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Conserved domains on  [gi|578812645|ref|XP_006715506|]
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E3 ubiquitin-protein ligase SHPRH isoform X7 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 702-903 1.75e-105

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


:

Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 336.24  E-value: 1.75e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070    57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDL 858
Cdd:cd18070   136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 578812645  859 FGLVVFLGIEPYCVKHWWVRLLYRP-YCKKNPQHLYSFIAKILWRS 903
Cdd:cd18070   212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
RING-HC_SHPRH-like cd16569
RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) ...
 1429-1482 1.50e-27

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: 106.27  E-value: 1.50e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 578812645 1429 PEPCPICARQLGKQWAVLTCGHCFCNECISIIIEQYSVgSHRSSIKCAICRQTT 1482
Cdd:cd16569     1 PEPCPICARPLGKQWSVLPCGHCFCLECIAILIDQYAQ-SRRRSLKCPICRETT 53
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.08e-24

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


:

Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 97.87  E-value: 1.08e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645  660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547     1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 1.37e-20

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


:

Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 1.37e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538    2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 304-409 7.47e-18

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd18070:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 257  Bit Score: 85.09  E-value: 7.47e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070     1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                          90       100
                  ....*....|....*....|....*.
gi 578812645  384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070    32 LALILLHPRPDNDLDAADDDSDEMVC 57
HepA super family cl33945
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 6.17e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


The actual alignment was detected with superfamily member COG0553:

Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 60.62  E-value: 6.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553   236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                          90
                  ....*....|.
gi 578812645  378 GKTVEVLALIL 388
Cdd:COG0553   272 GKTIQALALLL 282
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 702-903 1.75e-105

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 336.24  E-value: 1.75e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070    57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDL 858
Cdd:cd18070   136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 578812645  859 FGLVVFLGIEPYCVKHWWVRLLYRP-YCKKNPQHLYSFIAKILWRS 903
Cdd:cd18070   212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 707-987 7.04e-74

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 247.98  E-value: 7.04e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDG---FLQPHFLAEQDIVIITYDVLRselnyvd 783
Cdd:pfam00176   41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   784 iphsnsedgrrlrnqKRYMAIPSplvaVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVV 863
Cdd:pfam00176  114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLN 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   864 FLGIEPYCV----KHWWVRLLYRPYCKKNPQHLYSFIAKILWRSAKKDVidQIQIPPQTEEIHWLHFSPVERHFYHRqhe 939
Cdd:pfam00176  175 FLRPGPFGSlstfRNWFDRPIERGGGKKGVSRLHKLLKPFLLRRTKKDV--EKSLPPKVEYILFCRLSKLQRKLYQT--- 249

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 578812645   940 vccqdvvvKLRKISDWALKLSSLDRRTVTSILYPLLRLRQACCHPQAV 987
Cdd:pfam00176  250 --------FLLKKDLNAIKTGEGGREIKASLLNILMRLRKICNHPGLI 289
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 716-1024 5.18e-31

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 131.50  E-value: 5.18e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGvKKDGFLQPHFLAEQDIVIITYDVLRSelnyvDIPHsnsedgrrl 795
Cdd:COG0553   291 RPVLIVAPTSLVGNWQRELAKF--APGLRVLVLDG-TRERAKGANPFEDADLVITSYGLLRR-----DIEL--------- 353

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGiePycvkhw 875
Cdd:COG0553   354 ------------LAAVDWDLVILDEAQHIKNPATKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFLN--P------ 413

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  876 wvRLLY----------RPYCKKNPQ---HLYSFIAKILWRSAKKDVIDQIqiPPQTEEIHWLHFSPVERHFYhrqhevcc 942
Cdd:COG0553   414 --GLLGslkafrerfaRPIEKGDEEaleRLRRLLRPFLLRRTKEDVLKDL--PEKTEETLYVELTPEQRALY-------- 481

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  943 QDVVVKLRKisdwALKLSSLDRRTVTsILYPLLRLRQACCHPQAVRGEFLPLQKSTMTMEELLTSLQkkcgTECEEAHRQ 1022
Cdd:COG0553   482 EAVLEYLRR----ELEGAEGIRRRGL-ILAALTRLRQICSHPALLLEEGAELSGRSAKLEALLELLE----ELLAEGEKV 552


                  ..
gi 578812645 1023 LV 1024
Cdd:COG0553   553 LV 554
RING-HC_SHPRH-like cd16569
RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) ...
 1429-1482 1.50e-27

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: 106.27  E-value: 1.50e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 578812645 1429 PEPCPICARQLGKQWAVLTCGHCFCNECISIIIEQYSVgSHRSSIKCAICRQTT 1482
Cdd:cd16569     1 PEPCPICARPLGKQWSVLPCGHCFCLECIAILIDQYAQ-SRRRSLKCPICRETT 53
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.08e-24

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 97.87  E-value: 1.08e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645  660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547     1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 1.37e-20

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 1.37e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538    2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 304-409 7.47e-18

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 85.09  E-value: 7.47e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070     1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                          90       100
                  ....*....|....*....|....*.
gi 578812645  384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070    32 LALILLHPRPDNDLDAADDDSDEMVC 57
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 440-512 2.97e-14

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 69.57  E-value: 2.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578812645  440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGK 512
Cdd:cd00073     5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSK 77
H15 smart00526
Domain in histone families 1 and 5;
440-501 1.74e-09

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.28  E-value: 1.74e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578812645    440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKG 501
Cdd:smart00526    5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 6.17e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 60.62  E-value: 6.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553   236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                          90
                  ....*....|.
gi 578812645  378 GKTVEVLALIL 388
Cdd:COG0553   272 GKTIQALALLL 282
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 307-389 2.72e-07

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 53.84  E-value: 2.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   307 YQREAVNWMLQQECFRSSpatesalhflwreivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEVLAL 386
Cdd:pfam00176    1 YQIEGVNWMLSLENNLGR-------------------------------------------GGILADEMGLGKTLQTISL 37


                   ...
gi 578812645   387 ILT 389
Cdd:pfam00176   38 LLY 40
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 1432-1478 1.53e-05

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: 43.27  E-value: 1.53e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 578812645   1432 CPICARQLGKQWAVLTCGHCFCNECISIIIEQysvgshrSSIKCAIC 1478
Cdd:smart00184    1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLES-------GNNTCPIC 40
DEXDc smart00487
DEAD-like helicases superfamily;
718-869 1.61e-05

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 47.49  E-value: 1.61e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645    718 TLIISPS-SICHQWVDEINRHVRSSSLR-VLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELnyvdiphsnSEDGRRL 795
Cdd:smart00487   57 VLVLVPTrELAEQWAEELKKLGPSLGLKvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL---------ENDKLSL 127

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645    796 RNqkrymaipsplvaveWWRICLDEAQMV--ECPTVKAAEMAQRL-SGINRWCISGTP---VQRGLEDLFGLVVFLGIEP 869
Cdd:smart00487  128 SN---------------VDLVILDEAHRLldGGFGDQLEKLLKLLpKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGF 192
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
 1432-1475 8.73e-05

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: 41.23  E-value: 8.73e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 578812645  1432 CPICARQLGKqwAVLTCGHCFCNECISIiieqySVGSHRSSIKC 1475
Cdd:pfam13445    1 CPICLELFTD--PVLPCGHTFCRECLEE-----MSQKKGGKFKC 37
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 661-709 1.28e-04

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 40.94  E-value: 1.28e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 578812645   661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNY--DEKNLKIKPFYCPHCLVA 709
Cdd:pfam00628    3 AVCGKSD--DGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 675-706 2.51e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 40.27  E-value: 2.51e-04
                            10        20        30
                    ....*....|....*....|....*....|...
gi 578812645    675 VQCLKCHLWQHAKCVNY-DEKNLKIKPFYCPHC 706
Cdd:smart00249   15 LQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
 1415-1487 9.65e-04

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 42.96  E-value: 9.65e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578812645 1415 NLEKSQDKTSGGVNPEPCPICARQLGKQwAVLTCGHCFCNECIsiiieqYSVGSHRSSIKCAICRQTTSHKEI 1487
Cdd:COG5574   201 NLSKKNGLPFIPLADYKCFLCLEEPEVP-SCTPCGHLFCLSCL------LISWTKKKYEFCPLCRAKVYPKKV 266
 
Name Accession Description Interval E-value
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 702-903 1.75e-105

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 336.24  E-value: 1.75e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  702 YCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSsLRVLVYQGVKKDGFLQ---PHFLAEQDIVIITYDVLRSE 778
Cdd:cd18070    57 CCPDCLVAETPVSSKATLIVCPSAILAQWLDEINRHVPSS-LKVLTYQGVKKDGALAspaPEILAEYDIVVTTYDVLRTE 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  779 LNYVDIPHSNsedgRRLRNQKRYMAIPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDL 858
Cdd:cd18070   136 LHYAEANRSN----RRRRRQKRYEAPPSPLVLVEWWRVCLDEAQMVESSTSKAAEMARRLPRVNRWCVSGTPIQRGLDDL 211

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 578812645  859 FGLVVFLGIEPYCVKHWWVRLLYRP-YCKKNPQHLYSFIAKILWRS 903
Cdd:cd18070   212 FGLLSFLGVEPFCDSDWWARVLIRPqGRNKAREPLAALLKELLWRS 257
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 707-987 7.04e-74

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 247.98  E-value: 7.04e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDG---FLQPHFLAEQDIVIITYDVLRselnyvd 783
Cdd:pfam00176   41 LKHVDKNWGGPTLIVVPLSLLHNWMNEFERWVSPPALRVVVLHGNKRPQerwKNDPNFLADFDVVITTYETLR------- 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   784 iphsnsedgrrlrnqKRYMAIPSplvaVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVV 863
Cdd:pfam00176  114 ---------------KHKELLKK----VHWHRIVLDEGHRLKNSKSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLN 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   864 FLGIEPYCV----KHWWVRLLYRPYCKKNPQHLYSFIAKILWRSAKKDVidQIQIPPQTEEIHWLHFSPVERHFYHRqhe 939
Cdd:pfam00176  175 FLRPGPFGSlstfRNWFDRPIERGGGKKGVSRLHKLLKPFLLRRTKKDV--EKSLPPKVEYILFCRLSKLQRKLYQT--- 249

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*...
gi 578812645   940 vccqdvvvKLRKISDWALKLSSLDRRTVTSILYPLLRLRQACCHPQAV 987
Cdd:pfam00176  250 --------FLLKKDLNAIKTGEGGREIKASLLNILMRLRKICNHPGLI 289
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 693-902 3.66e-54

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 189.42  E-value: 3.66e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  693 EKNLKIKPFYCPHCLVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFlqPHFLAEQDIVIITY 772
Cdd:cd18008    40 PQDPKIPEELEENSSDPKKLYLSKTTLIVVPLSLLSQWKDEIEKHTKPGSLKVYVYHGSKRIKS--IEELSDYDIVITTY 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  773 DVLRSELNYVDIPHSNSEdgrrlrnqkrYMAIPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQ 852
Cdd:cd18008   118 GTLASEFPKNKKGGGRDS----------KEKEASPLHRIRWYRVILDEAHNIKNRSTKTSRAVCALKAERRWCLTGTPIQ 187

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578812645  853 RGLEDLFGLVVFLGIEPYCVKHWWVRLLYRPYCKKNP---QHLYSFIAKILWR 902
Cdd:cd18008   188 NSLDDLYSLLRFLRVEPFGDYPWFNSDISKPFSKNDRkalERLQALLKPILLR 240
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 707-902 2.01e-33

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 129.90  E-value: 2.01e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  707 LVAMEPVSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDgfLQPHFLAEQDIVIITYDVLRSElnyvdipH 786
Cdd:cd18071    63 LTTISLILANFTLIVCPLSVLSNWETQFEEHVKPGQLKVYTYHGGERN--RDPKLLSKYDIVLTTYNTLASD-------F 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  787 SNSEDgrrlrnqkrymaipSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLG 866
Cdd:cd18071   134 GAKGD--------------SPLHTINWLRVVLDEGHQIRNPNAQQTKAVLNLSSERRWVLTGTPIQNSPKDLGSLLSFLH 199

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 578812645  867 IEPYCVKHWWVRLLYRPYCKKNP---QHLYSFIAKILWR 902
Cdd:cd18071   200 LKPFSNPEYWRRLIQRPLTMGDPtglKRLQVLMKQITLR 238
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 716-1024 5.18e-31

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 131.50  E-value: 5.18e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGvKKDGFLQPHFLAEQDIVIITYDVLRSelnyvDIPHsnsedgrrl 795
Cdd:COG0553   291 RPVLIVAPTSLVGNWQRELAKF--APGLRVLVLDG-TRERAKGANPFEDADLVITSYGLLRR-----DIEL--------- 353

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGiePycvkhw 875
Cdd:COG0553   354 ------------LAAVDWDLVILDEAQHIKNPATKRAKAVRALKARHRLALTGTPVENRLEELWSLLDFLN--P------ 413

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  876 wvRLLY----------RPYCKKNPQ---HLYSFIAKILWRSAKKDVIDQIqiPPQTEEIHWLHFSPVERHFYhrqhevcc 942
Cdd:COG0553   414 --GLLGslkafrerfaRPIEKGDEEaleRLRRLLRPFLLRRTKEDVLKDL--PEKTEETLYVELTPEQRALY-------- 481

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  943 QDVVVKLRKisdwALKLSSLDRRTVTsILYPLLRLRQACCHPQAVRGEFLPLQKSTMTMEELLTSLQkkcgTECEEAHRQ 1022
Cdd:COG0553   482 EAVLEYLRR----ELEGAEGIRRRGL-ILAALTRLRQICSHPALLLEEGAELSGRSAKLEALLELLE----ELLAEGEKV 552


                  ..
gi 578812645 1023 LV 1024
Cdd:COG0553   553 LV 554
RING-HC_SHPRH-like cd16569
RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) ...
 1429-1482 1.50e-27

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: 106.27  E-value: 1.50e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 578812645 1429 PEPCPICARQLGKQWAVLTCGHCFCNECISIIIEQYSVgSHRSSIKCAICRQTT 1482
Cdd:cd16569     1 PEPCPICARPLGKQWSVLPCGHCFCLECIAILIDQYAQ-SRRRSLKCPICRETT 53
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 713-876 5.28e-27

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 111.42  E-value: 5.28e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  713 VSTRATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGflQPHFLAEQDIVIITYDVLRSELNyvdiphSNSEDG 792
Cdd:cd18072    71 VPSAGTLVVCPASLVHQWKNEVESRVASNKLRVCLYHGPNRER--IGEVLRDYDIVITTYSLVAKEIP------TYKEES 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  793 RrlrnqkrymaiPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGIEPYCV 872
Cdd:cd18072   143 R-----------SSPLFRIAWARIILDEAHNIKNPKVQASIAVCKLRAHARWALTGTPIQNNLLDMYSLLKFLRCSPFDD 211


                  ....
gi 578812645  873 KHWW 876
Cdd:cd18072   212 LKVW 215
PHD_SHPRH cd15547
PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, ...
 660-706 1.08e-24

PHD finger found in E3 ubiquitin-protein ligase SHPRH; SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain.


Pssm-ID: 277022 [Multi-domain]  Cd Length: 47  Bit Score: 97.87  E-value: 1.08e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645  660 ECICGELDQIDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15547     1 ECICGELDEIDNKHRVQCLKCGLWQHAECVNYDEESDKREPYLCPHC 47
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 440-508 1.37e-20

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 86.81  E-value: 1.37e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRY-DVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTF 508
Cdd:pfam00538    2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVgDVAKFNSLLKRALKKGVEKGTLVQPKGTGASGSF 71
DEXQc_SHPRH cd18070
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
 304-409 7.47e-18

DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350828 [Multi-domain]  Cd Length: 257  Bit Score: 85.09  E-value: 7.47e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhflwreivtseglklyynpytgciireypnsgpqLLGGILADEMGLGKTVEV 383
Cdd:cd18070     1 LLPYQRRAVNWML-------------------------------------------------VPGGILADEMGLGKTVEV 31

                          90       100
                  ....*....|....*....|....*.
gi 578812645  384 LALILTHTRQDVKQDALTLPEGKVVN 409
Cdd:cd18070    32 LALILLHPRPDNDLDAADDDSDEMVC 57
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 718-865 2.09e-17

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 81.84  E-value: 2.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  718 TLIISPSSICHQWVDEINRHVRSssLRVLVYQGVKKDGFLQPHF--LAEQDIVIITYDVLRSELNYvdiphsnsedgrrl 795
Cdd:cd17919    53 VLVVCPLSVLENWEREFEKWTPD--LRVVVYHGSQRERAQIRAKekLDKFDVVLTTYETLRRDKAS-------------- 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd17919   117 ------------LRKFRWDLVVVDEAHRLKNPKSQLSKALKALRAKRRLLLTGTPLQNNLEELWALLDFL 174
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 716-865 8.03e-16

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 77.99  E-value: 8.03e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  716 RATLIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKDgFLQPHFLAEQDIVIITYDVLRSELNYvdiphsnsedgrrl 795
Cdd:cd18012    54 GPSLVVAPTSLIYNWEEEAAKF--APELKVLVIHGTKRK-REKLRALEDYDLVITSYGLLRRDIEL-------------- 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd18012   117 ------------LKEVKFHYLVLDEAQNIKNPQTKTAKAVKALKADHRLALTGTPIENHLGELWSIFDFL 174
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 705-865 3.03e-15

DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350757 [Multi-domain]  Cd Length: 232  Bit Score: 76.62  E-value: 3.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  705 HCLVAMEPVST-RATLIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELNYvd 783
Cdd:cd17999    44 HHKRANSFNSEnLPSLVVCPPTLVGHWVAEIKKYFPNAFLKPLAYVGPPQERRRLREQGEKHNVIVASYDVLRNDIEV-- 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  784 iphsnsedgrrlrnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVV 863
Cdd:cd17999   122 ------------------------LTKIEWNYCVLDEGHIIKNSKTKLSKAVKQLKANHRLILSGTPIQNNVLELWSLFD 177


                  ..
gi 578812645  864 FL 865
Cdd:cd17999   178 FL 179
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 440-512 2.97e-14

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 69.57  E-value: 2.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578812645  440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKGHGFSGTFTLGK 512
Cdd:cd00073     5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLSK 77
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 304-394 7.53e-10

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 61.15  E-value: 7.53e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhflWReivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd18008     1 LLPYQKQGLAWML------------------PR-------------------------------GGILADEMGLGKTIQA 31

                          90
                  ....*....|.
gi 578812645  384 LALILTHTRQD 394
Cdd:cd18008    32 LALILATRPQD 42
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 304-400 8.03e-10

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 60.66  E-value: 8.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMlqqecfrsspatesalHFLWReivtseglklyYNpytgciireypnsgpqlLGGILADEMGLGKTVEV 383
Cdd:cd18012     5 LRPYQKEGFNWL----------------SFLRH-----------YG-----------------LGGILADDMGLGKTLQT 40

                          90
                  ....*....|....*..
gi 578812645  384 LALILTHTRQDVKQDAL 400
Cdd:cd18012    41 LALLLSRKEEGRKGPSL 57
H15 smart00526
Domain in histone families 1 and 5;
440-501 1.74e-09

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 55.28  E-value: 1.74e-09
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578812645    440 PPTRVMILTAVKEMNGKKGVSILSIYKYVSSIYRYDVQRNRSLLKRMLKCLIFEGLVKQIKG 501
Cdd:smart00526    5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANYKVLPNNFRKLLKLALKRLVASGKLVQVKG 66
DEXHc_HLTF1_SMARC3 cd18071
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
 304-389 4.18e-09

DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350829 [Multi-domain]  Cd Length: 239  Bit Score: 58.63  E-value: 4.18e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLQQEcfrSSPATESAlhflWREIVtseglKLYYNPYTGCIIREYPNSGpqlLGGILADEMGLGKTVEV 383
Cdd:cd18071     1 LLPHQKQALAWMVSRE---NSQDLPPF----WEEAV-----GLFLNTITNFSQKKRPELV---RGGILADDMGLGKTLTT 65


                  ....*.
gi 578812645  384 LALILT 389
Cdd:cd18071    66 ISLILA 71
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 298-388 6.17e-09

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 60.62  E-value: 6.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  298 PALIPVLRPYQREAVNWMLqqecfrsspatesalhFLWReivtseglklyynpytgciireypnsgpQLLGGILADEMGL 377
Cdd:COG0553   236 AGLKATLRPYQLEGAAWLL----------------FLRR----------------------------LGLGGLLADDMGL 271

                          90
                  ....*....|.
gi 578812645  378 GKTVEVLALIL 388
Cdd:COG0553   272 GKTIQALALLL 282
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 304-398 2.35e-08

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 55.26  E-value: 2.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglkLYYNPYtgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd17919     1 LRPYQLEGLNFLLE----------------------------LYENGP----------------GGILADEMGLGKTLQA 36

                          90
                  ....*....|....*
gi 578812645  384 LALILTHTRQDVKQD 398
Cdd:cd17919    37 IAFLAYLLKEGKERG 51
RING-HC_RNF170 cd16553
RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins; ...
 1432-1481 7.32e-08

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: 50.36  E-value: 7.32e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 578812645 1432 CPICARQLgkQWAVLT-CGHCFCNECisiIIEQYSVGSHRSSIKCAICRQT 1481
Cdd:cd16553     4 CPICLQDA--RFPVETnCGHLFCGPC---IITYWRHGSWLGAVSCPVCRQT 49
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 710-875 8.11e-08

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 55.08  E-value: 8.11e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  710 MEPVSTRA--TLIISPSSICHQWVDEINRHvrsSSLRVLVYQGVKKDGFLQPHFLAEQ-DIVIITYDVLRselnyvdiph 786
Cdd:cd18005    63 KPPASSAKkpVLIVAPLSVLYNWKDELDTW---GHFEVGVYHGSRKDDELEGRLKAGRlEVVVTTYDTLR---------- 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  787 snsedgrrlrnqkryMAIPSpLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFglvvflg 866
Cdd:cd18005   130 ---------------RCIDS-LNSINWSAVIADEAHRIKNPKSKLTQAMKELKCKVRIGLTGTLLQNNMKELW------- 186


                  ....*....
gi 578812645  867 iepyCVKHW 875
Cdd:cd18005   187 ----CLLDW 191
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 307-389 2.72e-07

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 53.84  E-value: 2.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645   307 YQREAVNWMLQQECFRSSpatesalhflwreivtseglklyynpytgciireypnsgpqllGGILADEMGLGKTVEVLAL 386
Cdd:pfam00176    1 YQIEGVNWMLSLENNLGR-------------------------------------------GGILADEMGLGKTLQTISL 37


                   ...
gi 578812645   387 ILT 389
Cdd:pfam00176   38 LLY 40
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 719-870 5.44e-07

DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350756 [Multi-domain]  Cd Length: 187  Bit Score: 51.62  E-value: 5.44e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHvrSSSLRVLVYQGVKKDGFLQPHFLAEQdivIITYDVLRSELNYVDiphSNSEDGRRLRNQ 798
Cdd:cd17998    53 LVVVPSSTLDNWLREFKRW--CPSLKVEPYYGSQEERKHLRYDILKG---LEDFDVIVTTYNLAT---SNPDDRSFFKRL 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 578812645  799 KRYMAIpsplvavewwricLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFLGIEPY 870
Cdd:cd17998   125 KLNYVV-------------YDEGHMLKNMTSERYRHLMTINANFRLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 713-864 1.89e-06

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 50.01  E-value: 1.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  713 VSTRATLIISPSSICHQWVDEINR----------HVRSSSLRVLVYQGVKKDGF-LQPHFLAEQDIVIITYDVLRSelny 781
Cdd:cd18000    48 LGLGPSLIVCPATVLKQWVKEFHRwwppfrvvvlHSSGSGTGSEEKLGSIERKSqLIRKVVGDGGILITTYEGFRK---- 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  782 vdiphsnsedgrrlrNQKrymaipsPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGL 861
Cdd:cd18000   124 ---------------HKD-------LLLNHNWQYVILDEGHKIRNPDAEITLACKQLRTPHRLILSGTPIQNNLKELWSL 181


                  ...
gi 578812645  862 VVF 864
Cdd:cd18000   182 FDF 184
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 718-865 2.39e-06

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 50.45  E-value: 2.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  718 TLIISPSSICHQWVDEINRhvRSSSLRVLVYQGVKKDG--FLQPHFLAEQDIVIITYDVLRSELNYVdiphsNSEDGRRL 795
Cdd:cd18001    52 VLVVMPTSLIPHWVKEFAK--WTPGLRVKVFHGTSKKEreRNLERIQRGGGVLLTTYGMVLSNTEQL-----SADDHDEF 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 RnqkrymaipsplvaveWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd18001   125 K----------------WDYVILDEGHKIKNSKTKSAKSLREIPAKNRIILTGTPIQNNLKELWALFDFA 178
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
 719-865 2.81e-06

DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350760 [Multi-domain]  Cd Length: 229  Bit Score: 50.20  E-value: 2.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHVrsSSLRVLVYQGVKKD-----GFLQPHFLAEQD----IVIITYDVLRSELNYvdiphsns 789
Cdd:cd18002    54 LVIAPASTLHNWQQEISRFV--PQFKVLPYWGNPKDrkvlrKFWDRKNLYTRDapfhVVITSYQLVVQDEKY-------- 123

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645  790 edgrrlrnqkrymaipspLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd18002   124 ------------------FQRVKWQYMVLDEAQAIKSSSSSRWKTLLSFHCRNRLLLTGTPIQNSMAELWALLHFI 181
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 719-865 4.40e-06

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 49.21  E-value: 4.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHVrSSSLRVLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSElnyvdiphsnsedgRRLRNQ 798
Cdd:cd18011    51 LILCPASLVEQWQDELQDKF-GLPFLILDRETAAQLRRLIGNPFEEFPIVIVSLDLLKRS--------------EERRGL 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578812645  799 krymaipspLVAVEWWRICLDEA-QMVECPTVKAA---EMAQRLSGINRWCI--SGTPVQRGLEDLFGLVVFL 865
Cdd:cd18011   116 ---------LLSEEWDLVVVDEAhKLRNSGGGKETkryKLGRLLAKRARHVLllTATPHNGKEEDFRALLSLL 179
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 304-397 6.03e-06

DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350753 [Multi-domain]  Cd Length: 223  Bit Score: 49.17  E-value: 6.03e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhFLWREivtseglklyynpYTGCIireypnsgpqllggiLADEMGLGKTVEV 383
Cdd:cd17995     1 LRDYQLEGVNWLL----------------FNWYN-------------RRNCI---------------LADEMGLGKTIQS 36

                          90
                  ....*....|....
gi 578812645  384 LALiLTHTRQDVKQ 397
Cdd:cd17995    37 IAF-LEHLYQVEGI 49
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 719-865 8.66e-06

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 48.47  E-value: 8.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHVrsSSLRVLVYQGVK--KDGFLQPHFLAEQ-DIVIITYDVLRSELNYVdiphsnsedgrrl 795
Cdd:cd17997    57 LIIVPKSTLDNWMREFKRWC--PSLRVVVLIGDKeeRADIIRDVLLPGKfDVCITSYEMVIKEKTVL------------- 121

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqKRYmaipsplvavEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd17997   122 ---KKF----------NWRYIIIDEAHRIKNEKSKLSQIVRLFNSRNRLLLTGTPLQNNLHELWALLNFL 178
PHD_MLL5 cd15550
PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that ...
 661-706 1.49e-05

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.


Pssm-ID: 277025 [Multi-domain]  Cd Length: 44  Bit Score: 43.46  E-value: 1.49e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 578812645  661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKpFYCPHC 706
Cdd:cd15550     2 CICGFEH--DDGFMICCDKCSVWQHGDCMGIDRENIPDS-YLCEQC 44
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 1432-1478 1.53e-05

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: 43.27  E-value: 1.53e-05
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*..
gi 578812645   1432 CPICARQLGKQWAVLTCGHCFCNECISIIIEQysvgshrSSIKCAIC 1478
Cdd:smart00184    1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLES-------GNNTCPIC 40
DEXDc smart00487
DEAD-like helicases superfamily;
718-869 1.61e-05

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 47.49  E-value: 1.61e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645    718 TLIISPS-SICHQWVDEINRHVRSSSLR-VLVYQGVKKDGFLQPHFLAEQDIVIITYDVLRSELnyvdiphsnSEDGRRL 795
Cdd:smart00487   57 VLVLVPTrELAEQWAEELKKLGPSLGLKvVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL---------ENDKLSL 127

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645    796 RNqkrymaipsplvaveWWRICLDEAQMV--ECPTVKAAEMAQRL-SGINRWCISGTP---VQRGLEDLFGLVVFLGIEP 869
Cdd:smart00487  128 SN---------------VDLVILDEAHRLldGGFGDQLEKLLKLLpKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGF 192
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 662-706 1.71e-05

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 43.31  E-value: 1.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 578812645  662 ICGELDQIDRKPRVQCLKCHLWQHAKCVNYD-EKNLKIKPFYCPHC 706
Cdd:cd15517     4 ICNLETAAVDELWVQCDGCDKWFHQFCLGLSnERYADEDKFKCPNC 49
RING-HC_ULS1-like cd23136
RING finger, HC subclass, found in Saccharomyces cerevisiae ubiquitin ligase for SUMO ...
 1432-1491 2.00e-05

RING finger, HC subclass, found in Saccharomyces cerevisiae ubiquitin ligase for SUMO conjugates protein 1 (ULS1) and similar proteins; ULS1, also called role in silencing protein 1, is an ATP-dependent helicase involved in mating type switching and in silencing interference through its interaction with the silencing regulator SIR4. It cooperates with UBC4 and UBC5 to mediate ubiquitination of SUMO conjugates. ULS1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438498 [Multi-domain]  Cd Length: 76  Bit Score: 44.22  E-value: 2.00e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1432 CPICARQLGKQWAVL--TCGHCFCNECISIIIEQYS---VGSHRSSIKCAICRQTTSHKE-ISYVF 1491
Cdd:cd23136     7 CPVCFDVVGEESIVIlaGCGHMICDGCVENFFEEQReekEGTGNRSAPCLTCKKLVKENDlVDYKL 72
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 304-396 2.63e-05

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 47.37  E-value: 2.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglkLYYNPYtgciireypnsgpqllGGILADEMGLGKTVEV 383
Cdd:cd18005     1 LRDYQREGVEFMYD----------------------------LYKNGR----------------GGILGDDMGLGKTVQV 36

                          90
                  ....*....|....*...
gi 578812645  384 LALIL-----THTRQDVK 396
Cdd:cd18005    37 IAFLAavlgkTGTRRDRE 54
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 304-415 4.09e-05

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 46.70  E-value: 4.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLqqecfrsspatesalhflWREivtseglklyynpytgciireypNSGPQllGGILADEMGLGKTVEV 383
Cdd:cd18072     1 LLLHQKQALAWLL------------------WRE-----------------------RQKPR--GGILADDMGLGKTLTM 37

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 578812645  384 LALILT-----HTRQDVKQDALTLPEGKVVNYFIPSH 415
Cdd:cd18072    38 IALILAqkntqNRKEEEKEKALTEWESKKDSTLVPSA 74
PHD_Cfp1 cd15553
PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding ...
 661-706 4.63e-05

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.


Pssm-ID: 277028  Cd Length: 46  Bit Score: 41.98  E-value: 4.63e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645  661 CICGELDqIDRKpRVQCLKCHLWQHAKCVNYDEKNLK-IKPFYCPHC 706
Cdd:cd15553     2 CICRSSD-ISRF-MIGCDNCEEWYHGDCINITEKEAKaIKEWYCQQC 46
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
 719-865 5.07e-05

DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350823 [Multi-domain]  Cd Length: 233  Bit Score: 46.55  E-value: 5.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHVrsSSLRVLVYQGVK--KDGFLQPHFL-AEQDIVIITYDVLRSElnyvdiphsnsedgrrl 795
Cdd:cd18065    69 MVLVPKSTLHNWMNEFKRWV--PSLRAVCLIGDKdaRAAFIRDVMMpGEWDVCVTSYEMVIKE----------------- 129

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  796 rnqkrymaiPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd18065   130 ---------KSVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFL 190
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 365-387 6.01e-05

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 45.78  E-value: 6.01e-05
                          10        20
                  ....*....|....*....|...
gi 578812645  365 QLLGGILADEMGLGKTVEVLALI 387
Cdd:cd18000    18 QRVGGILGDEMGLGKTIQIIAFL 40
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
 719-865 6.02e-05

DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350822 [Multi-domain]  Cd Length: 244  Bit Score: 46.20  E-value: 6.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  719 LIISPSSICHQWVDEINRHVRSSSLRVLVYQGVKKDGFLQPHFL-AEQDIVIITYDVLRSElnyvdiphsnsedgrrlrn 797
Cdd:cd18064    69 MVLVPKSTLHNWMAEFKRWVPTLRAVCLIGDKDQRAAFVRDVLLpGEWDVCVTSYEMLIKE------------------- 129

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578812645  798 qkrymaiPSPLVAVEWWRICLDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVFL 865
Cdd:cd18064   130 -------KSVFKKFNWRYLVIDEAHRIKNEKSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFL 190
zf-RING_UBOX pfam13445
RING-type zinc-finger; This zinc-finger is a typical RING-type of plant ubiquitin ligases.
 1432-1475 8.73e-05

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: 41.23  E-value: 8.73e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 578812645  1432 CPICARQLGKqwAVLTCGHCFCNECISIiieqySVGSHRSSIKC 1475
Cdd:pfam13445    1 CPICLELFTD--PVLPCGHTFCRECLEE-----MSQKKGGKFKC 37
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 661-706 8.78e-05

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 41.53  E-value: 8.78e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645  661 CICGELDQiDRKPRVQCLKCHLWQHAKCVNYDEK-NLKIKPFYCPHC 706
Cdd:cd15489     3 IVCGKGGD-LGGELLQCDGCGKWFHADCLGPPLSsFVPNGKWICPVC 48
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 303-387 9.14e-05

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 45.84  E-value: 9.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  303 VLRPYQREAVNWMLqqecfrsspatesalhflwreivtseglKLYYNPytgciireypnsgpqlLGGILADEMGLGKTVE 382
Cdd:cd18009     3 VMRPYQLEGMEWLR----------------------------MLWENG----------------INGILADEMGLGKTIQ 38


                  ....*
gi 578812645  383 VLALI 387
Cdd:cd18009    39 TIALL 43
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 367-387 1.14e-04

DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350754 [Multi-domain]  Cd Length: 233  Bit Score: 45.44  E-value: 1.14e-04
                          10        20
                  ....*....|....*....|.
gi 578812645  367 LGGILADEMGLGKTVEVLALI 387
Cdd:cd17996    23 LNGILADEMGLGKTIQTISLI 43
PHD pfam00628
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ...
 661-709 1.28e-04

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.


Pssm-ID: 425785 [Multi-domain]  Cd Length: 51  Bit Score: 40.94  E-value: 1.28e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 578812645   661 CICGELDqiDRKPRVQCLKCHLWQHAKCVNY--DEKNLKIKPFYCPHCLVA 709
Cdd:pfam00628    3 AVCGKSD--DGGELVQCDGCDDWFHLACLGPplDPAEIPSGEWLCPECKPK 51
RING-HC_AtBRCA1-like cd23147
RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 ...
 1432-1487 1.39e-04

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: 40.92  E-value: 1.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1432 CPICArQLGKQWAVLTCGHCFCNECIsiiieqysVGSHRSSIKCAICRQTTSHKEI 1487
Cdd:cd23147     7 CPICL-SLFKSAANLSCNHCFCAGCI--------GESLKLSAICPVCKIPATRRDT 53
RING-HC_RNF113A_B cd16539
RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins; ...
 1429-1483 2.22e-04

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: 40.27  E-value: 2.22e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578812645 1429 PEPCPICaRQLGKQWAVLTCGHCFCNECisiIIEQYsvgshRSSIKCAICRQTTS 1483
Cdd:cd16539     5 PFACFIC-RKPFKNPVVTKCGHYFCEKC---ALKHY-----RKSKKCFVCGKQTN 50
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 304-393 2.29e-04

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 44.58  E-value: 2.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVNWMLQqecfrsspatesalhflwreivtseglklyynpytgCIIReypNSGPQLLGGILADEMGLGKTVEV 383
Cdd:cd18004     1 LRPHQREGVQFLYD------------------------------------CLTG---RRGYGGGGAILADEMGLGKTLQA 41

                          90
                  ....*....|
gi 578812645  384 LALILTHTRQ 393
Cdd:cd18004    42 IALVWTLLKQ 51
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 675-706 2.51e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 40.27  E-value: 2.51e-04
                            10        20        30
                    ....*....|....*....|....*....|...
gi 578812645    675 VQCLKCHLWQHAKCVNY-DEKNLKIKPFYCPHC 706
Cdd:smart00249   15 LQCDGCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47
RING-HC_BAH1-like cd23127
RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 ...
 1432-1480 3.67e-04

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: 40.46  E-value: 3.67e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578812645 1432 CPICARQLGKQWAvLTCGHCFCNECI----SIIIEQySVGSHRSSIKCAICRQ 1480
Cdd:cd23127    11 CSICLDTVFDPVA-LGCGHLFCNSCAcsaaSVLIFQ-GLKAAPPEAKCPLCRQ 61
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
 1432-1478 3.70e-04

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: 39.39  E-value: 3.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 578812645 1432 CPICARQLgKQWAVLTCGHCFCNECISIIIEqysvgshRSSIKCAIC 1478
Cdd:cd16449     3 CPICLERL-KDPVLLPCGHVFCRECIRRLLE-------SGSIKCPIC 41
PHD_TAF3 cd15522
PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed ...
 662-706 4.01e-04

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).


Pssm-ID: 276997 [Multi-domain]  Cd Length: 46  Bit Score: 39.58  E-value: 4.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 578812645  662 ICGELDqiDRKPRVQCLKCHLWQHAKCVNYDEKNLKIKPFYCPHC 706
Cdd:cd15522     4 ICKKPD--DGSPMIGCDECDDWYHWECVGITDEPPEEDDWFCPKC 46
RING-HC_TRIM65_C-IV cd16609
RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar ...
 1432-1486 5.81e-04

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: 39.28  E-value: 5.81e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578812645 1432 CPICArQLGKQWAVLTCGHCFCNECisiiIEQYSVGSHRSSIKCAICRQTTSHKE 1486
Cdd:cd16609     6 CSICL-GLYQDPVTLPCQHSFCRAC----IEDHWRQKDEGSFSCPECRAPFPEGP 55
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 369-393 7.22e-04

DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350751 [Multi-domain]  Cd Length: 218  Bit Score: 42.73  E-value: 7.22e-04
                          10        20
                  ....*....|....*....|....*..
gi 578812645  369 GILADEMGLGKTVEVLALI--LTHTRQ 393
Cdd:cd17993    23 GILADEMGLGKTVQTISFLsyLFHSQQ 49
PHD_HAC_like cd15614
PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar ...
 675-706 7.41e-04

PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar proteins; This family includes A. thaliana HACs (HAC1/2/4/5/12), which are histone acetyltransferases of the p300/CREB-binding protein (CBP) co-activator family. CBP-type HAT proteins are also found in animals, but absent in fungi. The domain architecture of CBP-type HAT proteins differs between plants and animals. Members in this family contain an N-terminal partially conserved KIX domain, a Zf-TAZ domain, a Cysteine rich CBP-type HAT domain that harbors a plant homeodomain (PHD) finger, a Zf-ZZ domain, and a Zf-TAZ domain. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277086  Cd Length: 73  Bit Score: 39.64  E-value: 7.41e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 578812645  675 VQCLKCHLWQHAKCVNYDEKNLKIK--PFYCPHC 706
Cdd:cd15614    40 VQCDKCERWQHQICGLYNGRRNADEtaEYVCPLC 73
RING-HC_TRIM13_C-V cd16762
RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar ...
 1432-1482 9.42e-04

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: 38.74  E-value: 9.42e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 578812645 1432 CPICArQLGKQWAVLTCGHCFCNECISIIIEQYSVGSH-RSSIKCAICRQTT 1482
Cdd:cd16762     6 CPICC-CLFDDPRVLPCSHNFCKKCLEGILEGNVRTMLwRPPFKCPTCRKET 56
PEX10 COG5574
RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, ...
 1415-1487 9.65e-04

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


Pssm-ID: 227861 [Multi-domain]  Cd Length: 271  Bit Score: 42.96  E-value: 9.65e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 578812645 1415 NLEKSQDKTSGGVNPEPCPICARQLGKQwAVLTCGHCFCNECIsiiieqYSVGSHRSSIKCAICRQTTSHKEI 1487
Cdd:COG5574   201 NLSKKNGLPFIPLADYKCFLCLEEPEVP-SCTPCGHLFCLSCL------LISWTKKKYEFCPLCRAKVYPKKV 266
RING-HC_RNF222 cd16564
RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins; ...
 1432-1483 1.15e-03

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: 38.15  E-value: 1.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 578812645 1432 CPICARQLGKQWAVLTCGHCFCNECISIIIEQYsvgshrsSIKCAICRQTTS 1483
Cdd:cd16564     3 CPVCYEDFDDAPRILSCGHSFCEDCLVKQLVSM-------TISCPICRRVTF 47
RING-HC_RNF166 cd16549
RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins; ...
 1432-1479 1.26e-03

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: 38.25  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 578812645 1432 CPICARQLGKQWAVLTCGHCFCNECISIIIEQysvgshrSSIKCAICR 1479
Cdd:cd16549     4 CPICLEVYHKPVVITSCGHTFCGECLQPCLQV-------ASPLCPLCR 44
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 356-390 1.55e-03

DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350761 [Multi-domain]  Cd Length: 223  Bit Score: 41.95  E-value: 1.55e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 578812645  356 IREYPNSGPQLL--------GGILADEMGLGKTVEVLALiLTH 390
Cdd:cd18003     1 LREYQHIGLDWLatlyeknlNGILADEMGLGKTIQTIAL-LAH 42
zf-RING_2 pfam13639
Ring finger domain;
1432-1479 1.57e-03

Ring finger domain;


Pssm-ID: 433370 [Multi-domain]  Cd Length: 44  Bit Score: 37.77  E-value: 1.57e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 578812645  1432 CPICARQLGKQ--WAVLTCGHCFCNECISIIIeqysvgshRSSIKCAICR 1479
Cdd:pfam13639    3 CPICLEEFEEGdkVVVLPCGHHFHRECLDKWL--------RSSNTCPLCR 44
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
 342-393 1.75e-03

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 41.69  E-value: 1.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 578812645  342 EGLKLYYNPYTGCIIreyPNSGpqllGGILADEMGLGKTVEVLALILTHTRQ 393
Cdd:cd18067     7 EGVKFLYRCVTGRRI---RGSH----GCIMADEMGLGKTLQCITLMWTLLRQ 51
RING-HC_SpRad8-like cd16572
RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) ...
 1432-1487 1.88e-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: 37.87  E-value: 1.88e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1432 CPICARQLGKQWAVLTCGHCFCNECISIIIEQYSvgSHRSSIKCAICRQTTSHKEI 1487
Cdd:cd16572     7 CPICAEEPISELALTRCWHSACKDCLLDHIEFQK--SKNEVPLCPTCRQPINEQDI 60
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 304-393 1.96e-03

DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350765 [Multi-domain]  Cd Length: 239  Bit Score: 41.51  E-value: 1.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  304 LRPYQREAVnwmlqqecfrsspatesalHFLWREIVTSEGLklyYNPYTGCIireypnsgpqllggiLADEMGLGKTVEV 383
Cdd:cd18007     1 LKPHQVEGV-------------------RFLWSNLVGTDVG---SDEGGGCI---------------LAHTMGLGKTLQV 43

                          90
                  ....*....|
gi 578812645  384 LALILTHTRQ 393
Cdd:cd18007    44 ITFLHTYLAA 53
PHD_Bye1p_SIZ1_like cd15570
PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo ...
 661-706 1.99e-03

PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins; Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2.


Pssm-ID: 277045  Cd Length: 50  Bit Score: 37.82  E-value: 1.99e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 578812645  661 CICGELDQIDRKprVQCLKCHLWQHAKCVNYDEKNLKIKP-----FYCPHC 706
Cdd:cd15570     2 CPCGSSMEDGSM--IQCEGCKTWQHMDCVLIPDKPADGLPelpskFYCELC 50
RING-HC_TRIM13_like_C-V cd16581
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and ...
 1432-1479 2.46e-03

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: 37.49  E-value: 2.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 578812645 1432 CPICArQLGKQWAVLTCGHCFCNECISIIIEQySVGSHRSSIKCAICR 1479
Cdd:cd16581     5 CSICY-NIFDDPKILPCSHTFCKNCLEKLLAA-SGYYLLASLKCPTCR 50
RING-HC_TRIM21_C-IV cd16596
RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar ...
 1432-1480 2.49e-03

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: 38.34  E-value: 2.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 578812645 1432 CPICARQLGKQWAVlTCGHCFCNECISiiieqySVGSHRSSIkCAICRQ 1480
Cdd:cd16596    12 CPICLDPFVEPVSI-ECGHSFCQECIS------QVGKGGGSV-CPVCRQ 52
RING-HC_KEG-like cd23140
RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and ...
 1432-1482 2.61e-03

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: 37.62  E-value: 2.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 578812645 1432 CPICARQL---GKQWAVLTCGHCFCNECISiiieQYSVGSHRSSIKCAICRQTT 1482
Cdd:cd23140     4 CSVCSEGYnedERVPLLLQCGHTFCKDCLS----QMFIRCTDLTLKCPRCRQSV 53
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 711-864 3.47e-03

DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350824 [Multi-domain]  Cd Length: 235  Bit Score: 40.98  E-value: 3.47e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645  711 EPVSTRAtLIISPSSICHQWVDEINRHVRSSSLRVL-VYQGVKKDGFLQPHFLAeqdIVIITYDVLrselnyvdiphsns 789
Cdd:cd18066    57 KPVIKRA-LIVTPGSLVKNWKKEFQKWLGSERIKVFtVDQDHKVEEFIASPLYS---VLIISYEML-------------- 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 578812645  790 edgrrLRNQKRYMAIPSPLVavewwrIClDEAQMVECPTVKAAEMAQRLSGINRWCISGTPVQRGLEDLFGLVVF 864
Cdd:cd18066   119 -----LRSLDQISKLNFDLV------IC-DEGHRLKNTSIKTTTALTSLSCERRIILTGTPIQNDLQEFFALIDF 181
RING-HC_SH3RF1 cd16748
RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and ...
 1432-1479 3.74e-03

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: 36.91  E-value: 3.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 578812645 1432 CPICARQLGKQWAVLTCGHCFCNECISIIieqysVGShRSSIKCAICR 1479
Cdd:cd16748     5 CPVCLERLDATAKVLPCQHTFCRRCLLGI-----VGS-RSELRCPECR 46
RING-HC_TRIM5-like_C-IV cd16591
RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, ...
 1432-1498 3.90e-03

RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, TRIM34 and similar proteins; TRIM5, TRIM6, TRIM22, and TRIM34, four 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, 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. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections.


Pssm-ID: 438253 [Multi-domain]  Cd Length: 72  Bit Score: 37.42  E-value: 3.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 578812645 1432 CPICArQLGKQWAVLTCGHCFCNECISIIIEQYSVGSHRSSikCAICRqttshkeISYVFTSEKANQ 1498
Cdd:cd16591     9 CPICL-ELLTEPLSLDCGHSFCQACITANHKESVNQEGESS--CPVCR-------TSYQPENLRPNR 65
RING-HC_TRIM35_C-IV cd16599
RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar ...
 1432-1487 3.91e-03

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: 37.44  E-value: 3.91e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1432 CPICARQLgKQWAVLTCGHCFCNECISIIIEqysvgsHRSSIKCAICRQTTSHKEI 1487
Cdd:cd16599     7 CPICYEPF-REAVTLRCGHNFCKGCVSRSWE------RQPRAPCPVCKEASSSDDL 55
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 367-393 4.03e-03

DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350756 [Multi-domain]  Cd Length: 187  Bit Score: 40.06  E-value: 4.03e-03
                          10        20
                  ....*....|....*....|....*..
gi 578812645  367 LGGILADEMGLGKTVEVLALiLTHTRQ 393
Cdd:cd17998    20 LSGILADEMGLGKTIQVIAF-LAYLKE 45
RING-HC_AtBARD1-like cd23146
RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 ...
 1432-1487 4.15e-03

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: 36.68  E-value: 4.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1432 CPICARQLgKQWAVLTCGHCFCNECISIIIeqysvgSHRSSikCAICRQTTSHKEI 1487
Cdd:cd23146     7 CPICLKLL-NRPVLLPCDHIFCSSCITDST------KVGSD--CPVCKLPYHSQDL 53
RING-HC_RNF146 cd16546
RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins; ...
 1432-1480 5.35e-03

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: 36.59  E-value: 5.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 578812645 1432 CPICARQLgKQWAVLTCGHCFCNECISiiieqysvGSHRSSIKCAICRQ 1480
Cdd:cd16546     3 CPICLQTC-IHPVKLPCGHIFCYLCVK--------GVAWQSKRCALCRQ 42
RING-HC_RNF180 cd16554
RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins; ...
 1432-1495 5.58e-03

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: 36.52  E-value: 5.58e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 578812645 1432 CPICARQLGKQWAVLTCGHCFCNECISIIieqysVGSHRSSIKCAICRQTtshkeISYVFTSEK 1495
Cdd:cd16554     5 CPVCLDLYYDPYMCYPCGHIFCEPCLRQL-----AKSSPKNTPCPLCRTT-----IRRVFFQEE 58
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 368-385 5.77e-03

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 40.05  E-value: 5.77e-03
                          10
                  ....*....|....*...
gi 578812645  368 GGILADEMGLGKTVEVLA 385
Cdd:cd18001    21 GGILADDMGLGKTVQICA 38
PHD_MMD1_like cd15556
PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD ...
 660-706 6.04e-03

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.


Pssm-ID: 277031 [Multi-domain]  Cd Length: 46  Bit Score: 36.20  E-value: 6.04e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 578812645  660 ECICGELDQiDRKPRVQCLKCHLWQHAKCVNYDEkNLKIKP-FYCPHC 706
Cdd:cd15556     1 DCSCGTRDD-DGERMIACDVCEVWQHTRCVGIAD-NEEPPDhFLCRRC 46
RING-HC_CHR27-like cd23142
RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) ...
 1430-1487 6.63e-03

RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins; CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438504 [Multi-domain]  Cd Length: 55  Bit Score: 36.40  E-value: 6.63e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 578812645 1430 EPCPICARQLGKqwAVLT-CGHCFCNECisiIIEQYSVGSH-RSSIKCAICRQTTSHKEI 1487
Cdd:cd23142     1 AICPICNDPPED--AVVTlCGHVFCCEC---VFQYLSSDRTcRQFNHCPLCRQKLYLDDV 55
PHD_ash2p_like cd15583
PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and ...
 661-706 6.81e-03

PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins; spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity.


Pssm-ID: 277058  Cd Length: 50  Bit Score: 36.17  E-value: 6.81e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 578812645  661 CICGElDQIDRKPRVQCLKCHLWQHAKCVNYDekNLKIKP------FYCPHC 706
Cdd:cd15583     2 CYCGK-DRNLGEVELQCSICLKWFHAKCVSID--NGSCLPfmtnyqFVCKRC 50
RING-H2_RNF32 cd16471
RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins; RNF32 ...
 1431-1479 7.38e-03

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.


Pssm-ID: 438134 [Multi-domain]  Cd Length: 46  Bit Score: 36.07  E-value: 7.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 578812645 1431 PCPICARQL-GKQWAVLTCGHCFCNECISiIIEQYSVGSHRssiKCAICR 1479
Cdd:cd16471     1 ECPICLCAFkGRKCTLLSCSHVFHEACLS-AFEKFIESKNQ---KCPLCR 46
RING-HC_TRIM40-C-V cd16583
RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar ...
 1421-1485 7.70e-03

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: 36.35  E-value: 7.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 578812645 1421 DKTSGGVnpepCPICARQLGKqwAVLT-CGHCFCNECisiIIEQYSVGSHRSSIKCAICRQTTSHK 1485
Cdd:cd16583     1 DSDEEGV----CPICQEPLKE--AVSTdCGHLFCRMC---LTQHAKKASASGVFSCPVCRKPCSEG 57
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 367-393 9.23e-03

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 39.23  E-value: 9.23e-03
                          10        20
                  ....*....|....*....|....*....
gi 578812645  367 LGGILADEMGLGKTVEVLALI--LTHTRQ 393
Cdd:cd17997    23 INGILADEMGLGKTLQTISLLgyLKHYKN 51
RING-HC_TRIM47-like_C-IV cd16604
RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar ...
 1432-1481 9.86e-03

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: 35.47  E-value: 9.86e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 578812645 1432 CPICaRQLGKQWAVLTCGHCFCNECISIIIEQYSVGshrsSIKCAICRQT 1481
Cdd:cd16604     3 CPIC-LDLLKDPVTLPCGHSFCMGCLGALWGAGRGG----RASCPLCRQT 47
 
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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