gi 552953687 692 RI 693
Cdd:cd14953  319 RI 320
RING-HC_TRIM2_like_C-VII cd16586
RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and ...
 19-63 4.22e-27

RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438248 [Multi-domain]  Cd Length: 45  Bit Score: 103.68  E-value: 4.22e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  19 FLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16586    1 FLSCGICLERYKNPKVLPCLHTFCERCLQNYIPAESLSLSCPVCR 45
RING-HC_TRIM2 cd16767
RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also ...
 15-64 5.73e-26

RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2); TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438423 [Multi-domain]  Cd Length: 51  Bit Score: 100.86  E-value: 5.73e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  15 MDKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd16767    2 IDKQFLICSICLDRYKNPKVLPCLHTFCERCLQNYIPAHSLTLSCPVCRQ 51
NHL cd05819
NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in ...
 622-699 2.22e-25

NHL repeat unit of beta-propeller proteins; The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats.


Pssm-ID: 271320 [Multi-domain]  Cd Length: 269  Bit Score: 106.25  E-value: 2.22e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 622 FAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQVWRME 699
Cdd:cd05819    7 LNNPQGIAVDSSGNIYVADTGNNRIQVFDPDGNFITSFGSFGSGDGQFNEPAGVAVDSDGNLYVADTGNHRIQKFDPD 84
IG_FLMN smart00557
Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding ...
 322-419 2.37e-25

Filamin-type immunoglobulin domains; These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).


Pssm-ID: 214720 [Multi-domain]  Cd Length: 93  Bit Score: 100.37  E-value: 2.37e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   322 AHETVATGEGLRQALVGQPASLTVTTKDKdgrlvrtGSAELCAEITGPDGVRLAVPVVDHKNGTYELVYTARTEGDLLLS 401
Cdd:smart00557   1 ASKVKASGPGLEKGVVGEPAEFTVDTRDA-------GGGELEVEVTGPSGKKVPVEVKDNGDGTYTVSYTPTEPGDYTVT 73

                           90
                   ....*....|....*...
gi 552953687   402 VLLYGQPVRGSPFRVRAL 419
Cdd:smart00557  74 VKFGGEHIPGSPFTVKVG 91
Bbox2_TRIM2-like cd19759
B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and ...
 112-153 1.14e-23

B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380817 [Multi-domain]  Cd Length: 42  Bit Score: 94.05  E-value: 1.14e-23
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687 112 PLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRD 153
Cdd:cd19759    1 PLVCPNHDGETLEFYCESCETAVCRECTAGEHNEHRTVLLKD 42
Filamin pfam00630
Filamin/ABP280 repeat;
322-415 3.31e-23

Filamin/ABP280 repeat;


Pssm-ID: 395505  Cd Length: 89  Bit Score: 94.28  E-value: 3.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  322 AHETVATGEGLRQALVGQPASLTVTTKDKDGrlvrtgsaELCAEITGPDGVRLAVPVVDHKNGTYELVYTARTEGDLLLS 401
Cdd:pfam00630   4 ASKVKASGPGLEPGVVGKPAEFTVDTRDAGG--------EGEVEVTGPDGSPVPVEVTDNGDGTYTVSYTPTEPGDYTVS 75

                          90
                  ....*....|....
gi 552953687  402 VLLYGQPVRGSPFR 415
Cdd:pfam00630  76 VKFNGQHIPGSPFK 89
Vgb COG4257
Streptogramin lyase [Defense mechanisms];
484-693 7.50e-23

Streptogramin lyase [Defense mechanisms];


Pssm-ID: 443399 [Multi-domain]  Cd Length: 270  Bit Score: 98.94  E-value: 7.50e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 484 GEFTNLQGVSAASSGRIVVADSNNQCIQVFS-NEGQFKfrfgvrGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSP 562
Cdd:COG4257   14 APGSGPRDVAVDPDGAVWFTDQGGGRIGRLDpATGEFT------EYPLGGGSGPHGIAVDPDGNLWFTDNGNNRIGRIDP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 563 -EGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNksccvftfqpNGKLVGRF-GGRGATDRHF-----AGPHFVAVNNKNE 635
Cdd:COG4257   88 kTGEITTFALPGGGSNPHGIAFDPDGNLWFTDQ----------GGNRIGRLdPATGEVTEFPlptggAGPYGIAVDPDGN 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 636 IVVTDFHNHSVKVYSADGEFLFKFgshgEGNGQFNAPTGVAVDSNGNIIVADWGNSRI 693
Cdd:COG4257  158 LWVTDFGANAIGRIDPDTGTLTEY----ALPTPGAGPRGLAVDPDGNLWVADTGSGRI 211
NHL_PAL_like cd14958
Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the ...
 510-697 2.83e-22

Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the N-dealkylation of peptidyl-alpha-hydroxyglycine, which results in an alpha-amidated peptide and glyoxylate. Amidation of the C-terminus is required for the activity of many peptide hormones and neuropeptides. The catalytic residues of PAL are located on several NHL-repeats. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271328 [Multi-domain]  Cd Length: 300  Bit Score: 97.72  E-value: 2.83e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 510 IQVFSNEGQFKFRFGvrgrsPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAGRLMG----------PK 579
Cdd:cd14958   57 ILVFDPDGGFLRSWG-----AGLFYMPHGLTIDPDGNIWVTDVGLHQVFKFDPEGKLLPLLTLGERGEpgsdqthfckPT 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 580 GVAVDRNGHIIVVD---NKscCVFTFQPNGKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFL 656
Cdd:cd14958  132 DVAVAPDGDIFVADgycNS--RIVKFSPDGKLLKSWGEPGSGPGQFNLPHSIALDEDGRVYVADRENGRIQVFDADGKFL 209

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 657 --------------------------------------------------FKFGSHGEGNGQFNAPTGVAVDSNGNIIVA 686
Cdd:cd14958  210 tewtnpelgrpyalaidpdgllyvvdgpprlnrslpvrgfvirigkglilGRFGPGGKAPGQFQNPHDIAVDSGGDIYVG 289

                        250
                 ....*....|.
gi 552953687 687 DWGNSRIQVWR 697
Cdd:cd14958  290 ELGPNRVQKFV 300
NHL_PAL_like cd14958
Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the ...
 495-646 4.02e-22

Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5); PAL catalyzes the N-dealkylation of peptidyl-alpha-hydroxyglycine, which results in an alpha-amidated peptide and glyoxylate. Amidation of the C-terminus is required for the activity of many peptide hormones and neuropeptides. The catalytic residues of PAL are located on several NHL-repeats. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271328 [Multi-domain]  Cd Length: 300  Bit Score: 97.33  E-value: 4.02e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 495 ASSGRIVVADS-NNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAG 573
Cdd:cd14958  136 APDGDIFVADGyCNSRIVKFSPDGKLLKSWGEPGSGPGQFNLPHSIALDEDGRVYVADRENGRIQVFDADGKFLTEWTNP 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 574 RLMGPKGVAVDRNGHIIVVD-------NKSCCVFTFQPN-GKLVGRFGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHS 645
Cdd:cd14958  216 ELGRPYALAIDPDGLLYVVDgpprlnrSLPVRGFVIRIGkGLILGRFGPGGKAPGQFQNPHDIAVDSGGDIYVGELGPNR 295


                 .
gi 552953687 646 V 646
Cdd:cd14958  296 V 296
NHL_like_5 cd14963
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 616-695 1.82e-21

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271333 [Multi-domain]  Cd Length: 268  Bit Score: 94.67  E-value: 1.82e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 616 GATDRHFAGPHFVAVNNKNeIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14963    3 GPFGDPLNKPMGVAVSDGR-IYVADTNNHRVQVFDYEGKFKKSFGGPGTGPGEFKYPYGIAVDSDGNIYVADLYNGRIQV 81
Vgb COG4257
Streptogramin lyase [Defense mechanisms];
482-696 3.86e-21

Streptogramin lyase [Defense mechanisms];


Pssm-ID: 443399 [Multi-domain]  Cd Length: 270  Bit Score: 93.93  E-value: 3.86e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 482 EKGEFTNLQGVSAASSGRIVVADSNNQCIQVFS-NEGQFKfRFGVrgrsPGQLQRPTGVAVDTNGDIIVADYDNRWVSIF 560
Cdd:COG4257   54 PLGGGSGPHGIAVDPDGNLWFTDNGNNRIGRIDpKTGEIT-TFAL----PGGGSNPHGIAFDPDGNLWFTDQGGNRIGRL 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 561 SPE-GKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFggrgATDRHFAGPHFVAVNNKNEIVVT 639
Cdd:COG4257  129 DPAtGEVTEFPLPTGGAGPYGIAVDPDGNLWVTDFGANAIGRIDPDTGTLTEY----ALPTPGAGPRGLAVDPDGNLWVA 204

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687 640 DFHNHSVKVYS-ADGEFLfKFGSHGEGNGqfnaPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:COG4257  205 DTGSGRIGRFDpKTGTVT-EYPLPGGGAR----PYGVAVDGDGRVWFAESGANRIVRF 257
Bbox2_TRIM2_C-VII cd19824
B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar ...
 112-153 1.29e-20

B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar proteins; TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 Semi-independent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Aim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380882 [Multi-domain]  Cd Length: 42  Bit Score: 85.11  E-value: 1.29e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687 112 PLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRD 153
Cdd:cd19824    1 PLSCPNHDGNVMEFYCQSCETAMCQECTEGEHAEHPTVPLKD 42
NHL_PKND_like cd14952
NHL repeat domain of the protein kinase PknD; PknD is a mycobacterial transmembrane protein ...
 486-693 1.27e-19

NHL repeat domain of the protein kinase PknD; PknD is a mycobacterial transmembrane protein with a cytosolic kinase domain and an extracellular sensor domain that contains NHL repeats. It plays a key role in the development of central nervous system tuberculosis, by mediating the invasion of host brain endothelia. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271322 [Multi-domain]  Cd Length: 247  Bit Score: 88.80  E-value: 1.27e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 486 FTNL---QGVSAASSGRIVVADS-NNQCIQVFSN-EGQFKFRFgvrgrspGQLQRPTGVAVDTNGDIIVADYDNRWVSIF 560
Cdd:cd14952    6 FTGLdgpGGVAVDAAGNVYVADSgNNRVLKLAAGsTTQTVLPF-------TGLYQPQGVAVDAAGTVYVTDFGNNRVLKL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 561 SPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNksccvftfqPNGKLVGRFGGRGA-TDRHFAG---PHFVAVNNKNEI 636
Cdd:cd14952   79 AAGSTTQTVLPFTGLNDPTGVAVDAAGNVYVADT---------GNNRVLKLAAGSNTqTVLPFTGlsnPDGVAVDGAGNV 149

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 637 VVTDFHNHSVKVYSAdgeflfkfGSHGEGNGQF---NAPTGVAVDSNGNIIVADWGNSRI 693
Cdd:cd14952  150 YVTDTGNNRVLKLAA--------GSTTQTVLPFtglNSPSGVAVDTAGNVYVTDHGNNRV 201
NHL_like_3 cd14956
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 472-560 7.21e-19

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271326 [Multi-domain]  Cd Length: 274  Bit Score: 87.34  E-value: 7.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 LVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVAD 551
Cdd:cd14956  186 FLRKWGGRGTGPGQFNYPYGIAIDPDGNVFVADFGNNRIQKFTADGTFLTSWGSPGTGPGQFKNPWGVVVDADGTVYVAD 265


                 ....*....
gi 552953687 552 YDNRWVSIF 560
Cdd:cd14956  266 SNNNRVQRF 274
NHL_like_2 cd14957
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 471-561 4.82e-18

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271327 [Multi-domain]  Cd Length: 280  Bit Score: 85.01  E-value: 4.82e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 471 ELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVA 550
Cdd:cd14957  190 TFQYTFGSSGSGPGQFSDPYGIAVDSDGNIYVADTGNHRIQVFTSSGAYQYSIGTSGSGNGQFNYPYGIAVDNDGKIYVA 269

                         90
                 ....*....|.
gi 552953687 551 DYDNRWVSIFS 561
Cdd:cd14957  270 DSNNNRIQVFN 280
Vgb COG4257
Streptogramin lyase [Defense mechanisms];
530-694 5.32e-18

Streptogramin lyase [Defense mechanisms];


Pssm-ID: 443399 [Multi-domain]  Cd Length: 270  Bit Score: 84.69  E-value: 5.32e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 530 PGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLV 609
Cdd:COG4257   13 PAPGSGPRDVAVDPDGAVWFTDQGGGRIGRLDPATGEFTEYPLGGGSGPHGIAVDPDGNLWFTDNGNNRIGRIDPKTGEI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 610 GRFggrgATDRHFAGPHFVAVNNKNEIVVTDFHNHSV-KVYSADGEFLFKFGSHGEGNgqfnaPTGVAVDSNGNIIVADW 688
Cdd:COG4257   93 TTF----ALPGGGSNPHGIAFDPDGNLWFTDQGGNRIgRLDPATGEVTEFPLPTGGAG-----PYGIAVDPDGNLWVTDF 163


                 ....*.
gi 552953687 689 GNSRIQ 694
Cdd:COG4257  164 GANAIG 169
NHL_PKND_like cd14952
NHL repeat domain of the protein kinase PknD; PknD is a mycobacterial transmembrane protein ...
 533-696 6.76e-16

NHL repeat domain of the protein kinase PknD; PknD is a mycobacterial transmembrane protein with a cytosolic kinase domain and an extracellular sensor domain that contains NHL repeats. It plays a key role in the development of central nervous system tuberculosis, by mediating the invasion of host brain endothelia. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271322 [Multi-domain]  Cd Length: 247  Bit Score: 78.02  E-value: 6.76e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 533 LQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKsccvftfqpNGKLVGRF 612
Cdd:cd14952    9 LDGPGGVAVDAAGNVYVADSGNNRVLKLAAGSTTQTVLPFTGLYQPQGVAVDAAGTVYVTDFG---------NNRVLKLA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 613 GGRGA-TDRHFAG---PHFVAVNNKNEIVVTDFHNHSVkVYSADGEflfkfgshgegNGQF-------NAPTGVAVDSNG 681
Cdd:cd14952   80 AGSTTqTVLPFTGlndPTGVAVDAAGNVYVADTGNNRV-LKLAAGS-----------NTQTvlpftglSNPDGVAVDGAG 147

                        170
                 ....*....|....*
gi 552953687 682 NIIVADWGNSRIQVW 696
Cdd:cd14952  148 NVYVTDTGNNRVLKL 162
NHL_like_6 cd14962
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 477-562 8.53e-15

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271332 [Multi-domain]  Cd Length: 271  Bit Score: 75.32  E-value: 8.53e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRW 556
Cdd:cd14962  185 GERGDGPGSFARPKGIAVDSEGNIYVVDAAFDNVQIFNPEGELLLTVGGPGSGPGEFYLPSGIAIDKDDRIYVVDQFNRR 264


                 ....*.
gi 552953687 557 VSIFSP 562
Cdd:cd14962  265 IQVFQY 270
RING-HC_NHL-1-like cd16524
RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and ...
 17-63 2.14e-14

RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and similar proteins; NHL-1 functions as an E3 ubiquitin-protein ligase in the presence of both UBC-13 and UBC-1 within the ubiquitin pathway of Caenorhabditis elegans. It acts in chemosensory neurons to promote stress resistance in distal tissues by the transcription factor DAF-16 activation but is dispensable for the activation of heat shock factor 1 (HSF-1). NHL-1 belongs to the TRIM (tripartite motif)-NHL family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438187 [Multi-domain]  Cd Length: 53  Bit Score: 67.84  E-value: 2.14e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCER-CLQNYIPPQSLTLSCPVCR 63
Cdd:cd16524    3 EQLLTCPICLDRYRRPKLLPCQHTFCLSpCLEGLVDYVTRKLKCPECR 50
RING-HC_PML_C-V cd16579
RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; ...
 17-64 4.47e-14

RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins; Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438241 [Multi-domain]  Cd Length: 52  Bit Score: 66.81  E-value: 4.47e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIP--PQSLTLSCPVCRQ 64
Cdd:cd16579    2 FKFLRCPGCKAEYKCPKLLPCLHTVCSGCLEALAEqaSETTEFQCPICKA 51
NHL_like_4 cd14955
Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and ...
 655-694 2.69e-13

Uncharacterized NHL-repeat domain in bacterial and archaeal proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271325 [Multi-domain]  Cd Length: 279  Bit Score: 70.68  E-value: 2.69e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 552953687 655 FLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQ 694
Cdd:cd14955    1 FVTQWGSYGSGDGQFNSPSGIAVDSAGNVYVADTGNNRIQ 40
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
 20-64 3.63e-13

RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins; TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438271 [Multi-domain]  Cd Length: 58  Bit Score: 64.31  E-value: 3.63e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNY-IPPQSLTLSCPVCRQ 64
Cdd:cd16609    4 LTCSICLGLYQDPVTLPCQHSFCRACIEDHwRQKDEGSFSCPECRA 49
NHL_like_1 cd14953
Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat ...
 612-693 4.00e-13

Uncharacterized NHL-repeat domain in bacterial proteins; This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271323 [Multi-domain]  Cd Length: 323  Bit Score: 71.02  E-value: 4.00e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 612 FGGRGATDRHFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGE--FLFKFGSHGEGNG-----QFNAPTGVAVDSNGNII 684
Cdd:cd14953   12 FSGGGGTAARFNSPSGVAVDAAGNLYVADRGNHRIRKITPDGVvtTVAGTGTAGFADGggaaaQFNTPSGVAVDAAGNLY 91


                 ....*....
gi 552953687 685 VADWGNSRI 693
Cdd:cd14953   92 VADTGNHRI 100
YncE COG3391
DNA-binding beta-propeller fold protein YncE [General function prediction only];
472-701 6.10e-13

DNA-binding beta-propeller fold protein YncE [General function prediction only];


Pssm-ID: 442618 [Multi-domain]  Cd Length: 237  Bit Score: 68.95  E-value: 6.10e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 LVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDIIVAD 551
Cdd:COG3391    7 LLVAVLLAVLALAALAVAVAALGLGGGGPLLAAASGGVVGAAVGGGGVALLAGLGLGAAAVADADGADAGADGRRLYVAN 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 552 YDNRWVSIFSPE-GKFKTKIGAGRlmGPKGVAVDRNG-HIIVVDNKSCCVFTF-QPNGKLVGRFGGrgatdrhFAGPHFV 628
Cdd:COG3391   87 SGSGRVSVIDLAtGKVVATIPVGG--GPRGLAVDPDGgRLYVADSGNGRVSVIdTATGKVVATIPV-------GAGPHGI 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 629 AVN-NKNEIVVTDFHNHSVKVY-----SADGEFL--FKFGSHgegngqfnaPTGVAVDSNGNIIV--------ADWGNSR 692
Cdd:COG3391  158 AVDpDGKRLYVANSGSNTVSVIvsvidTATGKVVatIPVGGG---------PVGVAVSPDGRRLYvanrgsntSNGGSNT 228


                 ....*....
gi 552953687 693 IQVWRMESP 701
Cdd:COG3391  229 VSVIDLATL 237
BBOX smart00336
B-Box-type zinc finger;
110-151 7.33e-13

B-Box-type zinc finger;


Pssm-ID: 197662 [Multi-domain]  Cd Length: 42  Bit Score: 63.13  E-value: 7.33e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 552953687   110 GRPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLL 151
Cdd:smart00336   1 QRAPKCDSHGDEPAEFFCEECGALLCRTCDEAEHRGHTVVLL 42
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
 18-63 1.13e-12

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins; TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis.


Pssm-ID: 438243 [Multi-domain]  Cd Length: 50  Bit Score: 62.91  E-value: 1.13e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  18 QFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLT----LSCPVCR 63
Cdd:cd16581    1 EELTCSICYNIFDDPKILPCSHTFCKNCLEKLLAASGYYllasLKCPTCR 50
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
 20-62 1.72e-12

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 62.12  E-value: 1.72e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIppQSLTLSCPVC 62
Cdd:cd16449    1 LECPICLERLKDPVLLPCGHVFCRECIRRLL--ESGSIKCPIC 41
RING-HC_TRIM56_C-V cd16584
RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar ...
 19-76 2.51e-12

RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438246 [Multi-domain]  Cd Length: 56  Bit Score: 61.93  E-value: 2.51e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687  19 FLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltLSCPVCRQTSILPEQGVSAL 76
Cdd:cd16584    1 FLACKICLEQLRAPKTLPCLHTYCQDCLAQLADGGR--VRCPECRETVPVPPEGVASF 56
Vgb COG4257
Streptogramin lyase [Defense mechanisms];
484-655 5.50e-12

Streptogramin lyase [Defense mechanisms];


Pssm-ID: 443399 [Multi-domain]  Cd Length: 270  Bit Score: 66.97  E-value: 5.50e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 484 GEFTNLQGVSAASSGRIVVADSNNQCIQVFS-NEGQFKFrfgvrGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSP 562
Cdd:COG4257   99 GGGSNPHGIAFDPDGNLWFTDQGGNRIGRLDpATGEVTE-----FPLPTGGAGPYGIAVDPDGNLWVTDFGANAIGRIDP 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 563 E-GKFKTKIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFGGRGATdrhfAGPHFVAVNNKNEIVVTDF 641
Cdd:COG4257  174 DtGTLTEYALPTPGAGPRGLAVDPDGNLWVADTGSGRIGRFDPKTGTVTEYPLPGGG----ARPYGVAVDGDGRVWFAES 249

                        170
                 ....*....|....
gi 552953687 642 HNHSVKVYSADGEF 655
Cdd:COG4257  250 GANRIVRFDPDTEL 263
NHL_TRIM32_like cd14961
NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins; ...
 610-699 1.24e-11

NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins; The E3 ubiquitin-protein ligase TRIM32 (HT2A) is widely expressed and is responsible for ubiquinating a large variety of targets, including dysbindin (DTNBP1), NPHP7/Glis2, TAp73, and others. TRIM32 promotes disassociation of the plakoglobin-PI3K complex and reduces PI3K-Akt-FoxO signaling. Mutations in TRIM32 have been implemented in the two diverse diseases limb-girdle muscular dystrophy type 2H (LGMD2H) or sarcotubular myopathy (STM) and Bardet-Biedl syndrome type 11 (BBS11). The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271331 [Multi-domain]  Cd Length: 273  Bit Score: 65.76  E-value: 1.24e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 610 GRFGGRGATdrhFAGPHFVAVNNKNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWG 689
Cdd:cd14961    1 GSFGGWPGT---LNNPTGVAVTPTGRVVVADDGNKRIQVFDSDGNCLQQFGPKGDAGQDIRYPLDVAVTPDGHIVVTDAG 77

                         90
                 ....*....|
gi 552953687 690 NSRIQVWRME 699
Cdd:cd14961   78 DRSVKVFSFD 87
NHL_TRIM71_like cd14954
NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; ...
 647-695 4.69e-11

NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271324 [Multi-domain]  Cd Length: 285  Bit Score: 64.11  E-value: 4.69e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 552953687 647 KVYSADGEFLFKFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14954    1 RDYRAKGRPLLSFGKEGSKDGELCRPWGVAVDKDGRIIVADRSNNRVQV 49
RING-HC_RNF183-like cd16556
RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar ...
 22-69 1.69e-10

RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar proteins; RNF183 is an E3 ubiquitin-protein ligase that is upregulated during intestinal inflammation and is negatively regulated by miR-7. It promotes intestinal inflammation by increasing the ubiquitination and degradation of inhibitor of kappa B, thereby resulting in secondary activation of the Nuclear factor-kappaB (NF-kB) pathway. The interaction between RNF183-mediated ubiquitination and miRNA may be an important novel epigenetic mechanism in the pathogenesis of inflammatory bowel disease (IBD). The biological function of RNF223 and RNF225 remains unclear. Members of this family contain an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438218 [Multi-domain]  Cd Length: 57  Bit Score: 56.99  E-value: 1.69e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRY----RCPKVLPCLHTFCERCLQN---YIPPQSLTLSCPVCRQTSILP 69
Cdd:cd16556    3 CSICFSSYdntfKTPKLLDCGHTFCLECLARlslASPPQAERVPCPLCRQPTVLP 57
YvrE COG3386
Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase ...
 535-696 1.72e-10

Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 442613 [Multi-domain]  Cd Length: 266  Bit Score: 62.22  E-value: 1.72e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 535 RPTGVAVDTNGDIIVADYDNRwVSIFSPE-GKFKTKIGAG--RLMGPKGVAVDRNGHIivvdnksccVFT----FQPNGK 607
Cdd:COG3386   50 RPNGLAFDPDGRLLVADHGRG-LVRFDPAdGEVTVLADEYgkPLNRPNDGVVDPDGRL---------YFTdmgeYLPTGA 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 608 LVgRFGGRGATDRHFAGPHF---VAVNNKNEIV-VTDFHNHSVKVY--SADGEFLFK--FGSHGEGNGqfnAPTGVAVDS 679
Cdd:COG3386  120 LY-RVDPDGSLRVLADGLTFpngIAFSPDGRTLyVADTGAGRIYRFdlDADGTLGNRrvFADLPDGPG---GPDGLAVDA 195

                        170
                 ....*....|....*..
gi 552953687 680 NGNIIVADWGNSRIQVW 696
Cdd:COG3386  196 DGNLWVALWGGGGVVRF 212
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 22-62 3.47e-10

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 55.59  E-value: 3.47e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 552953687    22 CSICLDRY-RCPKVLPCLHTFCERCLQNYIppQSLTLSCPVC 62
Cdd:smart00184   1 CPICLEEYlKDPVILPCGHTFCRSCIRKWL--ESGNNTCPIC 40
RING-HC_TRIM59_C-V cd16763
RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar ...
 20-63 5.55e-10

RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins; TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain.


Pssm-ID: 438419 [Multi-domain]  Cd Length: 56  Bit Score: 55.30  E-value: 5.55e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIP---------PQSLTLSCPVCR 63
Cdd:cd16763    4 LTCSVCYSLFEDPRVLPCSHTFCRNCLENILQvsgnfsiwrPLRPPLKCPNCR 56
zf-B_box pfam00643
B-box zinc finger;
115-151 8.30e-10

B-box zinc finger;


Pssm-ID: 459886 [Multi-domain]  Cd Length: 42  Bit Score: 54.40  E-value: 8.30e-10
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 552953687  115 CPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLL 151
Cdd:pfam00643   6 CPEHEEEPLTLYCNDCQELLCEECSVGEHRGHTVVPL 42
NHL_like_3 cd14956
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 658-695 9.73e-10

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271326 [Multi-domain]  Cd Length: 274  Bit Score: 59.99  E-value: 9.73e-10
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 552953687 658 KFGSHGEGNGQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14956    1 SWGGRGSGPGQFKDPRGIAVDADDNVYVADARNGRIQV 38
RING-HC_TRIM77_C-IV cd16543
RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar ...
 20-66 1.04e-09

RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins; TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438205 [Multi-domain]  Cd Length: 54  Bit Score: 54.71  E-value: 1.04e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQTS 66
Cdd:cd16543    4 LTCSICLDLLKDPVTIPCGHSFCMNCITLLWDRKQGVPSCPQCRESF 50
RING-HC_CHFR cd16503
RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein ...
 20-65 2.88e-09

RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR); CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger.


Pssm-ID: 438166 [Multi-domain]  Cd Length: 55  Bit Score: 53.52  E-value: 2.88e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDR-YRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQT 65
Cdd:cd16503    3 LTCSICQDLlHDCVSLQPCMHNFCAACYSDWMERSNTE--CPTCRAT 47
RING-HC_TRIM69_C-IV cd16611
RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar ...
 18-64 3.04e-09

RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins; TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438273 [Multi-domain]  Cd Length: 59  Bit Score: 53.61  E-value: 3.04e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  18 QFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd16611    3 EELHCPLCLDFFRDPVMLSCGHNFCQSCITGFWELQAEDTTCPECRE 49
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
 22-60 4.99e-09

RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.


Pssm-ID: 463881 [Multi-domain]  Cd Length: 38  Bit Score: 52.02  E-value: 4.99e-09
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 552953687   22 CSICLDRYRCPkVLPCLHTFCERCLQNYIPPQSLTLSCP 60
Cdd:pfam13445   1 CPICLELFTDP-VLPCGHTFCRECLEEMSQKKGGKFKCP 38
rad18 TIGR00599
DNA repair protein rad18; All proteins in this family for which functions are known are ...
 6-88 5.26e-09

DNA repair protein rad18; All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273165 [Multi-domain]  Cd Length: 397  Bit Score: 58.86  E-value: 5.26e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687    6 DSPGPEVQPMDkQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRqtsiLPEQGvSALQNNFFISSL 85
Cdd:TIGR00599  14 TTPIPSLYPLD-TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP---KCPLCR----AEDQE-SKLRSNWLVSEI 84


                  ...
gi 552953687   86 MEA 88
Cdd:TIGR00599  85 VES 87
RING-HC_TRIM32_C-VII cd16587
RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar ...
 20-64 6.71e-09

RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins; TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs.


Pssm-ID: 438249 [Multi-domain]  Cd Length: 51  Bit Score: 52.02  E-value: 6.71e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  20 LVCSICLDRY----RCPKVLPCLHTFCERCLQNYIPPQSL-TLSCPVCRQ 64
Cdd:cd16587    1 LECPICLESFdegqLRPKLLHCGHTICEQCLEKLLASLSInGVRCPFCRK 50
RING-HC_TRIM25_C-IV cd16597
RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar ...
 20-65 7.05e-09

RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins; TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438259 [Multi-domain]  Cd Length: 71  Bit Score: 52.70  E-value: 7.05e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQ-SLTLSCPVCRQT 65
Cdd:cd16597    6 LTCSICLELFKDPVTLPCGHNFCGVCIEKTWDSQhGSEYSCPQCRAT 52
RING-HC_RNF208 cd16559
RING finger, HC subclass, found in RING finger protein 208 (RNF208) and similar proteins; ...
 20-68 8.31e-09

RING finger, HC subclass, found in RING finger protein 208 (RNF208) and similar proteins; RNF208 is an E3 ubiquitin-protein ligase whose activity can be modulated by S-nitrosylation. It contains a C3HC4-type RING-HC finger.


Pssm-ID: 438221 [Multi-domain]  Cd Length: 56  Bit Score: 52.24  E-value: 8.31e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRY----RCPKVLPCLHTFCERCLQNYIP--PQSLTLSCPVCRQTSIL 68
Cdd:cd16559    2 LLCPTCGHSYnftnKRPRILSCLHSVCEECLQILYEscPKYKFISCPTCKRETVL 56
RING-HC_RNF213 cd16561
RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; ...
 22-64 1.07e-08

RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins; RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex.


Pssm-ID: 438223 [Multi-domain]  Cd Length: 50  Bit Score: 51.51  E-value: 1.07e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:cd16561    5 CSICLEDLNDPVKLPCDHVFCEECIRQWLPGQM---SCPLCRT 44
RING-HC_TRIM62_C-IV cd16608
RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar ...
 14-66 1.32e-08

RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins; TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438270 [Multi-domain]  Cd Length: 52  Bit Score: 51.35  E-value: 1.32e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  14 PMDKQFLvCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLsCPVCRQTS 66
Cdd:cd16608    2 SLKDELL-CSICLSIYQDPVSLGCEHYFCRQCITEHWSRSEHRD-CPECRRTF 52
RING-HC_TRIM71_C-VII cd16589
RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar ...
 30-70 1.68e-08

RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and is therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438251 [Multi-domain]  Cd Length: 91  Bit Score: 52.41  E-value: 1.68e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  30 RCPKVLPCLHTFCERCLQNYIPP---QSLTLSCPVCRQTSILPE 70
Cdd:cd16589   48 RRLHVLPCLHAFCRQCLEAQRSPgagPALKLRCPVCDQKVVLSE 91
zf-RING_5 pfam14634
zinc-RING finger domain;
22-64 2.30e-08

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 50.50  E-value: 2.30e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 552953687   22 CSICLDRY---RCPKVLPCLHTFCERCLQNYIPPQsltlSCPVCRQ 64
Cdd:pfam14634   2 CNKCFKELsktRPFYLTSCGHIFCEECLTRLLQER----QCPICKK 43
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
 20-65 2.66e-08

RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain.


Pssm-ID: 438216 [Multi-domain]  Cd Length: 59  Bit Score: 50.77  E-value: 2.66e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCP-KVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQT 65
Cdd:cd16554    3 LTCPVCLDLYYDPyMCYPCGHIFCEPCLRQLAKSSPKNTPCPLCRTT 49
zf-C3HC4 pfam00097
Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a ...
 22-62 2.81e-08

Zinc finger, C3HC4 type (RING finger); The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway.


Pssm-ID: 395049 [Multi-domain]  Cd Length: 40  Bit Score: 50.05  E-value: 2.81e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 552953687   22 CSICLDRYRCPKV-LPCLHTFCERCLQNYIppQSLTLSCPVC 62
Cdd:pfam00097   1 CPICLEEPKDPVTlLPCGHLFCSKCIRSWL--ESGNVTCPLC 40
Bbox2 cd19756
B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of ...
 115-151 3.44e-08

B-box-type 2 zinc finger (Bbox2); The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2).


Pssm-ID: 380814 [Multi-domain]  Cd Length: 39  Bit Score: 49.72  E-value: 3.44e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 552953687 115 CPNHEGKTMEFYCEACETAMCGECR-AGEHREHGTVLL 151
Cdd:cd19756    2 CPEHPEEPLKLFCETCQELVCVLCLlSGEHRGHKVVPL 39
RING-HC_SH3RF3 cd16750
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 3 (SH3RF3) and ...
 20-63 3.84e-08

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 3 (SH3RF3) and similar proteins; SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in a screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1. Both contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438408 [Multi-domain]  Cd Length: 46  Bit Score: 49.73  E-value: 3.84e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRY-RCPKVLPCLHTFCERCLQNYIPPQSlTLSCPVCR 63
Cdd:cd16750    3 LECSVCLERLdTTSKVLPCQHTFCRRCLESIVSSRK-ELRCPECR 46
zf-RING_2 pfam13639
Ring finger domain;
22-63 4.60e-08

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 49.71  E-value: 4.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 552953687   22 CSICLDRY---RCPKVLPCLHTFCERCLQNYIppqSLTLSCPVCR 63
Cdd:pfam13639   3 CPICLEEFeegDKVVVLPCGHHFHRECLDKWL---RSSNTCPLCR 44
RING-HC_TRIM7-like_C-IV cd16594
RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and ...
 20-66 5.45e-08

RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins; TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells.


Pssm-ID: 438256 [Multi-domain]  Cd Length: 61  Bit Score: 49.99  E-value: 5.45e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQTS 66
Cdd:cd16594    6 LTCPICLDYFTDPVTLDCGHSFCRACIARCWEEPETSASCPQCRETC 52
RING-HC_RFPL4B cd16623
RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; ...
 20-69 5.94e-08

RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins; RFPL4B, also called RING finger protein 211 (RNF211), is an uncharacterized RING finger protein containing a typical C3HC4-type RING-HC finger.


Pssm-ID: 438285 [Multi-domain]  Cd Length: 63  Bit Score: 49.81  E-value: 5.94e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPP-QSLTLSCPVCRQTSILP 69
Cdd:cd16623    9 ATCPICLDFFSHPISLSCAHIFCFDCIQKWMTKrEDSILTCPLCRKEQKKP 59
vRING-HC-C4C4_RBBP6 cd16620
Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) ...
 20-70 8.64e-08

Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins; RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger.


Pssm-ID: 438282 [Multi-domain]  Cd Length: 55  Bit Score: 49.33  E-value: 8.64e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 552953687  20 LVCSICLDRYRCPKVLPCLH-TFCERCLQNYIPPQSLTlsCPVCRQTSILPE 70
Cdd:cd16620    4 LKCPICKDLMKDAVLTPCCGnSFCDECIRTALLEEDFT--CPTCKEPDVSPD 53
Bbox2_TRIM71_C-VII cd19796
B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar ...
 115-159 1.25e-07

B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins; TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7), and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs through mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380854 [Multi-domain]  Cd Length: 48  Bit Score: 48.46  E-value: 1.25e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687 115 CPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDVVEQHK 159
Cdd:cd19796    4 CEIHEHEVLRLYCDTCSVPICRECTMGEHRGHSFIYLQEAVQDSK 48
RING-HC_KEG-like cd23140
RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and ...
 21-67 1.43e-07

RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and similar proteins; KEG, also called RING-type E3 ubiquitin transferase KEG, is a RING E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It is essential for Arabidopsis growth and development. It acts as a negative regulator of abscisic acid signaling. It is required for ABSCISIC ACID-INSENSITIVE5 (ABI5) degradation, by mediating its ubiquitination. Together with EDR1, KEG may regulate endocytic trafficking and/or the formation of signaling complexes on trans-Golgi network (TGN)/ early endosome (EE) vesicles during stress responses. KEG is a multidomain protein that includes a C3HC4-type RING-HC finger, a kinase domain, ankyrin repeats, and 12 HERC2-like (for HECT and RCC1-like) repeats.


Pssm-ID: 438502 [Multi-domain]  Cd Length: 57  Bit Score: 48.79  E-value: 1.43e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 552953687  21 VCSICLDRY----RCPKVLPCLHTFCERCL-QNYIPPQSLTLSCPVCRQTSI 67
Cdd:cd23140    3 ECSVCSEGYnedeRVPLLLQCGHTFCKDCLsQMFIRCTDLTLKCPRCRQSVL 54
RING-HC_SH3RF1 cd16748
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and ...
 19-63 3.59e-07

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. It also plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and c-Jun N-terminal kinase (JNK) mediated apoptosis, linking Rac1 to downstream components. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. Moreover, SH3RF1 assembles an inhibitory complex with the actomyosin regulatory protein Shroom3, which links to the actin-myosin network to regulate neuronal process outgrowth. It also forms a complex with apoptosis-linked gene-2 (ALG-2) and ALG-2-interacting protein (ALIX/AIP1) in a calcium-dependent manner to play a role in the regulation of the JNK pathway. Furthermore, direct interaction of SH3RF1 and another molecular scaffold JNK-interacting protein (JIP) is required for apoptotic activation of JNKs. Interaction of SH3RF1 and E3 ubiquitin-protein isopeptide ligases, Siah proteins, further promotes JNK activation and apoptosis. In addition, SH3RF1 binds to and degrades TAK1, a crucial activator of both the JNK and the Relish signaling pathways. SH3RF1 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438406 [Multi-domain]  Cd Length: 48  Bit Score: 47.31  E-value: 3.59e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  19 FLVCSICLDRYRC-PKVLPCLHTFCERCLQNYIPPQSlTLSCPVCR 63
Cdd:cd16748    2 LLECPVCLERLDAtAKVLPCQHTFCRRCLLGIVGSRS-ELRCPECR 46
RING-HC_TRIM45_C-VII cd16588
RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar ...
 21-62 3.65e-07

RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain.


Pssm-ID: 438250 [Multi-domain]  Cd Length: 59  Bit Score: 47.52  E-value: 3.65e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIP-------------PQSLTLSCPVC 62
Cdd:cd16588    2 RCPVCGKLFQEPRLLPCLHTLCSPCLRQLEPfsvcglrggdrseKSNYSVLCPVC 56
RING-HC_TIF1_C-VI cd16585
RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) ...
 21-64 4.00e-07

RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) subfamily and similar proteins; The TIF1 subfamily of transcriptional cofactors containing RING-HC fingers includes TIF1alpha (TRIM24), TIF1beta (TRIM28), and TIF1gamma (TRIM33), which belong to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatin proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). TIF1delta (TRIM66) doesn't have a RING-HC finger and is not included in this model.


Pssm-ID: 438247 [Multi-domain]  Cd Length: 62  Bit Score: 47.58  E-value: 4.00e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687  21 VCSICLDRY--RCPKVLPCLHTFCERCLQNYIPPQSLT------------LSCPVCRQ 64
Cdd:cd16585    3 TCAVCKQSFqsREPKLLPCLHSFCKRCLPPADRAAANPspsggaagqvgvIRCPVCKQ 60
RING-HC_MmTRIM43-like cd23133
RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) ...
 17-64 4.67e-07

RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins; This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438495 [Multi-domain]  Cd Length: 57  Bit Score: 47.21  E-value: 4.67e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd23133    1 EETLTCSICQGIFMNPVYLRCGHKFCEACLLLFQEDIKFPAYCPMCRQ 48
RING-HC_ScPSH1-like cd16568
RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated ...
 20-64 4.76e-07

RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins; ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain.


Pssm-ID: 438230 [Multi-domain]  Cd Length: 54  Bit Score: 46.98  E-value: 4.76e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSlTLSCPVCRQ 64
Cdd:cd16568    5 QECIICHEYLYEPMVTTCGHTYCYTCLNTWFKSNR-SLSCPDCRT 48
Bbox2_TIF1g_C-VI cd19830
B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); ...
 111-159 5.07e-07

B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma); TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling. It inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis.


Pssm-ID: 380888  Cd Length: 53  Bit Score: 46.97  E-value: 5.07e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 552953687 111 RPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDVVEQHK 159
Cdd:cd19830    5 RPVFCPVHKQEQLKLFCETCDRLTCRDCQLLEHKEHRYQFLEEAFQNQK 53
RING-HC_malin cd16516
RING finger, HC subclass, found in malin and similar proteins; Malin ("mal" for seizure in ...
 20-65 5.20e-07

RING finger, HC subclass, found in malin and similar proteins; Malin ("mal" for seizure in French), also known as NHL repeat-containing protein 1 (NHLRC1), or EPM2B, is a nuclear E3 ubiquitin-protein ligase that ubiquitinates and promotes the degradation of laforin (EPM2A encoding protein phosphatase). Malin and laforin operate as a functional complex that play key roles in regulating cellular functions such as glycogen metabolism, unfolded cellular stress response, and proteolytic processes. They act as pro-survival factors that negatively regulate the Hipk2-p53 cell death pathway. They also negatively regulate cellular glucose uptake by preventing plasma membrane targeting of glucose transporters. Moreover, they degrade polyglucosan bodies in concert with glycogen debranching enzyme and brain isoform glycogen phosphorylase. Furthermore, they, together with Hsp70, form a new functional complex that suppress the cellular toxicity of misfolded proteins by promoting their degradation through the ubiquitin-proteasome system. Defects in either malin or laforin may cause Lafora disease (LD), a fatal form of teenage-onset autosomal recessive progressive myoclonus epilepsy. In addition, malin may have function, independent of laforin, in lysosomal biogenesis and/or lysosomal glycogen disposal. Malin contains six NHL-repeat protein-protein interaction domains and a C3HC4-type RING-HC finger.


Pssm-ID: 438179 [Multi-domain]  Cd Length: 52  Bit Score: 46.73  E-value: 5.20e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  20 LVCSICLDRY-----RCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQT 65
Cdd:cd16516    1 LECKVCFEKYshqqeHRPRNLPCGHVLCRECVTALAHPRRSKLECPFCRKA 51
mRING-HC-C3HC3D_LNX1-like cd16637
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, ...
 20-63 5.34e-07

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins; The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger.


Pssm-ID: 438299 [Multi-domain]  Cd Length: 42  Bit Score: 46.62  E-value: 5.34e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLtlsCPVCR 63
Cdd:cd16637    2 LTCHICLQPLVEPLDTPCGHTFCYKCLTNYLKIQQC---CPLDR 42
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
10-88 5.97e-07

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 52.40  E-value: 5.97e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552953687  10 PEVQPMDkQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLtlsCPVCRQtsilPEQgVSALQNNFFISSLMEA 88
Cdd:COG5432   17 PSLKGLD-SMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF---CPVCRE----DPC-ESRLRGSSGSREINES 86
RING-HC_AtRMA-like cd16745
RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) ...
 22-63 6.12e-07

RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins; AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region.


Pssm-ID: 438403 [Multi-domain]  Cd Length: 45  Bit Score: 46.32  E-value: 6.12e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16745    3 CNICLDLAQDPVVTLCGHLFCWPCLHKWLRRQSSQPECPVCK 44
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
 20-64 6.33e-07

RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins; TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain.


Pssm-ID: 438418 [Multi-domain]  Cd Length: 56  Bit Score: 46.83  E-value: 6.33e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTL------SCPVCRQ 64
Cdd:cd16762    4 LTCPICCCLFDDPRVLPCSHNFCKKCLEGILEGNVRTMlwrppfKCPTCRK 54
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
 22-65 7.47e-07

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome.


Pssm-ID: 438190 [Multi-domain]  Cd Length: 52  Bit Score: 46.45  E-value: 7.47e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIppqSLTLSCPVCRQT 65
Cdd:cd16527    3 CSLCLEERRHPTATPCGHLFCWSCITEWC---NEKPECPLCREP 43
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
 22-64 8.24e-07

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 46.14  E-value: 8.24e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIppQSLTLSCPVCRQ 64
Cdd:cd16509    6 CAICLDSLTNPVITPCAHVFCRRCICEVI--QREKAKCPMCRA 46
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
157-320 8.59e-07

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 52.46  E-value: 8.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 157 QHKAALQRQLEAVRGRLPQLSAAIALVggisQQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESICGAKQKvLQT 236
Cdd:COG4717  132 QELEALEAELAELPERLEELEERLEEL----RELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEE-LQQ 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 237 QLDTLRQGQEHIGSSCSFAEQALRlgsAPEVLLVRKHMRERLAALAAQAFPerphENAQLELVLEVDGLRRSVLNLGALL 316
Cdd:COG4717  207 RLAELEEELEEAQEELEELEEELE---QLENELEAAALEERLKEARLLLLI----AAALLALLGLGGSLLSLILTIAGVL 279


                 ....
gi 552953687 317 TTSA 320
Cdd:COG4717  280 FLVL 283
RING-HC_RNF112 cd16538
RING finger, HC subclass, found in RING finger protein 112 (RNF112) and similar proteins; ...
 22-65 9.66e-07

RING finger, HC subclass, found in RING finger protein 112 (RNF112) and similar proteins; RNF112, also known as brain finger protein (BFP), zinc finger protein 179 (ZNF179), or neurolastin, is a peripheral membrane protein that is predominantly expressed in the central nervous system and localizes to endosomes. It contains functional GTPase and C3HC4-type RING-HC finger domains and has been identified as a brain-specific dynamin family GTPase that affects endosome size and spine density. Moreover, RNF112 acts as a downstream target of sigma-1 receptor (Sig-1R) regulation and may play a novel role in neuroprotection by mediating the neuroprotective effects of dehydroepiandrosterone (DHEA) and its sulfated analog (DHEAS).


Pssm-ID: 438200 [Multi-domain]  Cd Length: 52  Bit Score: 46.14  E-value: 9.66e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQT 65
Cdd:cd16538    5 CSICLERLREPISLDCGHDFCIRCFSTHRIPGCEPPCCPECRKI 48
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 669-696 1.04e-06

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 45.47  E-value: 1.04e-06
                          10        20
                  ....*....|....*....|....*...
gi 552953687  669 FNAPTGVAVDSNGNIIVADWGNSRIQVW 696
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
RING-HC_TRIM9-like_C-I cd16576
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and ...
 20-64 1.04e-06

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins; Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate.


Pssm-ID: 438238 [Multi-domain]  Cd Length: 42  Bit Score: 45.86  E-value: 1.04e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNyippqsLTLSCPVCRQ 64
Cdd:cd16576    4 LKCPVCGSLFTEPVILPCSHNLCLGCALN------IQLTCPICHK 42
RING-HC_EHV1-like cd23130
RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) ...
 21-64 1.08e-06

RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) regulatory protein and similar proteins; EHV-1 regulatory protein belongs to the Vmw110 (IPC0) protein family. It contains a typical C3HC4-type RING-HC finger and binds zinc stably.


Pssm-ID: 438492 [Multi-domain]  Cd Length: 51  Bit Score: 45.81  E-value: 1.08e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  21 VCSICLD-RYRCPKVLPCLHTFCERCLQNYIppqSLTLSCPVCRQ 64
Cdd:cd23130    2 VCPICLDdPEDEAITLPCLHQFCYTCILRWL---QTSPTCPLCKT 43
Bbox2_TIF1a_C-VI cd19828
B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); ...
 111-162 1.09e-06

B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 380886  Cd Length: 57  Bit Score: 46.19  E-value: 1.09e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 552953687 111 RPLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDVVEQHKAAL 162
Cdd:cd19828    2 RPVFCPFHKKEQLKLYCETCDKLTCRDCQLLEHKEHRYQFIEEAFQNQKVII 53
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
 22-64 1.35e-06

RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438226 [Multi-domain]  Cd Length: 50  Bit Score: 45.47  E-value: 1.35e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYR-CPKVLPCLHTFCERCLQNYIPpqSLTLSCPVCRQ 64
Cdd:cd16564    3 CPVCYEDFDdAPRILSCGHSFCEDCLVKQLV--SMTISCPICRR 44
RING-HC_RNF182 cd16555
RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; ...
 20-66 1.84e-06

RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins; RNF182 is a brain-enriched E3 ubiquitin-protein ligase that stimulates E2-dependent polyubiquitination in vitro. It is upregulated in Alzheimer"s disease (AD) brains and neuronal cells exposed to injurious insults. It interacts with ATP6V0C and promotes its degradation by the ubiquitin-proteosome pathway, suggesting a very specific role in controlling the turnover of an essential component of the neurotransmitter release machinery. RNF182 contains an N-terminal C3HC4-type RING-HC finger, and a C-terminal transmembrane domain.


Pssm-ID: 438217 [Multi-domain]  Cd Length: 55  Bit Score: 45.51  E-value: 1.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRY----RCPKVLPCLHTFCERCLQNYI----PPQSLtLSCPVCRQTS 66
Cdd:cd16555    2 LECKICYNRYdlrqRRPKVLECCHRVCAKCLYKIVdlgdSSPSV-LVCPFCRFET 55
RING-HC_MID1 cd16753
RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as ...
 20-77 1.85e-06

RING finger, HC subclass, found in midline-1 (MID1) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID1 hetero-dimerizes in vitro with its paralog MID2.


Pssm-ID: 438411 [Multi-domain]  Cd Length: 72  Bit Score: 46.19  E-value: 1.85e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYI--------PPQSLT-LSCPVCRQTSILPEQGVSALQ 77
Cdd:cd16753    6 LTCPICLELFEDPLLLPCAHSLCFNCAHRILvshcasneSVESITaFQCPTCRYVITLNQRGLEGLK 72
RING-HC_RNF168 cd16550
RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; ...
 21-64 2.04e-06

RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins; RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin.


Pssm-ID: 438212 [Multi-domain]  Cd Length: 48  Bit Score: 45.06  E-value: 2.04e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQ 64
Cdd:cd16550    2 LCPICLEILVEPVTLPCNHTLCMPCFQSTVEKASLC--CPLCRL 43
RING-HC_RNF151 cd16547
RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; ...
 20-64 2.14e-06

RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins; RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain.


Pssm-ID: 438209 [Multi-domain]  Cd Length: 49  Bit Score: 45.14  E-value: 2.14e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:cd16547    4 LICSICHGVLRCPVRLSCSHIFCKKCILQWLKRQE---TCPCCRK 45
RING-HC_TRIM38_C-IV cd16600
RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar ...
 22-63 2.21e-06

RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar proteins; TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates Tumor necrosis factor alpha (TNF-alpha)- and interleukin-1beta-triggered Nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. TRIM38 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438262 [Multi-domain]  Cd Length: 58  Bit Score: 45.15  E-value: 2.21e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSL------TLSCPVCR 63
Cdd:cd16600    8 CSICLQLMTEPVSINCGHSYCKRCIVSFLENQSQlepgleTFSCPQCR 55
RING-HC_RNFT1-like cd16532
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein ...
 21-63 2.41e-06

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins; Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear.


Pssm-ID: 438194 [Multi-domain]  Cd Length: 41  Bit Score: 44.60  E-value: 2.41e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16532    2 ICPICQDEFKDPVVLRCKHIFCEDCVSEWFERER---TCPLCR 41
zf-C3HC4_3 pfam13920
Zinc finger, C3HC4 type (RING finger);
22-64 2.58e-06

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 464042 [Multi-domain]  Cd Length: 50  Bit Score: 44.67  E-value: 2.58e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 552953687   22 CSICLDRYRCPKVLPCLHT-FCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:pfam13920   5 CVICLDRPRNVVLLPCGHLcLCEECAERLLRKKK---KCPICRQ 45
WD40 COG2319
WD40 repeat [General function prediction only];
257-700 2.82e-06

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 50.29  E-value: 2.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 257 QALRLGSAPEVLLVRKHMRERLAALAAQAFPERPHENAQLELVLEVDGLRRsvlnlgALLTTSATAHETVATGEGLRQAL 336
Cdd:COG2319    1 ALSADGAALAAASADLALALLAAALGALLLLLLGLAAAVASLAASPDGARL------AAGAGDLTLLLLDAAAGALLATL 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 337 VGQPASLTVTTKDKDGRLVRTGSAELCAEITGPDGVRLAVPVVDHKNGTYELVYTArtEGDLLLSVllygqpvrGSPFRV 416
Cdd:COG2319   75 LGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSP--DGKTLASG--------SADGTV 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 417 RALRPGDlppspddvKRRVKSPGGPGSHVRQKAVRRPSSMYSTGGKrkDNPIedeLVFRVGSrGREKGEFTNLQGV--SA 494
Cdd:COG2319  145 RLWDLAT--------GKLLRTLTGHSGAVTSVAFSPDGKLLASGSD--DGTV---RLWDLAT-GKLLRTLTGHTGAvrSV 210

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 495 ASS--GRIVVADSNNQCIQVFS-NEGQFKFRFgvrgrsPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIG 571
Cdd:COG2319  211 AFSpdGKLLASGSADGTVRLWDlATGKLLRTL------TGHSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTL 284

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 572 AGRLMGPKGVAVDRNGHIIVV--DNKSCCVFTFQpNGKLVGRFGGrgatdrHFAGPHFVAVNNKNEIVVTDFHNHSVKVY 649
Cdd:COG2319  285 TGHSGGVNSVAFSPDGKLLASgsDDGTVRLWDLA-TGKLLRTLTG------HTGAVRSVAFSPDGKTLASGSDDGTVRLW 357

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|..
gi 552953687 650 SAD-GEFLFKFGSHGegngqfNAPTGVAVDSNGNIIVADWGNSRIQVWRMES 700
Cdd:COG2319  358 DLAtGELLRTLTGHT------GAVTSVAFSPDGRTLASGSADGTVRLWDLAT 403
Bbox2_TRIM16-like cd19769
B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, ...
 115-159 2.98e-06

B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, TRIM47 and similar proteins; This family includes a group of tripartite motif-containing proteins, such as TRIM16, TRIM29 and TRIM47. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor through affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. TRIM16 and TRIM29 belong to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. TRIM47 belongs to the C-IV subclass of TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380827 [Multi-domain]  Cd Length: 46  Bit Score: 44.62  E-value: 2.98e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687 115 CPNHeGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDVVEQHK 159
Cdd:cd19769    3 CPIH-KKPLELFCRTDQMCICELCAKEEHRGHDVVTVEEEREKKE 46
Bbox2_TRIM45_C-X cd19785
B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar ...
 112-154 3.40e-06

B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins; TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380843  Cd Length: 43  Bit Score: 44.33  E-value: 3.40e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687 112 PLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDV 154
Cdd:cd19785    1 PVLCPFHPAEELRLFCETCDKPVCRDCVLVEHRGHQCDFTSDV 43
RING-HC_TRIM9 cd16755
RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar ...
 20-65 3.51e-06

RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins; TRIM9, human ortholog of rat Spring, also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducin repeat-containing protein (beta-TrCP) through its N-terminal degron motif depending on the phosphorylation status, and thus negatively regulates nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and the exocytic soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438413 [Multi-domain]  Cd Length: 55  Bit Score: 44.64  E-value: 3.51e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYI-------PPQSlTLSCPVCRQT 65
Cdd:cd16755    4 LKCPVCGSFYREPIILPCSHNLCLACARNILvqtpeaeSPQS-CLTCPQCHRS 55
RING-HC_RNF5-like cd16534
RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 ...
 22-63 3.53e-06

RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins; RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438196 [Multi-domain]  Cd Length: 44  Bit Score: 44.21  E-value: 3.53e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16534    3 CNICLDTASDPVVTMCGHLFCWPCLYQWLETRPDRQTCPVCK 44
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 622-649 3.64e-06

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 43.93  E-value: 3.64e-06
                          10        20
                  ....*....|....*....|....*...
gi 552953687  622 FAGPHFVAVNNKNEIVVTDFHNHSVKVY 649
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
RING-H2_RNF167 cd16797
RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; ...
 21-64 3.67e-06

RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins; RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) ubiquitination. It ubiquitinates AMPA-type glutamate receptor subunit GluA2 and regulates its surface expression, and thus acts as a selective regulator of AMPAR-mediated neurotransmission. It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. RNF167 is widely conserved in metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, two transmembrane domains (TM1 and TM2), and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.


Pssm-ID: 319711 [Multi-domain]  Cd Length: 46  Bit Score: 44.26  E-value: 3.67e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYRCP---KVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQ 64
Cdd:cd16797    2 VCAICLDEYEEGdklRVLPCSHAYHSKCVDPWLTQTKKT--CPVCKQ 46
RING-HC_IRC20-like cd23135
RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers ...
 17-63 3.77e-06

RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers protein 20 (IRC20) and similar proteins; IRC20 is an uncharacterized ATP-dependent helicase that is probably involved in a pathway contributing to genomic integrity. IRC20 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438497 [Multi-domain]  Cd Length: 44  Bit Score: 44.04  E-value: 3.77e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd23135    1 KQKLSCSICFSEIRSGAILKCGHFFCLSCIASWLREKS---TCPLCK 44
RING-HC_RNF114 cd16540
RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; ...
 20-63 4.42e-06

RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins; RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438202 [Multi-domain]  Cd Length: 46  Bit Score: 43.98  E-value: 4.42e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCR 63
Cdd:cd16540    2 FTCPVCLEIFETPVRVPCGHVFCNACLQECLKPKKPV--CAVCR 43
Bbox2_BRAT-like cd19798
B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and ...
 111-143 4.65e-06

B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins; BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. This family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380856  Cd Length: 44  Bit Score: 43.83  E-value: 4.65e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 552953687 111 RPLSCPNHEGKTMEFYCEACETAMCGECRAGEH 143
Cdd:cd19798    2 KPVFCPKHPNEVLKFFCKTCNIPICKDCTLLDH 34
NHL-2_like cd14951
NHL repeat domain of NHL repeat-containing protein 2 and similar proteins; NHL ...
 477-695 4.90e-06

NHL repeat domain of NHL repeat-containing protein 2 and similar proteins; NHL repeat-containing protein 2 (NHLRC2) and related bacterial proteins; members of this eukaryotic and bacterial family are uncharacterized, the NHL repeat domain is found C-terminally of a thioredoxin domain. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271321 [Multi-domain]  Cd Length: 334  Bit Score: 49.11  E-value: 4.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 477 GSRGREKGEFT-----NLQGVSAASSGRIVVADSNNQCIQV--FSNE--------G-QFKFRFGVRGRSPGQLQRPTGVA 540
Cdd:cd14951    4 GERGLKDGSFAeasfnEPQGLALLPGNILYVADTENHALRKidLETGtvttlagtGeQGRDGEGGGPGREQPLSSPWDVA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 541 V-DTNGDIIVA----------DYDNRWVSIFSpegkfktkiGAGR---LMG----------PKGVAVDRNGHIIVVD--- 593
Cdd:cd14951   84 WgPEDDILYIAmagthqiwayDLDTGTCRVFA---------GSGNegnRNGpypheawfaqPSGLSLAGWGELFVADses 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 594 ----------NKSCCVFTFQPNGKLVGRFG---GRGATDR--HfagPHFVAVNNKNEIVVTDFHNHSVKVY-SADGE--F 655
Cdd:cd14951  155 sairavslkdGGVKTLVGGTRVGTGLFDFGdrdGPGAEALlqH---PLGVAALPDGSVYVADTYNHKIKRVdPATGEvsT 231

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 552953687 656 LFKFGSHGEGN--GQFNAPTGVAVDSNGNIIVADWGNSRIQV 695
Cdd:cd14951  232 LAGTGKAGYKDleAQFSEPSGLVVDGDGRLYVADTNNHRIRR 273
RING-HC_TRIM4_C-IV cd16590
RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar ...
 20-66 5.37e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins; TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria.


Pssm-ID: 438252 [Multi-domain]  Cd Length: 61  Bit Score: 44.25  E-value: 5.37e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQTS 66
Cdd:cd16590    7 LTCPICLDYFQDPVSIECGHNFCRGCLHRNWAPGGGPFPCPECRHPS 53
RING-HC_TRIM26_C-IV cd16598
RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar ...
 22-63 5.85e-06

RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins; TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438260 [Multi-domain]  Cd Length: 64  Bit Score: 44.38  E-value: 5.85e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLT--LSCPVCR 63
Cdd:cd16598    7 CSICLDYLRDPVTIDCGHNFCRSCITDYCPISGGHerPVCPLCR 50
RING-HC_SH3RF2 cd16749
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and ...
 20-63 5.92e-06

RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and similar proteins; SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438407 [Multi-domain]  Cd Length: 46  Bit Score: 43.77  E-value: 5.92e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRC-PKVLPCLHTFCERCLQNYIPPQSlTLSCPVCR 63
Cdd:cd16749    1 LECPVCFEKLDVtAKVLPCQHTFCKPCLQRIFKARK-ELRCPECR 44
RING-HC_SH3RFs cd16570
RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, ...
 20-63 6.22e-06

RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, SH3RF3, and similar proteins; SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH) that is required for pro-apoptotic JNK activation. SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2) and may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs.


Pssm-ID: 438232 [Multi-domain]  Cd Length: 44  Bit Score: 43.57  E-value: 6.22e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRC-PKVLPCLHTFCERCLQNYIPPQSlTLSCPVCR 63
Cdd:cd16570    1 LECPVCLERLDVsAKVLPCQHTFCKRCLQIIVASRG-ELRCPECR 44
DUF5128 pfam17170
6-bladed beta-propeller; This family is a 6-bladed beta-propeller structure of unknown ...
 498-657 7.47e-06

6-bladed beta-propeller; This family is a 6-bladed beta-propeller structure of unknown function. There is a highly conserved FDxxG motif which might be important.


Pssm-ID: 407298 [Multi-domain]  Cd Length: 321  Bit Score: 48.48  E-value: 7.47e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  498 GRIVVADSNNQCIQVFSNEGQFKFRFGVRGRSPGQLQRPTGVAVDTNGDII-VADYDNRWVSIFSPEG-KFKTKigagrl 575
Cdd:pfam17170  54 DRIFVFDSNTNNLFVFDKKGKFVRQIGAQGNGPGEYLQINDFIIDKSNNSIyILDFMQNKILTYDLDGySFIGE------ 127

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  576 mgpkgvavdrnghiIVVDNKSCCVFTFQPNgKLVgrFGGRGATDRHFAGPHFVAVNNKNEIVVTDF---------HNHSV 646
Cdd:pfam17170 128 --------------INLDLLPSDCCQLDKG-KLA--FDSSGFDDGKRSGFYLVITDELGNIISGFFpaeftlgilFNSSV 190

                         170
                  ....*....|.
gi 552953687  647 KVYSADGEFLF 657
Cdd:pfam17170 191 PFYEYGDNIYF 201
RING-HC_TRIM50_like_C-IV cd16605
RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 ...
 20-64 7.66e-06

RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins; TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. This subfamily also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins that may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by N-terminal RBCC domains only.


Pssm-ID: 438267 [Multi-domain]  Cd Length: 45  Bit Score: 43.20  E-value: 7.66e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd16605    1 LLCPICLEVFKEPLMLQCGHSYCKSCLVSLSGELDGQLLCPVCRQ 45
RING-HC_RNF141 cd16545
RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; ...
 21-63 7.70e-06

RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins; RNF141, also known as zinc finger protein 230 (ZNF230), is a RING finger protein present primarily in the nuclei of spermatogonia, the acrosome, and the tail of spermatozoa. It may have a broad function during early development of vertebrates. It plays an important role in spermatogenesis, including spermatogenic cell proliferation and sperm maturation, as well as motility and fertilization. It also exhibits DNA binding activity. RNF141/ZNF230 gene mutations may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription.


Pssm-ID: 438207 [Multi-domain]  Cd Length: 40  Bit Score: 43.23  E-value: 7.70e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  21 VCSICLDRyRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16545    2 ECCICMDR-KADLILPCAHSYCQKCIDKWSDRHR---TCPICR 40
RING-HC_DTX3-like cd16506
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like ...
 21-63 8.53e-06

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like (DTX3L) and similar proteins; This subfamily contains Deltex3 (DTX3) and Deltex-3-like (DTX3L), both of which are E3 ubiquitin-protein ligases belonging to the Deltex (DTX) family. DTX3, also known as RING finger protein 154 (RNF154), has a biological function that remains unclear. DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. In contrast to other DTXs, both DTX3 and DTX3L contain a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N termini and further enhance self-ubiquitination.


Pssm-ID: 438169 [Multi-domain]  Cd Length: 45  Bit Score: 43.12  E-value: 8.53e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  21 VCSICLDRYRCPKVLP-CLHTFCERCLQnyippQSLTL--SCPVCR 63
Cdd:cd16506    2 TCPICLDEIQNKKTLEkCKHSFCEDCID-----RALQVkpVCPVCG 42
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
 17-66 9.64e-06

RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins; TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438261 [Multi-domain]  Cd Length: 66  Bit Score: 43.60  E-value: 9.64e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSlTLSCPVCRQTS 66
Cdd:cd16599    2 KEELLCPICYEPFREAVTLRCGHNFCKGCVSRSWERQP-RAPCPVCKEAS 50
RING-HC_AtBARD1-like cd23146
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...
 20-65 1.08e-05

RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins; AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438508 [Multi-domain]  Cd Length: 54  Bit Score: 43.23  E-value: 1.08e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQT 65
Cdd:cd23146    5 LKCPICLKLLNRPVLLPCDHIFCSSCITDSTKVGS---DCPVCKLP 47
zf-C3HC4_2 pfam13923
Zinc finger, C3HC4 type (RING finger);
21-62 1.14e-05

Zinc finger, C3HC4 type (RING finger);


Pssm-ID: 404756 [Multi-domain]  Cd Length: 40  Bit Score: 42.81  E-value: 1.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 552953687   21 VCSICLDRYRCPKVL-PCLHTFCERCLQnyippQSLTLS--CPVC 62
Cdd:pfam13923   1 MCPICMDMLKDPSTTtPCGHVFCQDCIL-----RALRAGneCPLC 40
RING-HC_ScRAD18-like cd23148
RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 ...
 18-65 1.23e-05

RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins; RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438510 [Multi-domain]  Cd Length: 52  Bit Score: 42.91  E-value: 1.23e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  18 QFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQT 65
Cdd:cd23148    2 HALRCHICKDLLKAPMRTPCNHTFCSFCIRTHLNNDA---RCPLCKAE 46
RING-HC_RNF224 cd16565
RING finger, HC subclass, found in RING finger protein RNF224 and similar proteins; RNF224 is ...
 20-72 1.23e-05

RING finger, HC subclass, found in RING finger protein RNF224 and similar proteins; RNF224 is uncharacterized C3HC4-type RING-HC finger-containing proteins. It may function as an E3 ubiquitin-protein ligase.


Pssm-ID: 438227 [Multi-domain]  Cd Length: 59  Bit Score: 43.27  E-value: 1.23e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 552953687  20 LVCSICLDRY----RCPKVLPCLHTFCERCLQ--NYIPPQSLTLSCPVCRQTSILPEQG 72
Cdd:cd16565    1 LDCIICYSAYdlstRLPRRLYCGHTFCQACLKrlDTVINEQRWIPCPQCRQNTPTPRGG 59
RING-HC_RAD5 cd23131
RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; ...
 22-63 1.34e-05

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438493 [Multi-domain]  Cd Length: 65  Bit Score: 43.20  E-value: 1.34e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  22 CSICLDRYRCPK---VLPCLHTFCERCLQNYIPPQ---SLTLSCPVCR 63
Cdd:cd23131    6 CSICTQEPIEVGevvFTECGHSFCEDCLLEYIEFQnkkKLDLKCPNCR 53
WD40 COG2319
WD40 repeat [General function prediction only];
524-702 1.39e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 47.98  E-value: 1.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 524 GVRGRSPGQLQRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVV--DNKSCCVFT 601
Cdd:COG2319   69 ALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHTGAVRSVAFSPDGKTLASgsADGTVRLWD 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 602 FQpNGKLVGRFGGrgatdrHFAGPHFVAVNNKNEIVVTDFHNHSVKVYS-ADGEFLFKFGSHGegngqfNAPTGVAVDSN 680
Cdd:COG2319  149 LA-TGKLLRTLTG------HSGAVTSVAFSPDGKLLASGSDDGTVRLWDlATGKLLRTLTGHT------GAVRSVAFSPD 215

                        170       180
                 ....*....|....*....|..
gi 552953687 681 GNIIVADWGNSRIQVWRMESPR 702
Cdd:COG2319  216 GKLLASGSADGTVRLWDLATGK 237
RING-HC_Cbl-c cd16710
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; ...
 13-63 1.67e-05

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins; Cbl-c, also known as RING finger protein 57 (RNF57), SH3-binding protein Cbl-3, SH3-binding protein Cbl-c, or signal transduction protein Cbl-c, is an E3 ubiquitin-protein ligase expressed exclusively in epithelial cells. It contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a C3HC4-type RING-HC finger, and a short proline-rich region, but lacks the ubiquitin-associated (UBA) leucine zipper motif that are present in Cbl and Cbl-b. Cbl-c acts as a regulator of epidermal growth factor receptor (EGFR)-mediated signal transduction. It also suppresses v-Src-induced transformation through ubiquitin-dependent protein degradation. Moreover, Cbl-c ubiquitinates and downregulates RETMEN2A and implicates Enigma (PDLIM7) as a positive regulator of RETMEN2A by blocking Cbl-mediated ubiquitination and degradation. The ubiquitin ligase activity of Cbl-c is increased via the interaction of its RING-HC finger domain with a LIM domain of the paxillin homolog, hydrogen peroxide induced construct 5 (Hic-5).


Pssm-ID: 438370 [Multi-domain]  Cd Length: 65  Bit Score: 43.15  E-value: 1.67e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  13 QPMDKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCR 63
Cdd:cd16710    7 QAMNSTFELCKICAERDKDVRIEPCGHLLCSCCLAAWQHSDSQT--CPFCR 55
RING-HC_RNF170 cd16553
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...
 22-65 1.70e-05

RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438215 [Multi-domain]  Cd Length: 57  Bit Score: 42.66  E-value: 1.70e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSL--TLSCPVCRQT 65
Cdd:cd16553    4 CPICLQDARFPVETNCGHLFCGPCIITYWRHGSWlgAVSCPVCRQT 49
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
 20-63 1.71e-05

RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438211 [Multi-domain]  Cd Length: 47  Bit Score: 42.49  E-value: 1.71e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVL-PCLHTFCERCLQNYIppQSLTLSCPVCR 63
Cdd:cd16549    2 FSCPICLEVYHKPVVItSCGHTFCGECLQPCL--QVASPLCPLCR 44
mRING-HC-C3HC3D_LNX2 cd16780
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); ...
 20-64 1.83e-05

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2); LNX2, also known as numb-binding protein 2, or PDZ domain-containing RING finger protein 1 (PDZRN1), is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. It interacts with contactin-associated protein 4 (Caspr4, also known as CNTNAP4) in a PDZ domain-dependent manner, which modulates the proliferation and neuronal differentiation of neural progenitor cells (NPCs). LNX2 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAF motif for Numb/ Numblike-LNX interaction, and four PDZ domains necessary for the binding of substrates, including ErbB2, RhoC, the presynaptic protein CAST, the melanoma/cancer-testis antigen MAGEB18 and several proteins associated with cell junctions, such as JAM4 and the Coxsackievirus and adenovirus receptor (CAR).


Pssm-ID: 319694 [Multi-domain]  Cd Length: 45  Bit Score: 42.17  E-value: 1.83e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLtlsCPVCRQ 64
Cdd:cd16780    4 LVCHICLQPLLQPLDTPCGHTFCFKCLRNFLQEKDF---CPLDRK 45
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
 20-65 1.94e-05

RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins; TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle.


Pssm-ID: 438266 [Multi-domain]  Cd Length: 49  Bit Score: 42.41  E-value: 1.94e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPP-QSLTLSCPVCRQT 65
Cdd:cd16604    1 LSCPICLDLLKDPVTLPCGHSFCMGCLGALWGAgRGGRASCPLCRQT 47
RING-HC_TRIM72_C-IV cd16612
RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar ...
 18-71 1.95e-05

RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins; TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438274 [Multi-domain]  Cd Length: 60  Bit Score: 42.80  E-value: 1.95e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 552953687  18 QFLVCSICLDRYRCPKVLPCLHTFCERCLQNyIP--PQSLTLSCPVCrQTSILPEQ 71
Cdd:cd16612    3 QDLSCPLCLKLFQSPVTTECGHTFCQDCLSR-VPkeEDGGSTSCPTC-QAPTKPEQ 56
RING-HC_RNFT2 cd16742
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2 ...
 21-67 2.13e-05

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2(RNFT2); RNFT2, also known as transmembrane protein 118 (TMEM118), is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.


Pssm-ID: 438400 [Multi-domain]  Cd Length: 67  Bit Score: 42.94  E-value: 2.13e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQTSI 67
Cdd:cd16742   15 ICAICQAEFREPLILICQHVFCEECLCLWFDRER---TCPLCRSVVV 58
RING-HC_Topors cd16574
RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein ...
 22-64 2.16e-05

RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein (Topors) and similar proteins; Topors, also known as topoisomerase I-binding RING finger protein, tumor suppressor p53- binding protein 3, or p53-binding protein 3 (p53BP3), is a ubiquitously expressed nuclear E3 ubiquitin-protein ligase that can ligate both ubiquitin and small ubiquitin-like modifier (SUMO) to substrate proteins in the nucleus. It contains an N-terminal C3HC4-type RING-HC finger which ligates ubiquitin to its target proteins including DNA topoisomerase I, p53, NKX3.1, H2AX, and the AAV-2 Rep78/68 proteins. As a RING-dependent E3 ubiquitin ligase, Topors works with the E2 enzymes UbcH5a, UbcH5c, and UbcH6, but not with UbcH7, CDC34, or UbcH2b. Topors acts as a tumor suppressor in various malignancies. It regulates p53 modification, suggesting it may be responsible for astrocyte elevated gene-1 (AEG-1, also known as metadherin, or LYRIC) ubiquitin modification. Plk1-mediated phosphorylation of Topors inhibits Topors-mediated sumoylation of p53, whereas p53 ubiquitination is enhanced, leading to p53 degradation. It also functions as a negative regulator of the prostate tumor suppressor NKX3.1. Moreover, Topors is associated with promyelocytic leukemia nuclear bodies, and may be involved in the cellular response to camptothecin. It also plays a key role in the turnover of H2AX protein, discriminating the type of DNA damaging stress. Furthermore, Topors is a cilia-centrosomal protein associated with autosomal dominant retinal degeneration. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa (adRP).


Pssm-ID: 438236 [Multi-domain]  Cd Length: 47  Bit Score: 42.27  E-value: 2.16e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYRCPKVL--PCLHTFCERCLQNYippQSLTLSCPVCRQ 64
Cdd:cd16574    4 CPICLDRFENEKAFldGCFHAFCFTCILEW---SKVKNECPLCKQ 45
RING-HC_AtBRCA1-like cd23147
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...
 20-63 2.27e-05

RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins; AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438509 [Multi-domain]  Cd Length: 54  Bit Score: 42.46  E-value: 2.27e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQnyippQSLTLS--CPVCR 63
Cdd:cd23147    5 LKCPICLSLFKSAANLSCNHCFCAGCIG-----ESLKLSaiCPVCK 45
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
 22-64 2.30e-05

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 41.87  E-value: 2.30e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLqnyipPQSLTLS--CPVCRQ 64
Cdd:cd16514    4 CSLCLRLLYEPVTTPCGHTFCRACL-----ERCLDHSpkCPLCRT 43
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
 21-64 2.57e-05

RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins; TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438245 [Multi-domain]  Cd Length: 63  Bit Score: 42.51  E-value: 2.57e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLT--LSCPVCRQ 64
Cdd:cd16583    7 VCPICQEPLKEAVSTDCGHLFCRMCLTQHAKKASASgvFSCPVCRK 52
RING-HC_RNF10 cd16536
RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 ...
 22-62 2.62e-05

RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins; RNF10 is an E3 ubiquitin-protein ligase that interacts with mesenchyme Homeobox 2 (MEOX2) transcription factor, a regulator of the proliferation, differentiation and migration of vascular smooth muscle cells and cardiomyocytes; it enhances Meox2 activation of the p21 promoter. It also regulates the expression of myelin-associated glycoprotein (MAG) genes and is required for myelin production in Schwann cells of the peripheral nervous system. Moreover, RNF10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. RNF10 contains a C3HC4-type RING-HC finger and three putative nuclear localization signals.


Pssm-ID: 438198 [Multi-domain]  Cd Length: 54  Bit Score: 42.23  E-value: 2.62e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYippqsLTLS------CPVC 62
Cdd:cd16536    3 CPICLEPPVAPRITRCGHIFCWPCILRY-----LSLSekkwrkCPIC 44
RING-HC_RNFT1 cd16741
RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 ...
 21-63 3.29e-05

RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 (RNFT1); RNFT1, also known as protein PTD016, is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear.


Pssm-ID: 438399 [Multi-domain]  Cd Length: 58  Bit Score: 42.18  E-value: 3.29e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16741   16 ICAICQAEFRKPILLICQHVFCEECISLWFNREK---TCPLCR 55
RING-HC_TRIM60-like_C-IV cd16607
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 ...
 22-63 3.62e-05

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 and similar proteins; TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. RNF33 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. Both TRIM60 and TRIM75 belong the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B2-box, and two coiled coil domains, as well as a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of the TRIM family that contains RBCC domains only. Its biological function remains unclear.


Pssm-ID: 438269 [Multi-domain]  Cd Length: 48  Bit Score: 41.64  E-value: 3.62e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16607    4 CPICLDYLKDPVTINCGHNFCRSCISMSWKDLQDTFPCPVCR 45
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
152-307 3.80e-05

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 47.22  E-value: 3.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  152 RDVVEQHKAAL-----QRQLEAVRGRLPQLSAAIAlvggisqQLQERKAEALAQISAAFEDLEQALQQRKQALVSDLESI 226
Cdd:COG4913   271 LAELEYLRAALrlwfaQRRLELLEAELEELRAELA-------RLEAELERLEARLDALREELDELEAQIRGNGGDRLEQL 343

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  227 cGAKQKVLQTQLDTLRQGQEhigsscSFAEQALRLG-----SAPEVLLVRKHMRERLAALAAQafpERPHENAQLELVLE 301
Cdd:COG4913   344 -EREIERLERELEERERRRA------RLEALLAALGlplpaSAEEFAALRAEAAALLEALEEE---LEALEEALAEAEAA 413


                  ....*.
gi 552953687  302 VDGLRR 307
Cdd:COG4913   414 LRDLRR 419
RING-HC_TRIM8_C-V cd16580
RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar ...
 20-64 3.88e-05

RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins; TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1.


Pssm-ID: 438242 [Multi-domain]  Cd Length: 67  Bit Score: 42.19  E-value: 3.88e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd16580   12 LICPICLHVFVEPVQLPCKHNFCRGCIGEAWAKDAGLVRCPECNQ 56
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 153-312 4.03e-05

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 47.09  E-value: 4.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   153 DVVEQHkAALQRQLEAVRGRLPQ----LSAAIALV---GGISQQLQERKAEALAQISAAFEDLEQALQQRKQA------L 219
Cdd:pfam01576  219 DLQEQI-AELQAQIAELRAQLAKkeeeLQAALARLeeeTAQKNNALKKIRELEAQISELQEDLESERAARNKAekqrrdL 297

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   220 VSDLESicgakqkvLQTQL-DTLrqgqehigsSCSFAEQALRLGSAPEVLLVRKHMRERLAALAAQAFPERPHENAQL-E 297
Cdd:pfam01576  298 GEELEA--------LKTELeDTL---------DTTAAQQELRSKREQEVTELKKALEEETRSHEAQLQEMRQKHTQALeE 360

                          170
                   ....*....|....*
gi 552953687   298 LVLEVDGLRRSVLNL 312
Cdd:pfam01576  361 LTEQLEQAKRNKANL 375
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 533-560 4.18e-05

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 40.85  E-value: 4.18e-05
                          10        20
                  ....*....|....*....|....*...
gi 552953687  533 LQRPTGVAVDTNGDIIVADYDNRWVSIF 560
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
RING-H2_PA-TM-RING cd16454
RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family; The PA-TM-RING ...
 21-63 4.60e-05

RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family; The PA-TM-RING family represents a group of transmembrane-type E3 ubiquitin ligases, which has been characterized by an N-terminal transient signal peptide, a PA (protease-associated) domain, a TM (transmembrane) domain, as well as a C-terminal C3H2C3-type RING-H2 finger domain. It includes RNF13, RNF167, ZNRF4 (zinc and RING finger 4), GRAIL (gene related to anergy in lymphocytes)/RNF128, RNF130, RNF133, RNF148, RNF149 and RNF150 (which are more closely related), as well as RNF43 and ZNRF3, which have substantially longer C-terminal tail extensions compared with the others. PA-TM-RING proteins are expressed at low levels in all mammalian tissues and species, but they are not present in yeast. They play a common regulatory role in intracellular trafficking/sorting, suggesting that abrogation of their function may result in dysregulation of cellular signaling events in cancer.


Pssm-ID: 438118 [Multi-domain]  Cd Length: 43  Bit Score: 41.11  E-value: 4.60e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  21 VCSICLDRYRCP---KVLPCLHTFCERCLqnyIPPQSLTLSCPVCR 63
Cdd:cd16454    1 TCAICLEEFKEGekvRVLPCNHLFHKDCI---DPWLEQHNTCPLCR 43
RING-HC_TIF1gamma cd16766
RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); ...
 21-64 4.73e-05

RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma); TIF1gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling, inhibiting the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 proteins, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis.


Pssm-ID: 438422  Cd Length: 67  Bit Score: 41.77  E-value: 4.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 552953687  21 VCSICLDRYRC-PKVLPCLHTFCERCLQNyiPPQSLT----------------LSCPVCRQ 64
Cdd:cd16766    7 VCKQSLQSRDAePKLLPCLHSFCRRCLPE--PERQLSvpvpggsngdiqqvgvIRCPVCRQ 65
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
 22-63 5.19e-05

RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; RNF219 may function as a modulator of late-onset Alzheimer's disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus, a genetic variant of RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438224 [Multi-domain]  Cd Length: 45  Bit Score: 40.88  E-value: 5.19e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16562    4 CHICLGKVRQPVICSNNHVFCSSCMDVWLKNNN---QCPACR 42
RING-HC_TRIM41-like_C-IV cd16602
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and ...
 21-65 5.56e-05

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins; TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain.


Pssm-ID: 438264 [Multi-domain]  Cd Length: 53  Bit Score: 41.07  E-value: 5.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQnyippQSLTLSCPVCRQT 65
Cdd:cd16602    5 VCAICLDYFKDPVSIGCGHNFCRVCVT-----QLWGFTCPQCRKS 44
RING-HC_MID2 cd16754
RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as ...
 20-73 6.23e-05

RING finger, HC subclass, found in midline-2 (MID2) and similar proteins; MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1.


Pssm-ID: 438412 [Multi-domain]  Cd Length: 70  Bit Score: 41.51  E-value: 6.23e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYI-----------PPQSltLSCPVCRQTSILPEQGV 73
Cdd:cd16754    8 LTCPICLELFEDPLLLPCAHSLCFSCAHRILtsgcasgesiePPSA--FQCPTCRYVISLNHRGL 70
RING-H2 cd16448
H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type ...
 22-63 7.98e-05

H2 subclass of RING (RING-H2) fingers and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438112 [Multi-domain]  Cd Length: 43  Bit Score: 40.46  E-value: 7.98e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRY--RCPKV-LPCLHTFCERCLQNYIppQSLTLSCPVCR 63
Cdd:cd16448    1 CVICLEEFeeGDVVRlLPCGHVFHLACILRWL--ESGNNTCPLCR 43
RING-HC_RNF169 cd16551
RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; ...
 20-63 8.34e-05

RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins; RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain.


Pssm-ID: 438213 [Multi-domain]  Cd Length: 55  Bit Score: 40.61  E-value: 8.34e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16551    2 LTCAGCLEVPVEPATLPCGHTLCRGCANRALDAAEAGPTCPRCR 45
zf-C3HC4_4 pfam15227
zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like ...
 22-62 8.57e-05

zinc finger of C3HC4-type, RING; This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, pfam11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme.


Pssm-ID: 464570 [Multi-domain]  Cd Length: 42  Bit Score: 40.50  E-value: 8.57e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 552953687   22 CSICLDRYRCPKVLPCLHTFCERCLQNY-IPPQSLTLSCPVC 62
Cdd:pfam15227   1 CPICLDYLEKPVSIECGHSFCLSCINSLqKEPDGESLLCPQC 42
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 486-513 8.73e-05

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 40.08  E-value: 8.73e-05
                          10        20
                  ....*....|....*....|....*...
gi 552953687  486 FTNLQGVSAASSGRIVVADSNNQCIQVF 513
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
 22-64 8.79e-05

RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases.


Pssm-ID: 438201 [Multi-domain]  Cd Length: 54  Bit Score: 40.65  E-value: 8.79e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERC-LQNYIPPQsltlSCPVCRQ 64
Cdd:cd16539    8 CFICRKPFKNPVVTKCGHYFCEKCaLKHYRKSK----KCFVCGK 47
RING-HC_ORTHRUS_rpt1 cd23138
first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; ...
 20-65 8.98e-05

first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins; This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one.


Pssm-ID: 438500 [Multi-domain]  Cd Length: 48  Bit Score: 40.50  E-value: 8.98e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQT 65
Cdd:cd23138    3 LNCSFCMQLPERPVTTPCGHNFCLKCFQKWMGQGKKT--CGTCRSP 46
RING-HC_COP1 cd16504
RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and ...
 20-62 9.51e-05

RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins; COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger.


Pssm-ID: 438167 [Multi-domain]  Cd Length: 47  Bit Score: 40.30  E-value: 9.51e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVC 62
Cdd:cd16504    3 FLCPICFDIIKEAFVTKCGHSFCYKCIVKHLEQKN---RCPKC 42
Bbox2_TIF1_C-VI cd19775
B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This ...
 112-147 9.52e-05

B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family; This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs).


Pssm-ID: 380833  Cd Length: 43  Bit Score: 40.39  E-value: 9.52e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 552953687 112 PLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHG 147
Cdd:cd19775    1 PLFCPVHPQEPLKLFCETCDKLTCRDCQLLEHKDHK 36
mRING-HC-C3HC3D_arc-1-like cd23124
Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative ...
 19-64 9.68e-05

Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative GTP-binding protein trim-23 homolog (arc-1) and similar proteins; arc-1, also called RING-type E3 ubiquitin transferase arc-1, is an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. arc-1 contains a modified C3HC3D-type RING-HC finger.


Pssm-ID: 438486 [Multi-domain]  Cd Length: 55  Bit Score: 40.56  E-value: 9.68e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  19 FLVCSICLDRY------RCPKVLP-CLHTFCERCLQNYIPPQSLTLSCPVCRQ 64
Cdd:cd23124    1 ELECGICQQEYsaddplLIPRILTeCGHTICTNCAGTILGQSSGSIFCPFDRI 53
RING-HC_Cbl-like cd16502
RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor ...
 19-63 1.02e-04

RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins; The Cbl adaptor protein family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity, which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-c, as well as two invertebrate Cbl-family proteins, D-Cbl in Drosophila and Sli-1 in C. elegans. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating activated tyrosine kinases and targeting them for degradation. D-Cbl associates with the Drosophila epidermal growth factor receptor (EGFR) and overexpression of D-Cbl in the eye of Drosophila embryos inhibits EGFR-dependent photoreceptor cell development. Sli-1 is a negative regulator of the Let-23 receptor tyrosine kinase, an EGFR homolog, in vulva development. Cbl proteins in this subfamily consist of a highly conserved N-terminal half that includes a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain) and a C3HC4-type RING-HC finger, both of which are required for Cbl-mediated downregulation of RTKs, and a divergent C-terminal region.


Pssm-ID: 438165 [Multi-domain]  Cd Length: 43  Bit Score: 40.02  E-value: 1.02e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  19 FLVCSICLDRYRCPKVLPCLHTFCERCLQNYIppQSLTLSCPVCR 63
Cdd:cd16502    1 FQLCKICAENDKDVRIEPCGHLLCTPCLTSWQ--DSDGQTCPFCR 43
NHL_TRIM71_like cd14954
NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; ...
 469-513 1.05e-04

NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins; The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271324 [Multi-domain]  Cd Length: 285  Bit Score: 44.85  E-value: 1.05e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687 469 EDELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVF 513
Cdd:cd14954  241 DGEFLCSFGTEGNGEGQFDRPSGVAVTPDGRIVVVDRGNHRIQVF 285
RING-HC_RNF186 cd16557
RING finger, HC subclass, found in RING finger protein 186 (RNF186) and similar proteins; ...
 20-64 1.10e-04

RING finger, HC subclass, found in RING finger protein 186 (RNF186) and similar proteins; RNF186 is an E3 ubiquitin-protein ligase with an N-terminal C3HC4-type RING-HC finger and two putative C-terminal transmembrane domains which enable it to localize in a certain organelle. It regulates RING-dependent self-ubiquitination, as well as endoplasmic reticulum (ER) stress-mediated apoptosis through interaction with the Bcl-2 family protein BNip1.


Pssm-ID: 438219 [Multi-domain]  Cd Length: 52  Bit Score: 40.22  E-value: 1.10e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  20 LVCSICLDRYRC----PKVLPCLHTFCERCLQNYIPPQSLT--LSCPVCRQ 64
Cdd:cd16557    2 LECLVCRNPYSCfvrkPKLLACQHAFCAICLKLILCEQDGTwsVTCPLCRR 52
RING-HC_RAD18 cd16529
RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; ...
 20-63 1.18e-04

RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins; RAD18, also known as HR18 or RING finger protein 73 (RNF73), is an E3 ubiquitin-protein ligase involved in post replication repair of UV-damaged DNA via its recruitment to stalled replication forks. It associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on K164. It also interacts with another E2 ubiquitin conjugating enzyme RAD6 to form a complex that monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Moreover, Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins. It can function as a mediator for DNA damage response signals to activate the G2/M checkpoint in order to maintain genome integrity and cell survival after ionizing radiation (IR) exposure. RAD18 contains a C3HC4-type RING-HC finger, a ubiquitin-binding zinc finger domain (UBZ), a SAP (SAF-A/B, Acinus and PIAS) domain, and a RAD6-binding domain (R6BD).


Pssm-ID: 438192 [Multi-domain]  Cd Length: 54  Bit Score: 40.36  E-value: 1.18e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLP-CLHTFCERCLQNYIppqSLTLSCPVCR 63
Cdd:cd16529    5 LRCPICFEYFNTAMMITqCSHNYCSLCIRRFL---SYKTQCPTCR 46
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
155-307 1.24e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 44.89  E-value: 1.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 155 VEQHKAALQRQLEAVRGRLPQ----LSAAIALVGGISQQLQERKAEAlAQISAAFEDLE---QALQQRKQAL---VSDLE 224
Cdd:COG4372   64 LEEELEQARSELEQLEEELEElneqLQAAQAELAQAQEELESLQEEA-EELQEELEELQkerQDLEQQRKQLeaqIAELQ 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 225 SICGAKQKvlqtQLDTLRQGQEHIgsscsfAEQALRLGSAPEVLLVRKHmRERLAALAAQAFPERPHENAQLELVLEVDG 304
Cdd:COG4372  143 SEIAEREE----ELKELEEQLESL------QEELAALEQELQALSEAEA-EQALDELLKEANRNAEKEEELAEAEKLIES 211


                 ...
gi 552953687 305 LRR 307
Cdd:COG4372  212 LPR 214
RING-HC_RNF207 cd16558
RING finger, HC subclass, found in RING finger protein 207 (RNF207) and similar proteins; ...
 20-62 1.44e-04

RING finger, HC subclass, found in RING finger protein 207 (RNF207) and similar proteins; RNF207 is a cardiac-specific E3 ubiquitin-protein ligase that plays an important role in the regulation of cardiac repolarization. It regulates action potential duration, likely via effects on human ether-a-go-go-related gene (HERG) trafficking and localization in a heat shock protein-dependent manner. RNF207 contains a C3HC4-type RING-HC finger, Bbox 1 and Bbox C-terminal (BBC) domain, as well as a C-terminal non-homologous region (CNHR).


Pssm-ID: 438220 [Multi-domain]  Cd Length: 43  Bit Score: 39.65  E-value: 1.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVC 62
Cdd:cd16558    2 LVCYLCHEQYEHPCLLDCYHTFCASCLRGRAADGRLT--CPLC 42
RING-HC_RNF5 cd16743
RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, ...
 22-63 1.46e-04

RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins; RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438401 [Multi-domain]  Cd Length: 54  Bit Score: 39.87  E-value: 1.46e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16743    3 CNICLETARDAVVSLCGHLFCWPCLHQWLETRPERQECPVCK 44
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
 22-64 1.49e-04

RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 44.11  E-value: 1.49e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSlTLSCPVCRQ 64
Cdd:COG5574  218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKK-YEFCPLCRA 259
RING-H2_RNF13 cd16796
RING finger, H2 subclass, found in RING finger protein 13 (RNF13) and similar proteins; RNF13 ...
 18-64 1.68e-04

RING finger, H2 subclass, found in RING finger protein 13 (RNF13) and similar proteins; RNF13 is a widely expressed membrane-associated E3 ubiquitin-protein ligase that is functionally significant in the regulation of cancer development, muscle cell growth, and neuronal development. Its expression is developmentally regulated during myogenesis and is upregulated in various tumors. RNF13 negatively regulates cell proliferation through its E3 ligase activity. It functions as an important regulator of inositol-requiring transmembrane kinase/endonuclease IRE1alpha, mediating endoplasmic reticulum (ER) stress-induced apoptosis through the activation of the IRE1alpha-TRAF2-JNK signaling pathway. Moreover, RNF13 is involved in the regulation of the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) complex via the ubiquitination of snapin, a SNAP25-interacting protein, which thereby controls synaptic function. In addition, RNF13 participates in regulating the function of satellite cells by modulating cytokine composition. RNF13 is evolutionarily conserved among many metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.


Pssm-ID: 438450 [Multi-domain]  Cd Length: 59  Bit Score: 40.03  E-value: 1.68e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  18 QFLVCSICLDRYRCP---KVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQ 64
Cdd:cd16796    7 EYDVCAICLDEYEEGdklRILPCSHAYHCKCVDPWLTKTKKT--CPVCKQ 54
RING-HC_RING1-like cd16531
RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and ...
 20-63 1.92e-04

RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and similar proteins; RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), is a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. Both RING1 and RING2 are core components of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members of this family contain a C3HC4-type RING-HC finger.


Pssm-ID: 438193 [Multi-domain]  Cd Length: 66  Bit Score: 39.94  E-value: 1.92e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPK-VLPCLHTFCERCLQNYIppQSLTLSCPVCR 63
Cdd:cd16531    2 LMCPICLGIIKNTMtVKECLHRFCAECIEKAL--RLGNKECPTCR 44
RING-HC_TRIM36_C-I cd16756
RING finger, HC subclass, found in tripartite motif-containing protein 36 (TRIM36) and similar ...
 20-63 2.01e-04

RING finger, HC subclass, found in tripartite motif-containing protein 36 (TRIM36) and similar proteins; TRIM36, the human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation by interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438414 [Multi-domain]  Cd Length: 49  Bit Score: 39.51  E-value: 2.01e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPpqslTLSCPVCR 63
Cdd:cd16756    4 LICPSCKELFTHPLILPCQHSVCHKCVKELLT----TFPCPGCQ 43
WD40 COG2319
WD40 repeat [General function prediction only];
392-702 2.15e-04

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 44.13  E-value: 2.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 392 ARTEGDLLLSVLLYGQPVRGSPFRVRALRPGDLPPSPDDVKRRVKSPGGPGSHVRQKAVRRPSSMYSTGGKRKDNPIEDE 471
Cdd:COG2319   21 LAAALGALLLLLLGLAAAVASLAASPDGARLAAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADG 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 472 LV--FRVgSRGREKGEFTNLQG----VSAASSGRIVVADSNNQCIQVFS-NEGQFKFRFgvrgrsPGQLQRPTGVAVDTN 544
Cdd:COG2319  101 TVrlWDL-ATGLLLRTLTGHTGavrsVAFSPDGKTLASGSADGTVRLWDlATGKLLRTL------TGHSGAVTSVAFSPD 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 545 GDIIVADYDNRWVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVV--DNKSCCVFTFQpNGKLVGRFGGrgatdrHF 622
Cdd:COG2319  174 GKLLASGSDDGTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKLLASgsADGTVRLWDLA-TGKLLRTLTG------HS 246

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 623 AGPHFVAVNNKNEIVVTDFHNHSVKVYSAD-GEFLFKFGSHGegngqfNAPTGVAVDSNGNIIVADWGNSRIQVWRMESP 701
Cdd:COG2319  247 GSVRSVAFSPDGRLLASGSADGTVRLWDLAtGELLRTLTGHS------GGVNSVAFSPDGKLLASGSDDGTVRLWDLATG 320


                 .
gi 552953687 702 R 702
Cdd:COG2319  321 K 321
Bbox2_TRIM56_C-V cd19789
B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar ...
 115-145 2.19e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins; TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380847  Cd Length: 47  Bit Score: 39.45  E-value: 2.19e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 552953687 115 CPNHEGKTMEFYCEACETAMCGECRAGEHRE 145
Cdd:cd19789    5 CREHRDERLLLYCTPCEAAVCRECRLRPHLS 35
mRING-HC-C3HC3D_Roquin cd16638
Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar ...
 19-46 2.43e-04

Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins; The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition.


Pssm-ID: 438300 [Multi-domain]  Cd Length: 44  Bit Score: 39.25  E-value: 2.43e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 552953687  19 FLVCSICL----DRYRCPKVLPCLHTFCERCL 46
Cdd:cd16638    1 FLSCPVCTnefdGTQRKPISLGCGHTVCKTCL 32
RING-HC_DTX3L cd16712
RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, ...
 17-62 2.45e-04

RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins; DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. DTX3L has a unique N-terminus, but lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex (DTX) family members, such as DTX1, DTX2, and DTX4. Moreover, its C-terminal region is highly homologous to DTX3. It includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N-terminus and further enhance self-ubiquitination.


Pssm-ID: 438372 [Multi-domain]  Cd Length: 56  Bit Score: 39.34  E-value: 2.45e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  17 KQFLVCSICLDRYRCPKVLP-CLHTFCERCLQ---NYIPpqsltlSCPVC 62
Cdd:cd16712    1 QEEDECPICMDRISNKKVLPkCKHVFCAACIDkamKYKP------VCPVC 44
Bbox2_TIF1b_C-VI cd19829
B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); ...
 112-155 2.48e-04

B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD) and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-beta acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 380887  Cd Length: 44  Bit Score: 39.04  E-value: 2.48e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687 112 PLSCPNHEGKTMEFYCEACETAMCGECRAGEHREHGTVLLRDVV 155
Cdd:cd19829    1 TVYCSIHKQEPLKLFCETCDTLTCRDCQLNAHKDHQYQFLEDAV 44
RING-HC_BRCA1 cd16498
RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and ...
 11-93 2.75e-04

RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus.


Pssm-ID: 438161 [Multi-domain]  Cd Length: 94  Bit Score: 40.36  E-value: 2.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  11 EVQPMDKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCRqTSILPeqgvSALQNNFFISSLMEAMQ 90
Cdd:cd16498    8 EVISAMQKNLECPICLELLKEPVSTKCDHQFCRFCILKLLQKKKKPAPCPLCK-KSVTK----RSLQESTRFKQLVEAVK 82


                 ...
gi 552953687  91 QAP 93
Cdd:cd16498   83 KLI 85
RING-HC_RBR_TRIAD1 cd16773
RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 ...
 21-60 2.82e-04

RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, also known as ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48, as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438429 [Multi-domain]  Cd Length: 54  Bit Score: 39.26  E-value: 2.82e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYRCPKV--LPCLHTFCERCLQNYIPPQ-----SLTLSCP 60
Cdd:cd16773    2 TCGVCCEDVPKDELfsLACGHYFCNDCWKQYLTVKikdgvSTGIECM 48
RING-HC_RNF152 cd16548
RING finger, HC subclass, found in RING finger protein 152 (RNF152) and similar proteins; ...
 20-63 2.98e-04

RING finger, HC subclass, found in RING finger protein 152 (RNF152) and similar proteins; RNF152 is a lysosome-anchored E3 ubiquitin-protein ligase involved in apoptosis. It is polyubiquitinated through K48 linkage. It negatively regulates the activation of the mTORC1 pathway by targeting RagA GTPase for K63-linked ubiquitination. It interacts with and ubiquitinates RagA in an amino-acid-sensitive manner. The ubiquitination of RagA recruits its inhibitor GATOR1, a GAP complex for Rag GTPases, to the Rag complex, thereby inactivating mTORC1 signaling. RNF152 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal transmembrane domain, both of which are responsible for its E3 ligase activity.


Pssm-ID: 438210 [Multi-domain]  Cd Length: 46  Bit Score: 38.82  E-value: 2.98e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  20 LVCSICLDRY---RCPKVLPCLHTFCERCLQNYIPPQSlTLSCPVCR 63
Cdd:cd16548    1 LECQICFNYYsprRRPKLLDCKHTCCSVCLQQMRTSQK-DLRCPWCR 46
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
 22-64 3.23e-04

RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail.


Pssm-ID: 438208 [Multi-domain]  Cd Length: 50  Bit Score: 38.91  E-value: 3.23e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNyIPPQSLTlsCPVCRQ 64
Cdd:cd16546    3 CPICLQTCIHPVKLPCGHIFCYLCVKG-VAWQSKR--CALCRQ 42
RING-HC_SHPRH-like cd16569
RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) ...
 34-66 3.38e-04

RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins; SHPRH is a yeast RAD5 homolog found in mammals. It functions as an E3 ubiquitin-protein ligase that associates with proliferating cell nuclear antigen (PCNA), RAD18, and the ubiquitin-conjugating enzyme UBC13 (E2), and suppresses genomic instability by proliferating methyl methanesulfonate (MMS)-induced PCNA polyubiquitination. SHPRH contains a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a linker histone domain (H15), a PHD-finger, and a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA. This subfamily also includes tripartite motif-containing protein 15 (TRIM15). TRIM15, also known as RING finger protein 93 (RNF93), zinc finger protein 178 (ZNF178), or zinc finger protein B7 (ZNFB7), is a focal adhesion protein that regulates focal adhesion disassembly. It localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. TRIM15 can also associate with coronin 1B, cortactin, filamin binding LIM protein1, and vasodilator-stimulated phosphoprotein, which are involved in actin cytoskeleton dynamics. As an additional component of the integrin adhesome, it regulates focal adhesion turnover and cell migration. TRIM15 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438231 [Multi-domain]  Cd Length: 53  Bit Score: 38.86  E-value: 3.38e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 552953687  34 VLPCLHTFCERCLQ----NYIPPQSLTLSCPVCRQTS 66
Cdd:cd16569   17 VLPCGHCFCLECIAilidQYAQSRRRSLKCPICRETT 53
RING-HC_TRIM39_C-IV cd16601
RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar ...
 22-62 3.61e-04

RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins; TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438263 [Multi-domain]  Cd Length: 44  Bit Score: 38.62  E-value: 3.61e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVC 62
Cdd:cd16601    4 CSLCKEYLKDPVIIECGHNFCRACITRFWEELDGDFPCPQC 44
RING-HC_RNF185 cd16744
RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; ...
 22-63 3.68e-04

RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins; RNF185 is an E3 ubiquitin-protein ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). It controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical ERAD model substrates. It also negatively regulates osteogenic differentiation by targeting dishevelled2 (Dvl2), a key mediator of the Wnt signaling pathway, for degradation. Moreover, RNF185 regulates selective mitochondrial autophagy through interaction with the Bcl-2 family protein BNIP1. It also plays an important role in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. RNF185 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438402 [Multi-domain]  Cd Length: 57  Bit Score: 39.14  E-value: 3.68e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVCR 63
Cdd:cd16744    3 CNICLDTAKDAVVSLCGHLFCWPCLHQWLETRPNRQVCPVCK 44
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
141-323 3.85e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 44.14  E-value: 3.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  141 GEHREHGT--------VLLRDVVEQhKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKA--EALAQISAAFEDLEQ 210
Cdd:COG4913   587 GTRHEKDDrrrirsryVLGFDNRAK-LAALEAELAELEEELAEAEERLEALEAELDALQERREalQRLAEYSWDEIDVAS 665

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  211 A------LQQRKQAL---VSDLESIcGAKQKVLQTQLDTLRQGQEHIGSSCSFAEQAL------------RLGSAPEvlL 269
Cdd:COG4913   666 AereiaeLEAELERLdasSDDLAAL-EEQLEELEAELEELEEELDELKGEIGRLEKELeqaeeeldelqdRLEAAED--L 742

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 552953687  270 VRKHMRERLAALAAQAFPERPHENAQLELVLEVDGLRRSVLNLGALLTTSATAH 323
Cdd:COG4913   743 ARLELRALLEERFAAALGDAVERELRENLEERIDALRARLNRAEEELERAMRAF 796
RING-H2_RNF32_rpt1 cd16677
first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; ...
 21-64 4.59e-04

first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. This model corresponds to the first RING-H2 finger.


Pssm-ID: 438339 [Multi-domain]  Cd Length: 49  Bit Score: 38.43  E-value: 4.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  21 VCSICLDRYRC-PKV-LPCLHTFCERCLQNYiPPQSLTLSCPVCRQ 64
Cdd:cd16677    1 PCPICLEDFGLqQQVlLSCSHVFHRACLESF-ERFSGKKTCPMCRK 45
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 142-261 4.99e-04

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 43.42  E-value: 4.99e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   142 EHREHGTVLLRD----VVEQHKAALQRQLEAVRGRLPQLSAAIAlvggisQQLQERKAEALAQISAAfedleQALQQRKQ 217
Cdd:TIGR00618  405 LQREQATIDTRTsafrDLQGQLAHAKKQQELQQRYAELCAAAIT------CTAQCEKLEKIHLQESA-----QSLKEREQ 473

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 552953687   218 ALvSDLESICgakQKVLQTQLDTLRQGQEHIGSSCSFAEQALRL 261
Cdd:TIGR00618  474 QL-QTKEQIH---LQETRKKAVVLARLLELQEEPCPLCGSCIHP 513
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 152-402 5.24e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 43.39  E-value: 5.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 152 RDVVEQHKAALQRQLEAVRGRLPQLSAAIAlvggisqQLQERKAEALAQISAAFEDLEQALQQRKQALvSDLESICGAKQ 231
Cdd:COG1196  304 IARLEERRRELEERLEELEEELAELEEELE-------ELEEELEELEEELEEAEEELEEAEAELAEAE-EALLEAEAELA 375

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 232 KVLQTQLDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVRKHMRER--------LAALAAQAFPERPHENAQLELVLEVD 303
Cdd:COG1196  376 EAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEeleeleeaLAELEEEEEEEEEALEEAAEEEAELE 455

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 304 GLRRSVLN-LGALLTTSATAHETVATGEGLRQALVGQPASLTVTTKDKDGRLVRTGSAELcaeITGPDGVRLAVPVVDHK 382
Cdd:COG1196  456 EEEEALLElLAELLEEAALLEAALAELLEELAEAAARLLLLLEAEADYEGFLEGVKAALL---LAGLRGLAGAVAVLIGV 532

                        250       260
                 ....*....|....*....|
gi 552953687 383 NGTYELVYTARTEGDLLLSV 402
Cdd:COG1196  533 EAAYEAALEAALAAALQNIV 552
RING-HC_RNF39 cd16592
RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, ...
 21-63 6.35e-04

RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins; RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438254 [Multi-domain]  Cd Length: 58  Bit Score: 38.20  E-value: 6.35e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNY--IPPQSLT----LSCPVCR 63
Cdd:cd16592    6 TCPICLGYFKDPVILDCEHSFCRACIARHwgQEAMEGNgaegVFCPQCG 54
RING-H2_PJA1_2 cd16465
RING finger, H2 subclass, found in protein E3 ubiquitin-protein ligase Praja-1, Praja-2, and ...
 22-65 6.52e-04

RING finger, H2 subclass, found in protein E3 ubiquitin-protein ligase Praja-1, Praja-2, and similar proteins; This family includes two highly similar E3 ubiquitin-protein ligases, Praja-1 and Praja-2. Praja-1, also known as RING finger protein 70, is a RING-H2 finger ubiquitin ligase encoded by gene PJA1, a novel human X chromosome gene abundantly expressed in the brain. It has been implicated in bone and liver development, as well as memory formation and X-linked mental retardation (MRX). Praja-1 interacts with and activates the ubiquitin-conjugating enzyme UbcH5B, and shows E2-dependent E3 ubiquitin ligase activity. It is a 3-deazaneplanocin A (DZNep)-induced ubiquitin ligase that directly ubiquitinates individual polycomb repressive complex 2 (PRC2) subunits in a cell free system, which leads to their proteasomal degradation. It also plays an important role in neuronal plasticity, which is the basis for learning and memory. Moreover, Praja-1 ubiquitinates embryonic liver fodrin (ELF) and Smad3, but not Smad4, in a transforming growth factor-beta (TGF-beta)-dependent manner. It controls ELF abundance through ubiquitin-mediated degradation, and further regulates TGF-beta signaling, which plays a key role in the suppression of gastric carcinoma. Praja-1 also regulates the transcription function of the homeodomain protein Dlx5 by controlling the stability of Dlxin-1, via a ubiquitin-dependent degradation pathway. Praja-2, also known as RING finger protein 131, NEURODAP1, or KIAA0438, is an E2-dependent E3 ubiquitin ligase that interacts with and activates the ubiquitin-conjugating enzyme UbcH5B. It functions as an A-kinase anchoring protein (AKAP)-like E3 ubiquitin ligase that plays a critical role in controlling cyclic AMP (cAMP)-dependent PKA activity and pro-survival signaling, and further promotes cell proliferation and growth. Praja-2 is also involved in protein sorting at the postsynaptic density region of axosomatic synapses and possibly plays a role in synaptic communication and plasticity. Together with the AMPK-related kinase SIK2 and the CDK5 activator CDK5R1/p35, it forms a SIK2-p35-PJA2 complex that plays an essential role for glucose homeostasis in pancreatic beta cell functional compensation. Praja-2 ubiquitylates and degrades Mob, a core component of NDR/LATS kinase and a positive regulator of the tumor-suppressor Hippo signaling. Both Praja-1 and Praja-2 contain a potential nuclear localization signal (NLS) and a C-terminal C3H2C3-type RING-H2 motif.


Pssm-ID: 438128 [Multi-domain]  Cd Length: 46  Bit Score: 37.82  E-value: 6.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  22 CSICLDRYRCPKV---LPCLHTFCERCLQNYIpPQSLTlsCPVCRQT 65
Cdd:cd16465    2 CPICCSEYVKDEIateLPCHHLFHKPCITAWL-QKSGT--CPVCRHV 45
PLN02919 PLN02919
haloacid dehalogenase-like hydrolase family protein
 611-690 7.07e-04

haloacid dehalogenase-like hydrolase family protein


Pssm-ID: 215497 [Multi-domain]  Cd Length: 1057  Bit Score: 42.92  E-value: 7.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  611 RFGGRGATDRhFAGPHFVAVNNKNEIVVTDFhnhsvkvysaDGEFLFKFGSHGE--------GNGQFNAPTGVAVDSNGN 682
Cdd:PLN02919  568 KFPGKLAIDL-LNNRLFISDSNHNRIVVTDL----------DGNFIVQIGSTGEeglrdgsfEDATFNRPQGLAYNAKKN 636


                  ....*....
gi 552953687  683 II-VADWGN 690
Cdd:PLN02919  637 LLyVADTEN 645
RING-HC_TRIM10_C-IV cd16593
RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar ...
 22-64 7.29e-04

RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins; TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438255 [Multi-domain]  Cd Length: 61  Bit Score: 38.35  E-value: 7.29e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYI----PPQSLTLSCPVCRQ 64
Cdd:cd16593    8 CPICQGTLREPVTIDCGHNFCRACLTRYCeipgPDLEEPPTCPLCKE 54
RING-HC_PCGF cd16525
RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and ...
 20-63 7.31e-04

RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins; This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger.


Pssm-ID: 438188 [Multi-domain]  Cd Length: 42  Bit Score: 37.59  E-value: 7.31e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCP-KVLPCLHTFCERCLQNYIppqSLTLSCPVCR 63
Cdd:cd16525    1 LTCSLCKGYLIDAtTITECLHSFCKSCIVRHL---ETSKNCPVCD 42
RING-HC_RNF138 cd16544
RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; ...
 20-64 7.40e-04

RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins; RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM).


Pssm-ID: 438206 [Multi-domain]  Cd Length: 53  Bit Score: 38.15  E-value: 7.40e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCP-KVLPCLHTFCERCLQNYIPPQSltLSCPVCRQ 64
Cdd:cd16544    3 LTCPVCQEVLKDPvELPPCRHIFCKACILLALRSSG--ARCPLCRG 46
RING-H2_RNF6 cd16673
RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins; RNF6 ...
 21-64 7.42e-04

RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins; RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. Moreover, RNF6 regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 also binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. RNF6 also acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF6 contains an N-terminal coiled-coil domain, a Lys-X-X-Leu/Ile-X-X-Leu/Ile (KIL) motif, and a C-terminal C3H2C3-type RING-H2 finger which is responsible for its ubiquitin ligase activity. The KIL motif is present in a subset of RING-H2 proteins from organisms as evolutionarily diverse as human, mouse, chicken, Drosophila, Caenorhabditis elegans, and Arabidopsis thaliana.


Pssm-ID: 438335 [Multi-domain]  Cd Length: 52  Bit Score: 38.01  E-value: 7.42e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYRCP---KVLPCLHTFCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:cd16673    2 TCSVCINEYATGnklRRLPCAHEFHIHCIDRWLSENS---TCPICRQ 45
RING-HC_TRIM67 cd16758
RING finger, HC subclass, found in tripartite motif-containing protein 67 (TRIM67) and similar ...
 20-64 7.63e-04

RING finger, HC subclass, found in tripartite motif-containing protein 67 (TRIM67) and similar proteins; TRIM67, also known as TRIM9-like protein (TNL), is selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438416 [Multi-domain]  Cd Length: 57  Bit Score: 38.14  E-value: 7.63e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIP---------PQSLTLSCPVCRQ 64
Cdd:cd16758    4 LKCPVCGSLFREPIILPCSHNVCLPCARTIAVqtpeseqhlPHSSSITCPQCHR 57
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
 22-91 7.74e-04

RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins; TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438258 [Multi-domain]  Cd Length: 77  Bit Score: 38.73  E-value: 7.74e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYipPQSLTLSCPVCRQTSILpeqgvSALQNNFFISSLMEAMQQ 91
Cdd:cd16596   12 CPICLDPFVEPVSIECGHSFCQECISQV--GKGGGSVCPVCRQRFLL-----KNLRPNRQLANMVNNLKE 74
RING-HC_MuRF_C-II cd16577
RING finger, HC subclass, found in muscle-specific RING finger proteins TRIM63/MuRF-1, TRIM55 ...
 20-63 7.75e-04

RING finger, HC subclass, found in muscle-specific RING finger proteins TRIM63/MuRF-1, TRIM55/MuRF-2 and TRIM54/MuRF-3; This subfamily corresponds to a group of striated muscle-specific tripartite motif (TRIM) proteins, including TRIM63/MuRF-1, TRIM55/MuRF-2, and TRIM54/MuRF-3, which function as E3 ubiquitin ligases in ubiquitin-mediated muscle protein turnover. They are tightly developmentally regulated in skeletal muscle and associate with different cytoskeleton components, such as microtubules, Z-disks and M-bands, as well as with metabolic enzymes and nuclear proteins. They also cooperate with diverse proteins implicated in selective protein degradation by the proteasome and autophagosome, and target proteins of metabolic regulation, sarcomere assembly and transcriptional regulation. Moreover, MURFs display variable fibre-type preferences. TRIM63/MuRF-1 is predominantly fast (type II) fibre-associated in skeletal muscle. TRIM55/MuRF-2 is predominantly slow-fibre associated. TRIM54/MuRF-3 is ubiquitously present. They play an active role in microtubule-mediated sarcomere assembly. MuRFs belong to the C-II subclass of the TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain positioned C-terminal to the RBCC domain. They also harbor a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.


Pssm-ID: 438239 [Multi-domain]  Cd Length: 56  Bit Score: 37.95  E-value: 7.75e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 552953687  20 LVCSICLDRYRCPKV-LPCLHTFCERC----LQNYIPPQSLTLS-------CPVCR 63
Cdd:cd16577    1 LICPICLEMFTKPVViLPCQHNLCRKCandiFQARNPYWPTTTMgsggrfrCPSCR 56
MukB COG3096
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ...
 132-301 7.82e-04

Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442330 [Multi-domain]  Cd Length: 1470  Bit Score: 43.02  E-value: 7.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  132 TAMCGECRAGEHREHGTVLLRDVVEQhKAALQRqLEAVRGRLPQLSAAIAlvggiSQQLQERKAEALAQISA----AFED 207
Cdd:COG3096   482 CKIAGEVERSQAWQTARELLRRYRSQ-QALAQR-LQQLRAQLAELEQRLR-----QQQNAERLLEEFCQRIGqqldAAEE 554

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  208 LEqALQQRKQALVSDLE---SICGAKQKVLQTQLDTLRQGQEhigsscSFAEQALRLGSAPEVLlvrkhmrERLAALAAQ 284
Cdd:COG3096   555 LE-ELLAELEAQLEELEeqaAEAVEQRSELRQQLEQLRARIK------ELAARAPAWLAAQDAL-------ERLREQSGE 620

                         170
                  ....*....|....*..
gi 552953687  285 AFPERPHENAQLELVLE 301
Cdd:COG3096   621 ALADSQEVTAAMQQLLE 637
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 537-702 8.54e-04

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 41.94  E-value: 8.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 537 TGVAVDTNGDIIV-ADYDNRwVSIFSPEGKFKTKIGAGRLMGPKGVAVDRNGHIIVV--DNKSCCVFTFQpNGKLVGRFG 613
Cdd:cd00200   13 TCVAFSPDGKLLAtGSGDGT-IKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASgsSDKTIRLWDLE-TGECVRTLT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 614 GrgatdrHFAGPHFVAVNNKNEIVVTDFHNHSVKVYS-ADGEFLFKFGSHGegngqfNAPTGVAVDSNGNIIVADWGNSR 692
Cdd:cd00200   91 G------HTSYVSSVAFSPDGRILSSSSRDKTIKVWDvETGKCLTTLRGHT------DWVNSVAFSPDGTFVASSSQDGT 158

                        170
                 ....*....|
gi 552953687 693 IQVWRMESPR 702
Cdd:cd00200  159 IKLWDLRTGK 168
RING-H2_RNF215 cd16670
RING finger, H2 subclass, found in RING finger protein 215 (RNF215) and similar proteins; This ...
 22-63 8.83e-04

RING finger, H2 subclass, found in RING finger protein 215 (RNF215) and similar proteins; This family includes uncharacterized protein RNF215 and similar proteins. Although its biological function remains unclear, RNF215 shares high sequence similarity with PA-TM-RING ubiquitin ligases, which have been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438332 [Multi-domain]  Cd Length: 50  Bit Score: 37.82  E-value: 8.83e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRY---RCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16670    3 CAVCLDQFyknQCLRVLPCLHEFHRDCVDPWLLLQQ---TCPLCK 44
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
150-314 8.95e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 42.59  E-value: 8.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  150 LLRDVVEQHKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQALQQRKQalvsdlesicga 229
Cdd:COG4913   292 LLEAELEELRAELARLEAELERLEARLDALREELDELEAQIRGNGGDRLEQLEREIERLERELEERER------------ 359

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  230 KQKVLQTQLDTLrqGQEHIGSSCSFAEQALRLGSAPEVLLVRKH-MRERLAALAAQafpERPHENAQLELVLEVDGLRRS 308
Cdd:COG4913   360 RRARLEALLAAL--GLPLPASAEEFAALRAEAAALLEALEEELEaLEEALAEAEAA---LRDLRRELRELEAEIASLERR 434


                  ....*.
gi 552953687  309 VLNLGA 314
Cdd:COG4913   435 KSNIPA 440
mRING-H2-C3H2C2D_ZSWM2 cd16486
Modified RING finger, H2 subclass (C3H2C2D-type), found in zinc finger SWIM domain-containing ...
 21-64 9.11e-04

Modified RING finger, H2 subclass (C3H2C2D-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins; ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3 and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination, and two modified RING-H2 fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the second RING-H2 finger, which is not a canonical C3H2C3-type, but a modified C3H2C2D-type.


Pssm-ID: 438149 [Multi-domain]  Cd Length: 49  Bit Score: 37.74  E-value: 9.11e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYR---CPKVLPCLHTFCERCLQNYIPPQSltLSCPVCRQ 64
Cdd:cd16486    1 QCRICLKAFQlgqHVRTLPCRHKFHRDCIDNWLLHSR--NSCPIDGQ 45
Bbox2_TRIM66-like cd19794
B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar ...
 113-146 9.62e-04

B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins; TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif.


Pssm-ID: 380852  Cd Length: 43  Bit Score: 37.44  E-value: 9.62e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 552953687 113 LSCPNHEGKTMEFYCEACETAMCGECRAGEHREH 146
Cdd:cd19794    1 LMCPLHNQEPLKLFCETCDVLVCRSCLLSEHKEH 34
RING-HC_TRIM46_C-I cd16757
RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar ...
 20-63 9.78e-04

RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins; TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438415 [Multi-domain]  Cd Length: 43  Bit Score: 37.49  E-value: 9.78e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPqsltlsCPVCR 63
Cdd:cd16757    5 LLCPVCKEMYKQPLVLPCMHNVCQVCASEVLFP------CPPCQ 42
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
151-243 1.02e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 42.20  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 151 LRDVVEQhKAALQRQLEAVRGRLPQLSAAIAlvgGISQQLQERKAEalaqisaaFEDLEQALQQRKQALVSDLESICGAK 230
Cdd:COG4372   33 LRKALFE-LDKLQEELEQLREELEQAREELE---QLEEELEQARSE--------LEQLEEELEELNEQLQAAQAELAQAQ 100

                         90
                 ....*....|....*
gi 552953687 231 Q--KVLQTQLDTLRQ 243
Cdd:COG4372  101 EelESLQEEAEELQE 115
RING-HC_LONFs_rpt1 cd16513
first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
 22-64 1.02e-03

first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger.


Pssm-ID: 438176 [Multi-domain]  Cd Length: 47  Bit Score: 37.29  E-value: 1.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQnyippQSLTLSCPVCRQ 64
Cdd:cd16513    5 CPLCRGLLFEPVTLPCGHTFCKRCLE-----RDPSSRCRLCRL 42
NHL_like_6 cd14962
Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) ...
 440-513 1.04e-03

Uncharacterized NHL-repeat domain in bacterial proteins; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures.


Pssm-ID: 271332 [Multi-domain]  Cd Length: 271  Bit Score: 41.42  E-value: 1.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 440 GPGSHVRQK--AVRRPSSMYSTGGKrKDNPI----EDELVFRVGSRGREKGEFTNLQGVSAASSGRIVVADSNNQCIQVF 513
Cdd:cd14962  190 GPGSFARPKgiAVDSEGNIYVVDAA-FDNVQifnpEGELLLTVGGPGSGPGEFYLPSGIAIDKDDRIYVVDQFNRRIQVF 268
RING-HC_TRIM58_C-IV cd16606
RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar ...
 22-63 1.08e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins; TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438268 [Multi-domain]  Cd Length: 53  Bit Score: 37.53  E-value: 1.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYI----PPQSLTLSCPVCR 63
Cdd:cd16606    5 CPVCLDFLQEPVSVDCGHSFCLRCISEFCeksdSAQGGVYACPQCR 50
RING-HC_GEFO-like cd16507
RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange ...
 22-63 1.13e-03

RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange factor O (RasGEFO) and similar proteins; RasGEFO, also known as RasGEF domain-containing protein O, functions as a Ras guanine-nucleotide exchange factor (RasGEFs), activating Ras by catalyzing the replacement of GDP with GTP. RasGEFs are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contains a C3HC4-type RING-HC finger that may be responsible for E3 ubiquitin ligase activity.


Pssm-ID: 438170 [Multi-domain]  Cd Length: 58  Bit Score: 37.71  E-value: 1.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLP-CLHTFCERCLQNYIPPQsltlSCPVCR 63
Cdd:cd16507   12 CGICQNLFKDPNTLIpCGHAFCLDCLTTNASIK----NCIQCK 50
RING-H2_RHA1-like cd23121
RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) ...
 21-64 1.16e-03

RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) and similar proteins; This subfamily includes Arabidopsis thaliana RHA1A, RHA1B and XERICO. RHA1A is a probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. RHA1B possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro. XERICO functions on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate-specific degradation. Members of this subfamily contain a C3H2C3-type RING-H2 finger.


Pssm-ID: 438483 [Multi-domain]  Cd Length: 50  Bit Score: 37.46  E-value: 1.16e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  21 VCSICLDRY----RCPKVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQ 64
Cdd:cd23121    3 CCAICLSDFnsdeKLRQLPKCGHIFHHHCLDRWIRYNKIT--CPLCRA 48
RING-HC_MID_C-I cd16575
RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; ...
 20-63 1.17e-03

RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins; MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis. Functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438237 [Multi-domain]  Cd Length: 54  Bit Score: 37.60  E-value: 1.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYI--------PPQSLT-LSCPVCR 63
Cdd:cd16575    1 LTCPICLELFEDPLLLPCAHSLCFNCAHRILvshcasneSVESITaFQCPTCR 53
RING-HC_TRIM17_C-IV cd16595
RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar ...
 22-66 1.17e-03

RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins; TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438257 [Multi-domain]  Cd Length: 70  Bit Score: 38.05  E-value: 1.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQ---------NYIPPQSLTLSCPVCRQTS 66
Cdd:cd16595    8 CSICLDYFTDPVMTTCGHNFCRACIQlswekargkKGRRKQKGSFPCPECREMS 61
RING-HC_TIF1alpha cd16764
RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha); ...
 22-60 1.20e-03

RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha); TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of RAR that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development.


Pssm-ID: 438420  Cd Length: 71  Bit Score: 37.92  E-value: 1.20e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 552953687  22 CSICLD--RYRCPKVLPCLHTFCERCLQNyiPPQSLTLSCP 60
Cdd:cd16764    4 CGVCKQhiQSREPRLLPCLHSFCQRCLPQ--PERYLMLPAP 42
RING-HC_PCGF5 cd16737
RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, ...
 19-62 1.24e-03

RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins; PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438395 [Multi-domain]  Cd Length: 95  Bit Score: 38.58  E-value: 1.24e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  19 FLVCSICLDRYRCPKVLP-CLHTFCERCLQNYIPPqslTLSCPVC 62
Cdd:cd16737   10 YITCRICKGYLIKPTTVTeCLHTFCKSCIVQHFED---SNDCPEC 51
WD40 COG2319
WD40 repeat [General function prediction only];
491-702 1.25e-03

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 41.82  E-value: 1.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 491 GVSAASSGRIVVADSNNQCIQVFS-NEGQFKFRFgvrgrsPGQLQRPTGVAVDTNGDIIV-ADYDNRwVSIFSPEGKFKT 568
Cdd:COG2319  167 SVAFSPDGKLLASGSDDGTVRLWDlATGKLLRTL------TGHTGAVRSVAFSPDGKLLAsGSADGT-VRLWDLATGKLL 239

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 569 KIGAGRLMGPKGVAVDRNGHIIVV--DNKSCCVFTFQpNGKLVGRFGGrgatdrHFAGPHFVAVNNKNEIVVTDFHNHSV 646
Cdd:COG2319  240 RTLTGHSGSVRSVAFSPDGRLLASgsADGTVRLWDLA-TGELLRTLTG------HSGGVNSVAFSPDGKLLASGSDDGTV 312

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 552953687 647 KVYSAD-GEFLFKFGSHGegngqfNAPTGVAVDSNGNIIVADWGNSRIQVWRMESPR 702
Cdd:COG2319  313 RLWDLAtGKLLRTLTGHT------GAVRSVAFSPDGKTLASGSDDGTVRLWDLATGE 363
RING-H2_RNF13-like cd16665
RING finger, H2 subclass, found in RING finger protein 13 (RNF13), RING finger protein 167 ...
 21-64 1.31e-03

RING finger, H2 subclass, found in RING finger protein 13 (RNF13), RING finger protein 167 (RNF167), and similar proteins; This subfamily includes RING finger protein 13 (RNF13), RING finger protein 167 (RNF167), Zinc/RING finger protein 4 (ZNRF4), and similar proteins, which belong to a larger PA-TM-RING ubiquitin ligase family that has been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane domain (TM), and a C-terminal C3H2C3-type RING-H2 finger followed by a putative PEST sequence. RNF13 is a widely expressed membrane-associated E3 ubiquitin-protein ligase that functions in the regulation of cancer development, muscle cell growth, and neuronal development. Its expression is developmentally regulated during myogenesis and is upregulated in various tumors. RNF13 negatively regulates cell proliferation through its E3 ligase activity. RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in the ubiquitination of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR). It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. ZNRF4, also known as RING finger protein 204 (RNF204), or Nixin, is an endoplasmic reticulum (ER) membrane-anchored ubiquitin ligase that physically interacts with the ER-localized chaperone calnexin in a glycosylation-independent manner, inducing calnexin ubiquitination, and p97-dependent degradation. The murine protein sperizin (spermatid-specific ring zinc finger) is a homolog of human ZNRF4. It is specifically expressed in Haploid germ cells and is involved in spermatogenesis.


Pssm-ID: 438327 [Multi-domain]  Cd Length: 46  Bit Score: 37.03  E-value: 1.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 552953687  21 VCSICLDRYRCP---KVLPCLHTFCERCLQNYIPPQSLTlsCPVCRQ 64
Cdd:cd16665    2 VCAICLDDYEEGdklRILPCSHAYHCKCIDPWLTKNKRT--CPVCKR 46
mRING-HC-C3HC3D_LNX1 cd16779
Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); ...
 20-63 1.32e-03

Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1); LNX1, also known as numb-binding protein 1 or PDZ domain-containing RING finger protein 2, is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX1 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAY motif for Numb-LNX interaction, and four PDZ domains necessary for the binding of substrates, including CAR, ErbB2, SKIP, JAM4, CAST, c-Src, Claudins, RhoC, KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2, PDZ-binding kinase (PBK), LNX2, and itself.


Pssm-ID: 438435 [Multi-domain]  Cd Length: 42  Bit Score: 37.09  E-value: 1.32e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLtlsCPVCR 63
Cdd:cd16779    2 LICHICLQALIQPLDTPCGHTYCTLCLTNFLVEKDF---CPMDR 42
YvrE COG3386
Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase ...
 569-687 1.32e-03

Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 442613 [Multi-domain]  Cd Length: 266  Bit Score: 41.03  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 569 KIGAGRLMGPKGVAVDRNGHIIVVDNKSCCVFTFQPNGKLVGRFggrgATDRHFAGphFVAVNNKNEIVVTDfHNHSVKV 648
Cdd:COG3386    1 KLADAGFRLGEGPVWDPDGRLYWVDIPGGRIHRYDPDGGAVEVF----AEPSGRPN--GLAFDPDGRLLVAD-HGRGLVR 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 552953687 649 YS-ADGEFLFKFGSHGEGNGQFNaptGVAVDSNGNIIVAD 687
Cdd:COG3386   74 FDpADGEVTVLADEYGKPLNRPN---DGVVDPDGRLYFTD 110
RING-HC_Bre1-like cd16499
RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ...
 17-62 1.41e-03

RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes; Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, the Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438162 [Multi-domain]  Cd Length: 59  Bit Score: 37.54  E-value: 1.41e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  17 KQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYIppQSLTLSCPVC 62
Cdd:cd16499    4 RELLKCSVCNDRFKDVIITKCGHVFCNECVQKRL--ETRQRKCPGC 47
RING-HC_RAD16-like cd16567
RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, ...
 20-64 1.47e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins; Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain.


Pssm-ID: 438229 [Multi-domain]  Cd Length: 48  Bit Score: 36.94  E-value: 1.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIppQSL---TLSCPVCRQ 64
Cdd:cd16567    1 LVCGICHEEAEDPVVARCHHVFCRACVKEYI--ESApggKVTCPTCHK 46
RING-HC_SpRad8-like cd16572
RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) ...
 22-65 1.55e-03

RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) and similar proteins; SpRad8 is a conserved protein homologous to Saccharomyces cerevisiae DNA repair protein Rad5 and human helicase-like transcription factor (HLTF) that is required for error-free postreplication repair by contributing to polyubiquitylation of PCNA. SpRad8 contains a C3HC4-type RING-HC finger responsible for the E3 ubiquitin ligase activity, a SNF2-family helicase domain including an ATP binding site, and a family-specific HIRAN domain (HIP116, Rad5p N-terminal domain) that contributes to nuclear localization.


Pssm-ID: 438234 [Multi-domain]  Cd Length: 61  Bit Score: 37.49  E-value: 1.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  22 CSICL-DRYRCPKVLPCLHTFCERCLQNYIPPQ---SLTLSCPVCRQT 65
Cdd:cd16572    7 CPICAeEPISELALTRCWHSACKDCLLDHIEFQkskNEVPLCPTCRQP 54
RING-H2_AMFR cd16455
RING finger, H2 subclass, found in autocrine motility factor receptor (AMFR) and similar ...
 22-63 1.72e-03

RING finger, H2 subclass, found in autocrine motility factor receptor (AMFR) and similar proteins; AMFR, also known as AMF receptor, or RING finger protein 45, or ER-protein gp78, is an internalizing cell surface glycoprotein localized in both plasma membrane caveolae and the endoplasmic reticulum (ER). It is involved in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. AMFR also functions as a RING finger-dependent ubiquitin protein ligase (E3) implicated in the degradation from the ER. AMFR contains an N-terminal RING-H2 finger and a C-terminal ubiquitin-associated (UBA)-like CUE domain.


Pssm-ID: 438119 [Multi-domain]  Cd Length: 44  Bit Score: 36.66  E-value: 1.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQsltLSCPVCR 63
Cdd:cd16455    3 CAICWESMQSARKLPCGHLFHNSCLRSWLEQD---TSCPTCR 41
COG5152 COG5152
Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function ...
 2-62 1.75e-03

Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only];


Pssm-ID: 227481 [Multi-domain]  Cd Length: 259  Bit Score: 40.83  E-value: 1.75e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 552953687   2 AKREDSPGPEvQPMDKQFLVCSICLDRYRCPKVLPCLHTFCERClqnYIPPQSLTLSCPVC 62
Cdd:COG5152  180 AEYEEAPVIS-GPGEKIPFLCGICKKDYESPVVTECGHSFCSLC---AIRKYQKGDECGVC 236
NHL pfam01436
NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is ...
 575-602 1.78e-03

NHL repeat; The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats.


Pssm-ID: 396153 [Multi-domain]  Cd Length: 28  Bit Score: 36.23  E-value: 1.78e-03
                          10        20
                  ....*....|....*....|....*...
gi 552953687  575 LMGPKGVAVDRNGHIIVVDNKSCCVFTF 602
Cdd:pfam01436   1 FNRPHGVAVDSNGDIYVADSENHRVQVF 28
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 155-336 1.96e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 41.58  E-value: 1.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   155 VEQHKAALQRQLEAVRGRLPQLSAAIALVggisQQLQERKAEALAQISAAFEDLE------QALQQRKQALVSDLESICG 228
Cdd:TIGR02168  300 LEQQKQILRERLANLERQLEELEAQLEEL----ESKLDELAEELAELEEKLEELKeeleslEAELEELEAELEELESRLE 375

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687   229 AKQKVLQTQLDTLRQGQEHIgsscsfAEQALRLGSAPEVLLVRKHMRERLAALAAQAfPERPHENAQLELVLEVDGLRRs 308
Cdd:TIGR02168  376 ELEEQLETLRSKVAQLELQI------ASLNNEIERLEARLERLEDRRERLQQEIEEL-LKKLEEAELKELQAELEELEE- 447

                          170       180
                   ....*....|....*....|....*...
gi 552953687   309 vlnlgALLTTSATAHETVATGEGLRQAL 336
Cdd:TIGR02168  448 -----ELEELQEELERLEEALEELREEL 470
RING-H2_RNF181 cd16669
RING finger, H2 subclass, found in RING finger protein 181 (RNF181) and similar proteins; ...
 22-63 2.00e-03

RING finger, H2 subclass, found in RING finger protein 181 (RNF181) and similar proteins; RNF181, also known as HSPC238, is a platelet E3 ubiquitin-protein ligase containing a C3H2C3-type RING-H2 finger. It interacts with the KVGFFKR motif of platelet integrin alpha(IIb)beta3, suggesting a role for RNF181-mediated ubiquitination in integrin and platelet signaling. It also suppresses the tumorigenesis of hepatocellular carcinoma (HCC) through the inhibition of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling in the liver.


Pssm-ID: 438331 [Multi-domain]  Cd Length: 46  Bit Score: 36.58  E-value: 2.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYR---CPKVLPCLHTFCERCLqnyIPPQSLTLSCPVCR 63
Cdd:cd16669    2 CPICLLEFEegeTVKQLPCKHSFHSDCI---LPWLGKTNSCPLCR 43
PLN02919 PLN02919
haloacid dehalogenase-like hydrolase family protein
 459-554 2.03e-03

haloacid dehalogenase-like hydrolase family protein


Pssm-ID: 215497 [Multi-domain]  Cd Length: 1057  Bit Score: 41.76  E-value: 2.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  459 TGGKR---KDNPIEDELVFRVGSRGREKGE--FTNLQGVSAASSGRIVVADSNNQCIQVF----------SNEGQFKFRF 523
Cdd:PLN02919  771 TGGSRllaGGDPTFSDNLFKFGDHDGVGSEvlLQHPLGVLCAKDGQIYVADSYNHKIKKLdpatkrvttlAGTGKAGFKD 850

                          90       100       110
                  ....*....|....*....|....*....|.
gi 552953687  524 GvRGRSpGQLQRPTGVAVDTNGDIIVADYDN 554
Cdd:PLN02919  851 G-KALK-AQLSEPAGLALGENGRLFVADTNN 879
RING-H2_RNF103 cd16473
RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; ...
 22-64 2.13e-03

RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins; RNF103, also known as KF-1 or zinc finger protein 103 homolog (Zfp-103), is an endoplasmic reticulum (ER)-resident E3 ubiquitin-protein ligase that is widely expressed in many different organs, including brain, heart, kidney, spleen, and lung. It is involved in the ER-associated degradation (ERAD) pathway by interacting with components of the ERAD pathway, including Derlin-1 and VCP. RNF103 contains several hydrophobic regions at its N-terminal and middle regions, as well as a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438136 [Multi-domain]  Cd Length: 55  Bit Score: 36.87  E-value: 2.13e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYR---CPKVLPCLHTFCERCLQNYIppQSLTLSCPVCRQ 64
Cdd:cd16473    7 CAICLENYQngdLLRGLPCGHVFHQNCIDVWL--ERDNHCCPVCRW 50
COG5540 COG5540
RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, ...
 22-69 2.22e-03

RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227827 [Multi-domain]  Cd Length: 374  Bit Score: 41.13  E-value: 2.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 552953687  22 CSICL------DRYRcpkVLPCLHTFCERCLQNYIPPQSltLSCPVCRqTSILP 69
Cdd:COG5540  326 CAICMsnfiknDRLR---VLPCDHRFHVGCVDKWLLGYS--NKCPVCR-TAIPP 373
RING-H2_synoviolin cd16479
RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as ...
 21-63 2.27e-03

RING finger, H2 subclass, found in synoviolin and similar proteins; Synoviolin, also known as synovial apoptosis inhibitor 1 (Syvn1), Hrd1, or Der3, is an endoplasmic reticulum (ER)-anchoring E3 ubiquitin ligase that functions as a suppressor of ER stress-induced apoptosis and plays a role in homeostasis maintenance. It also targets tumor suppressor gene p53 for proteasomal degradation, suggesting crosstalk between ER associated degradation (ERAD) and p53 mediated apoptotic pathway under ER stress. Moreover, synoviolin controls body weight and mitochondrial biogenesis through negative regulation of the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1beta. It upregulates amyloid beta production by targeting a negative regulator of gamma-secretase, Retention in endoplasmic reticulum 1 (Rer1), for degradation. It is also involved in the degradation of endogenous immature nicastrin, and affects amyloid beta-protein generation. Moreover, synoviolin is highly expressed in rheumatoid synovial cells and may be involved in the pathogenesis of rheumatoid arthritis (RA). It functions as an anti-apoptotic factor that is responsible for the outgrowth of synovial cells during the development of RA. It promotes inositol-requiring enzyme 1 (IRE1) ubiquitination and degradation in synovial fibroblasts with collagen-induced arthritis. Furthermore, the upregulation of synoviolin may represent a protective response against neurodegeneration in Parkinson's disease (PD). In addition, synoviolin is involved in liver fibrogenesis. Synoviolin contains a C3H2C2-type RING-H2 finger.


Pssm-ID: 438142 [Multi-domain]  Cd Length: 43  Bit Score: 36.18  E-value: 2.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  21 VCSICLDRYR-CPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16479    3 TCIICREEMTvGAKKLPCGHIFHLSCLRSWLQRQQ---TCPTCR 43
RING-HC_TRIM43-like_C-IV cd16603
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, ...
 20-66 2.55e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins; The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger.


Pssm-ID: 438265 [Multi-domain]  Cd Length: 59  Bit Score: 36.69  E-value: 2.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQ-NYIPPQSLTlSCPVCRQTS 66
Cdd:cd16603    5 LTCPICMNYFIDPVTIDCGHSFCRPCLYlNWQDIPFLA-QCPECRKTT 51
RING-HC_BAR cd16497
RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as ...
 22-64 2.61e-03

RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR); BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s).


Pssm-ID: 438160 [Multi-domain]  Cd Length: 52  Bit Score: 36.33  E-value: 2.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIpPQSLTLSCPVCRQ 64
Cdd:cd16497    4 CHCCYDLLVNPTTLNCGHSFCRHCLALWW-KSSKKTECPECRQ 45
RING-HC_TIF1beta cd16765
RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta); ...
 22-64 2.68e-03

RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta); TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domain of TIF1-beta is responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.


Pssm-ID: 438421 [Multi-domain]  Cd Length: 63  Bit Score: 36.82  E-value: 2.68e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687  22 CSICLDRYRC---PKVLPCLHTFCERCLQNYIPPQSLT------------LSCPVCRQ 64
Cdd:cd16765    4 CGVCRERLRPerePRLLPCLHSVCSACLGPAAPAAANSsgdggaagdgtvVDCPVCKQ 61
RING-H2_RNF122 cd16676
RING finger, H2 subclass, found in RING finger protein 122 (RNF122) and similar proteins; ...
 22-64 2.76e-03

RING finger, H2 subclass, found in RING finger protein 122 (RNF122) and similar proteins; RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergo degradation through its RING finger in a proteasome-dependent manner. It interacts with calcium-modulating cyclophilin ligand (CAML), which is not a substrate, but a stabilizer of RNF122. RNF122 contains an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438338 [Multi-domain]  Cd Length: 47  Bit Score: 36.09  E-value: 2.76e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYRCPK---VLPCLHTFCERCLQNYIPPQSLtlsCPVCRQ 64
Cdd:cd16676    3 CAVCLEDFKTKDelgVLPCQHAFHRKCLVKWLEIRCV---CPMCNK 45
CHASE3 COG5278
Extracytoplasmic sensor domain CHASE3 (specificity unknown) [Signal transduction mechanisms];
196-375 2.79e-03

Extracytoplasmic sensor domain CHASE3 (specificity unknown) [Signal transduction mechanisms];


Pssm-ID: 444089 [Multi-domain]  Cd Length: 530  Bit Score: 41.05  E-value: 2.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 196 EALAQISAAFEDLEQALQ--QRKQALVSDLESICGAKQKVLQTQLDTLRQGQehigsscsfAEQALRLGSAPEVLLVRKH 273
Cdd:COG5278   83 EARAEIDELLAELRSLTAdnPEQQARLDELEALIDQWLAELEQVIALRRAGG---------LEAALALVRSGEGKALMDE 153

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 274 MRERLAALAAQAFPERPHENAQLELVLEVDGLRRSVLNLGALLTTSATAHETVATGEGLRQALVGQPASLTVTTKDKDGR 353
Cdd:COG5278  154 IRARLLLLALALAALLLAAAALLLLLLALAALLALAELLLLALARALAALLLLLLLEAELAAAAALLAAAAALAALAALE 233

                        170       180
                 ....*....|....*....|..
gi 552953687 354 LVRTGSAELCAEITGPDGVRLA 375
Cdd:COG5278  234 LLAALALALALLLAALLLALLA 255
RING-HC_TRIM31_C-V cd16582
RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar ...
 20-62 2.87e-03

RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar proteins; TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM31 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain.


Pssm-ID: 438244 [Multi-domain]  Cd Length: 44  Bit Score: 35.96  E-value: 2.87e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSLTLSCPVC 62
Cdd:cd16582    2 VICPICLDILQKPVTIDCGHNFCLQCITQIGETSCGFFKCPLC 44
RING-HC_MuRF2 cd16760
RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar ...
 20-64 2.91e-03

RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar proteins; MuRF-2, also known as tripartite motif-containing protein 55 (TRIM55) or RING finger protein 29 (RNF29), is a muscle-specific E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover and is also a ligand of the transactivation domain of the serum response transcription factor (SRF). It is predominantly slow-fibre associated and highly expressed in embryonic skeletal muscle. MuRF-2 associates transiently with microtubules, myosin, and titin during sarcomere assembly. It has been implicated in microtubule, intermediate filament, and sarcomeric M-line maintenance in striated muscle development, as well as in signaling from the sarcomere to the nucleus. It plays an important role in the earliest stages of skeletal muscle differentiation and myofibrillogenesis. It is developmentally downregulated and is assembled at the M-line region of the sarcomere and with microtubules. MuRF-2 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains.


Pssm-ID: 438417 [Multi-domain]  Cd Length: 64  Bit Score: 36.89  E-value: 2.91e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  20 LVCSICLDRYRCPKV-LPCLHTFCERCLQN-------YIPPQSLT-------LSCPVCRQ 64
Cdd:cd16760    4 LICPICLEMFTKPVViLPCQHNLCRKCANDifqasnpYLPTRGGTtvasggrFRCPSCRH 63
RING-HC_RNF220 cd16563
RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; ...
 20-62 2.97e-03

RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins; RNF220 is an E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of Sin3B, a scaffold protein of the Sin3/HDAC (histone deacetylase) corepressor complex. It can also bind E2 and mediate auto-ubiquitination of itself. Moreover, RNF220 specifically interacts with beta-catenin, and enhances canonical Wnt signaling through ubiquitin-specific protease 7 (USP7)-mediated deubiquitination and stabilization of beta-catenin, which is independent of its E3 ligase activity. RNF220 contains a characteristic C3HC4-type RING-HC finger at its C-terminus.


Pssm-ID: 438225 [Multi-domain]  Cd Length: 52  Bit Score: 36.28  E-value: 2.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 552953687  20 LVCSICLDRYRCPKV-LPCLHTFCERCLQNYIPPQSLtlsCPVC 62
Cdd:cd16563    1 YKCLICMDSYTMPLVsIQCWHVHCEECWLRTLGAKKL---CPQC 41
mRING-HC-C3HC3D_TRIM23_C-IX cd16645
Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein ...
 20-64 3.01e-03

Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 438307 [Multi-domain]  Cd Length: 50  Bit Score: 36.27  E-value: 3.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 552953687  20 LVCSICLDRYR-----CPKVLPCLHTFCERCLQNyIPPQSLTLSCPVCRQ 64
Cdd:cd16645    2 LECGVCEDVFSlqgdkVPRLLLCGHTVCHDCLTR-LPLHGRAVRCPFDRQ 50
RING-HC_ITT1-like cd23134
RING finger, HC subclass, found in Saccharomyces cerevisiae translation termination inhibitor ...
 21-49 3.23e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae translation termination inhibitor protein ITT1 and similar proteins; ITT1 is a protein that modulates the efficiency of translation termination, resulting in the readthrough of all three types of nonsense codons UAA, UAG and UGA. ITT1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438496  Cd Length: 60  Bit Score: 36.53  E-value: 3.23e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 552953687  21 VCSICLDRYR---CPKvLPCLHTFCERCLQNY 49
Cdd:cd23134    6 HCGICFEEKKgsdFIK-LPCGHVFCRECLQDY 36
RING-HC_PRT1-like cd23132
RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and ...
 22-63 3.39e-03

RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and similar proteins; PRT1, also called RING-type E3 ubiquitin transferase PRT1, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with an N-terminal bulky aromatic amino acid (Phe). It does not act on aliphatic hydrophobic and basic N-terminal residues (Arg or Leu) containing proteins. PRT1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438494 [Multi-domain]  Cd Length: 52  Bit Score: 36.24  E-value: 3.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYRCPKVLPCLHTFC----ERCLQNYippqsLTLSCPVCR 63
Cdd:cd23132    5 CCICLDLLYKPVVLECGHVFCfwcvHRCMNGY-----DESHCPLCR 45
RING-H2_RNF139-like cd16476
RING finger, H2 subclass, found in RING finger proteins RNF139, RNF145, and similar proteins; ...
 21-62 3.66e-03

RING finger, H2 subclass, found in RING finger proteins RNF139, RNF145, and similar proteins; RNF139, also known as translocation in renal carcinoma on chromosome 8 protein (TRC8), is an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. It is a tumor suppressor that has been implicated in a novel regulatory relationship linking the cholesterol/lipid biosynthetic pathway with cellular growth control. A mutation in RNF139 has been identified in families with hereditary renal (RCC) and thyroid cancers. RNF145 is an uncharacterized RING finger protein encoded by the RNF145 gene, which is expressed in T lymphocytes, and its expression is altered in acute myelomonocytic and acute promyelocytic leukemias. Although its biological function remains unclear, RNF145 shows high sequence similarity with RNF139. Both RNF139 and RNF145 contain a C3H2C3-type RING-H2 finger with possible E3-ubiquitin ligase activity.


Pssm-ID: 438139 [Multi-domain]  Cd Length: 41  Bit Score: 35.89  E-value: 3.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687  21 VCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVC 62
Cdd:cd16476    2 VCAICYQEMKEARITPCNHFFHGLCLRKWLYVQD---TCPLC 40
RING-HC_RNF8 cd16535
RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is ...
 20-64 3.71e-03

RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins; RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal forkhead-associated (FHA) domain and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438197 [Multi-domain]  Cd Length: 64  Bit Score: 36.22  E-value: 3.71e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:cd16535    2 LQCSICSELFIEAVTLNCSHSFCSYCITEWMKRKK---ECPICRK 43
RING-HC_TRIM68_C-IV cd16610
RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar ...
 20-63 3.72e-03

RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar proteins; TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogre's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain.


Pssm-ID: 438272 [Multi-domain]  Cd Length: 49  Bit Score: 36.03  E-value: 3.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERCLQNY--IPPQSLT--LSCPVCR 63
Cdd:cd16610    2 VACPICMTFLREPVSIDCGHSFCHSCLSGLweVPGESQNwgYTCPLCR 49
RING-HC_DTX3 cd16711
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar ...
 21-63 3.97e-03

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins; DTX3, also known as RING finger protein 154 (RNF154), is an E3 ubiquitin-protein ligase that belongs to the Deltex (DTX) family. In contrast to other DTXs, DTX3 does not contain two N-terminal Notch-binding WWE domains, but a short unique N-terminal domain, suggesting it does not interact with the intracellular domain of Notch. Its C-terminal region includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain.


Pssm-ID: 438371 [Multi-domain]  Cd Length: 54  Bit Score: 35.86  E-value: 3.97e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  21 VCSICLDRYRCPKVL-PCLHTFCERCLQnyippQSLTL--SCPVCR 63
Cdd:cd16711    3 TCPICLGEIQNKKTLdKCKHSFCEDCIT-----RALQVkkACPMCG 43
RING-HC_PCGF1 cd16733
RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar ...
 18-64 4.11e-03

RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar proteins; PCGF1, also known as nervous system Polycomb-1 (NSPc1) or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438391 [Multi-domain]  Cd Length: 71  Bit Score: 36.48  E-value: 4.11e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 552953687  18 QFLVCSICLDRY-RCPKVLPCLHTFCERCLQNYIppqSLTLSCPVCRQ 64
Cdd:cd16733    8 EHIVCYLCAGYFiDATTITECLHTFCKSCIVKYL---QTSKYCPMCNI 52
RING-H2_RNF38-like cd16472
RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins; ...
 22-63 4.31e-03

RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins; This subfamily includes RING finger proteins RNF38, RNF44, and similar proteins. RNF38 is a nuclear E3 ubiquitin protein ligase that plays a role in regulating p53. RNF44 is an uncharacterized RING finger protein that shows high sequence similarity to RNF38. Both RNF38 and RNF44 contain a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), and a C3H2C3-type RING-H2 finger. In addition, RNF38 harbors two potential nuclear localization signals.


Pssm-ID: 438135 [Multi-domain]  Cd Length: 46  Bit Score: 35.77  E-value: 4.31e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRY---RCPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16472    5 CVVCMCDYekrQLLRVLPCSHEFHAKCIDKWLKTNR---TCPICR 46
PRK08268 PRK08268
3-hydroxy-acyl-CoA dehydrogenase; Validated
 148-229 4.44e-03

3-hydroxy-acyl-CoA dehydrogenase; Validated


Pssm-ID: 236211 [Multi-domain]  Cd Length: 507  Bit Score: 40.22  E-value: 4.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 148 TVLLRDV----VEQHKAALQRQLE--AVRGRLPQlSAAIALVGGIS--QQLQERKAEALAqISAAFEDLEQalqqrKQAL 219
Cdd:PRK08268  32 TVLLYDAragaAAAARDGIAARLAklVEKGKLTA-EQADAALARLRpvEALADLADCDLV-VEAIVERLDV-----KQAL 104

                         90
                 ....*....|
gi 552953687 220 VSDLESICGA 229
Cdd:PRK08268 105 FAQLEAIVSP 114
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 156-324 4.48e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 40.31  E-value: 4.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 156 EQHKAALQRQLEAVRGRLPQLSAAIALVGGISQQLQERKAEALAQISAAFEDLEQA------LQQRKQALVSDLESICGA 229
Cdd:COG1196  280 ELELEEAQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELeeeleeLEEELEEAEEELEEAEAE 359

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 230 KQKVLQTQLDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLVR-KHMRERLAALAAQAfpERpHENAQLELVLEVDGLRRS 308
Cdd:COG1196  360 LAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQlEELEEAEEALLERL--ER-LEEELEELEEALAELEEE 436

                        170
                 ....*....|....*.
gi 552953687 309 VLNLGALLTTSATAHE 324
Cdd:COG1196  437 EEEEEEALEEAAEEEA 452
zf-ANAPC11 pfam12861
Anaphase-promoting complex subunit 11 RING-H2 finger; Apc11 is one of the subunits of the ...
 21-65 4.61e-03

Anaphase-promoting complex subunit 11 RING-H2 finger; Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability.


Pssm-ID: 403920 [Multi-domain]  Cd Length: 85  Bit Score: 36.69  E-value: 4.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 552953687   21 VCSICLDRY------------RCPKVL-PCLHTFCERCLQNYIPPQSLTLSCPVCRQT 65
Cdd:pfam12861  23 VCGICRVSFdgtcpdckfpgdDCPLVWgKCSHNFHMHCILKWLHTETSKGLCPMCRQT 80
RING-HC_Cbl cd16708
RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl and similar proteins; Cbl, ...
 15-63 5.56e-03

RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl and similar proteins; Cbl, also known as Casitas B-lineage lymphoma proto-oncogene, proto-oncogene c-Cbl, RING finger protein 55 (RNF55), or signal transduction protein Cbl, is a multi-domain protein that acts as a key negative regulator of various receptor and non-receptor tyrosine kinase signaling. It contains a tyrosine kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a proline-rich domain, a C3HC4-type RING-HC finger, and an ubiquitin-associated (UBA) domain. TKB is responsible for the interactions with many tyrosine kinases, such as the colony-stimulating factor-1 (CSF-1) receptor, Syk/ZAP-70, and Src-family of protein tyrosine kinases. The proline-rich domain can recruit proteins with a SH3 domain. Moreover, Cbl functions as an E3 ubiquitin ligase that can bind ubiquitin-conjugating enzymes (E2s) through the RING-HC finger.


Pssm-ID: 438368 [Multi-domain]  Cd Length: 77  Bit Score: 36.22  E-value: 5.56e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 552953687  15 MDKQFLVCSICLDRYRCPKVLPCLHTFCERCLQNYipPQSLTLSCPVCR 63
Cdd:cd16708   17 MGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSW--QESEGQGCPFCR 63
MscS_porin pfam12795
Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part ...
 152-312 5.84e-03

Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux.


Pssm-ID: 432790 [Multi-domain]  Cd Length: 238  Bit Score: 39.21  E-value: 5.84e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  152 RDVVEQHKAALQRQLEAVRGRLPQLSAAIAlvggisqQLQERKAEALAQISAA--FEDLEQALQQRKQALVSDLESICGA 229
Cdd:pfam12795  32 IDASKQRAAAYQKALDDAPAELRELRQELA-------ALQAKAEAAPKEILASlsLEELEQRLLQTSAQLQELQNQLAQL 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  230 KQKV--LQTQLDTLRQGQEHIGSSCSFAEQALRLGSAPEVLLV---RKHMRERLAALAAQafperpheNAQLELVLEVDG 304
Cdd:pfam12795 105 NSQLieLQTRPERAQQQLSEARQRLQQIRNRLNGPAPPGEPLSeaqRWALQAELAALKAQ--------IDMLEQELLSNN 176


                  ....*...
gi 552953687  305 LRRSVLNL 312
Cdd:pfam12795 177 NRQDLLKA 184
Bbox2_TRIM23_C-IX_rpt2 cd19774
second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and ...
 115-151 5.85e-03

second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins; TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition.


Pssm-ID: 380832  Cd Length: 50  Bit Score: 35.47  E-value: 5.85e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 552953687 115 CPNHEGKTMEFYC--EACETA--MCGECR-AGEHREHGTVLL 151
Cdd:cd19774    5 CPIHPDHLIEFVCleEDCQESplMCIICKeYGKHQGHKHELL 46
RING-HC_MKRN cd16521
RING finger, HC subclass, found in the makorin (MKRN) proteins; The MKRN protein subfamily ...
 20-63 6.03e-03

RING finger, HC subclass, found in the makorin (MKRN) proteins; The MKRN protein subfamily includes ribonucleoproteins that are characterized by a variety of zinc-finger motifs, including typical arrays of one to four C3H1-type zinc fingers and a C3HC4-type RING-HC finger. Another motif rich in Cys and His residues (CH), with so far unknown function, is also generally present in MKRN proteins. MKRN proteins may have E3 ubiquitin ligase activity.


Pssm-ID: 438184 [Multi-domain]  Cd Length: 53  Bit Score: 35.33  E-value: 6.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 552953687  20 LVCSICLDRYRCPK----VLP-CLHTFCERCLQNY----IPPQSLTLSCPVCR 63
Cdd:cd16521    1 IECGICMEVVLEKErrfgILSnCNHVFCLECIREWrsskDFENSIVRSCPICR 53
RING-H2_RNF6-like cd16467
RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6, RNF12, and similar ...
 22-63 6.16e-03

RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6, RNF12, and similar proteins; RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. RNF6 also regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. It acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF12, also known as LIM domain-interacting RING finger protein, or RING finger LIM domain-binding protein (R-LIM), is an E3 ubiquitin-protein ligase encoded by gene RLIM that is crucial for normal embryonic development in some species and for normal X inactivation in mice. It thus functions as a major sex-specific epigenetic regulator of female mouse nurturing tissues. RNF12 is widely expressed during embryogenesis, and mainly localizes to the cell nucleus, where it regulates the levels of many proteins, including CLIM, LMO, HDAC2, TRF1, SMAD7, and REX1, by proteasomal degradation. Both RNF6 and RNF12 contain a well conserved C3H2C3-type RING-H2 finger.


Pssm-ID: 438130 [Multi-domain]  Cd Length: 43  Bit Score: 35.12  E-value: 6.16e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYRCPKVL---PCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16467    2 CTICLGEYETGEKLrrlPCSHEFHSECVDRWLKENS---SCPICR 43
YvrE COG3386
Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase ...
 533-619 6.52e-03

Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 442613 [Multi-domain]  Cd Length: 266  Bit Score: 39.10  E-value: 6.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 533 LQRPTGVAVDTNGDI-IVADYDNRWVSIF--SPEGK-------FKTKIGAGrlmGPKGVAVDRNGHIIVVDNKSCCVFTF 602
Cdd:COG3386  136 LTFPNGIAFSPDGRTlYVADTGAGRIYRFdlDADGTlgnrrvfADLPDGPG---GPDGLAVDADGNLWVALWGGGGVVRF 212

                         90       100
                 ....*....|....*....|....*....
gi 552953687 603 QPNGKLVGR------------FGGRGATD 619
Cdd:COG3386  213 DPDGELLGRielperrptnvaFGGPDLRT 241
DUF5128 pfam17170
6-bladed beta-propeller; This family is a 6-bladed beta-propeller structure of unknown ...
 633-693 7.08e-03

6-bladed beta-propeller; This family is a 6-bladed beta-propeller structure of unknown function. There is a highly conserved FDxxG motif which might be important.


Pssm-ID: 407298 [Multi-domain]  Cd Length: 321  Bit Score: 39.23  E-value: 7.08e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 552953687  633 KNEIVVTDFHNHSVKVYSADGEFLFKFGSHGEGNGQFNAPTGVAVD-SNGNIIVADWGNSRI 693
Cdd:pfam17170  53 DDRIFVFDSNTNNLFVFDKKGKFVRQIGAQGNGPGEYLQINDFIIDkSNNSIYILDFMQNKI 114
PRK10246 PRK10246
exonuclease subunit SbcC; Provisional
 152-297 7.66e-03

exonuclease subunit SbcC; Provisional


Pssm-ID: 182330 [Multi-domain]  Cd Length: 1047  Bit Score: 39.78  E-value: 7.66e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687  152 RDVVEQHKAALQRQLEAVRGRLPQLSaaialvggisQQLQERKAEAlaqisaafedleQALQQRKQALVSDLESICGAKQ 231
Cdd:PRK10246  532 LDALEKEVKKLGEEGAALRGQLDALT----------KQLQRDESEA------------QSLRQEEQALTQQWQAVCASLN 589

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 552953687  232 KVLQTQLDT---LRQGQEHigsscsfaEQALRlgsapevLLVRKHMRErlAALAAQAFPERPHEnAQLE 297
Cdd:PRK10246  590 ITLQPQDDIqpwLDAQEEH--------ERQLR-------LLSQRHELQ--GQIAAHNQQIIQYQ-QQIE 640
RING-HC_UHRF cd16613
RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing ...
 22-64 7.75e-03

RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438275 [Multi-domain]  Cd Length: 46  Bit Score: 35.02  E-value: 7.75e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIPPQslTLSCPVCRQ 64
Cdd:cd16613    3 CICCQELVYKPITTPCKHNICKSCLQRSFKAE--VYTCPACRH 43
RING-HC_BAH1-like cd23127
RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 ...
 20-70 7.80e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 (BAH1) and similar proteins; This subfamily includes Arabidopsis thaliana BAH1 and BAH1-like. BAH1, also known as protein NITROGEN LIMITATION ADAPTATION (NLA), or RING-type E3 ubiquitin transferase BAH1, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It plays a role in salicylic acid-mediated negative feedback regulation of salicylic acid (SA) accumulation. It may be involved in the overall regulation of SA, benzoic acid and phenylpropanoid biosynthesis. It controls the adaptability to nitrogen limitation by channeling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis. BAH1-like, also known as RING finger protein 178, or RING-type E3 ubiquitin transferase BAH1-like, is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438489 [Multi-domain]  Cd Length: 74  Bit Score: 35.84  E-value: 7.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 552953687  20 LVCSICLDRYRCPKVLPCLHTFCERC--------LQNYIPPQSLTLSCPVCRQTSILPE 70
Cdd:cd23127    9 LTCSICLDTVFDPVALGCGHLFCNSCacsaasvlIFQGLKAAPPEAKCPLCRQDGVYAD 67
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
160-243 7.88e-03

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 39.61  E-value: 7.88e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 552953687 160 AALQRQLEAVRGRL----PQLSAAIALVGGISQQLQERKAEALAQISAAFEDL---EQALQQRKQALVSDLESICG--AK 230
Cdd:COG3206  273 AELEAELAELSARYtpnhPDVIALRAQIAALRAQLQQEAQRILASLEAELEALqarEASLQAQLAQLEARLAELPEleAE 352

                         90
                 ....*....|...
gi 552953687 231 QKVLQTQLDTLRQ 243
Cdd:COG3206  353 LRRLEREVEVARE 365
RING-H2_RNF130 cd16803
RING finger, H2 subclass, found in RING finger protein 130 (RNF130) and similar proteins; ...
 22-63 8.34e-03

RING finger, H2 subclass, found in RING finger protein 130 (RNF130) and similar proteins; RNF130, also known as Goliath homolog (H-Goliath), is a paralog of RNF128, also known as gene related to anergy in lymphocytes protein (GRAIL). It is a transmembrane E3 ubiquitin-protein ligase expressed in leukocytes. It has a self-ubiquitination property, and controls the development of T cell clonal anergy by ubiquitination. RNF130 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence.


Pssm-ID: 319717 [Multi-domain]  Cd Length: 49  Bit Score: 34.95  E-value: 8.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYR---CPKVLPCLHTFCERCLQNYIPPQSltlSCPVCR 63
Cdd:cd16803    3 CAVCIEGYKqndVVRILPCKHVFHKSCVDPWLNEHC---TCPMCK 44
RING-H2_RNF126-like cd16667
RING finger, H2 subclass, found in RING finger proteins RNF126, RNF115, and similar proteins; ...
 22-63 8.39e-03

RING finger, H2 subclass, found in RING finger proteins RNF126, RNF115, and similar proteins; This subfamily includes RING finger proteins RNF126, RNF115, and similar proteins. RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control. It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR). RNF126 promotes cancer cell proliferation by targeting the tumor suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers. It is also able to ubiquitylate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. RNF115, also known as Rab7-interacting ring finger protein (Rabring 7), or zinc finger protein 364 (ZNF364), or breast cancer-associated gene 2 (BCA2), is an E3 ubiquitin-protein ligase that is an endogenous inhibitor of adenosine monophosphate-activated protein kinase (AMPK) activation; this inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a cofactor in the restriction imposed by tetherin on HIV-1, and targets HIV-1 Gag for lysosomal degradation, impairing virus assembly and release, in a tetherin-independent manner. Moreover, RNF115 is a Rab7-binding protein that stimulates c-Myc degradation through mono-ubiquitination of MM-1. It also plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis. RNF115 and RNF126 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. Both of them contain an N-terminal BCA2 Zinc-finger domain (BZF), AKT-phosphorylation sites, and a C-terminal C3H2C3-type RING-H2 finger.


Pssm-ID: 438329 [Multi-domain]  Cd Length: 43  Bit Score: 34.59  E-value: 8.39e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 552953687  22 CSICLDRYRCP---KVLPCLHTFCERCLqnyIPPQSLTLSCPVCR 63
Cdd:cd16667    2 CAVCKEDFEVGeevRQLPCKHLFHPDCI---VPWLELHNSCPVCR 43
RING-H2_RNF12 cd16674
RING finger, H2 subclass, found in RING finger protein 12 (RNF12) and similar proteins; RNF12, ...
 22-64 9.63e-03

RING finger, H2 subclass, found in RING finger protein 12 (RNF12) and similar proteins; RNF12, also known as LIM domain-interacting RING finger protein or RING finger LIM domain-binding protein (R-LIM), is an E3 ubiquitin-protein ligase encoded by gene RLIM that is crucial for normal embryonic development in some species and for normal X inactivation in mice. It thus functions as a major sex-specific epigenetic regulator of female mouse nurturing tissues. RNF12 is widely expressed during embryogenesis, and mainly localizes to the cell nucleus, where it regulates the levels of many proteins, including CLIM, LMO, HDAC2, TRF1, SMAD7, and REX1, by proteasomal degradation. Its functional activity is regulated by phosphorylation-dependent nucleocytoplasmic shuttling. It is negatively regulated by pluripotency factors in embryonic stem cells. p53 represses its transcription through Sp1. RNF12 is the primary factor responsible for X chromosome inactivation (XCI) in female placental mammals. It is an indispensable factor in up-regulation of Xist transcription, thereby leading to initiation of random XCI. It also targets REX1, an inhibitor of XCI, for proteasomal degradation. RNF12 also acts as a co-regulator for a range of transcription factors, particularly those containing a LIM homeodomain, and modulates the formation of transcriptional multiprotein complexes. It is a negative regulator of Smad7, which in turn negatively regulates the signaling of type I receptors from the transforming growth factor beta (TGF-beta) superfamily. In addition, paternal RNF12 is a critical survival factor for milk-producing alveolar cells. RNF12 contains an nuclear localization signal (NLS) and a C3H2C3-type RING-H2 finger.


Pssm-ID: 438336 [Multi-domain]  Cd Length: 51  Bit Score: 34.70  E-value: 9.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 552953687  22 CSICLDRYRCP---KVLPCLHTFCERCLQNYIPPQSltlSCPVCRQ 64
Cdd:cd16674    3 CSVCITEYTEGnklRKLPCSHEYHVHCIDRWLSENS---TCPICRR 45
RING-HC_RNF125 cd16542
RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as ...
 22-72 9.67e-03

RING finger, HC subclass, found in RING finger protein 125 (RNF125); RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination.


Pssm-ID: 438204 [Multi-domain]  Cd Length: 50  Bit Score: 34.85  E-value: 9.67e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 552953687  22 CSICLDRYRCPKVLPCLHTFCERCLQNYIppQSLTLSCPVCRqtSILPEQG 72
Cdd:cd16542    4 CAVCLEVLHQPVRTRCGHVFCRPCIATSL--RNNTWTCPYCR--AYLSSEG 50
YvrE COG3386
Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase ...
 502-570 9.73e-03

Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]; Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway


Pssm-ID: 442613 [Multi-domain]  Cd Length: 266  Bit Score: 38.33  E-value: 9.73e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 552953687 502 VADSNNQCIQVF--SNEGQFKFR--FGVRGRSPGqlqRPTGVAVDTNGDIIVADYDNRWVSIFSPEGKFKTKI 570
Cdd:COG3386  153 VADTGAGRIYRFdlDADGTLGNRrvFADLPDGPG---GPDGLAVDADGNLWVALWGGGGVVRFDPDGELLGRI 222
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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