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Conserved domains on  [gi|1075637951|ref|NP_001333292|]
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splicing factor 1 isoform 9 [Homo sapiens]

Protein Classification

C2HC-type zinc finger protein( domain architecture ID 13420122)

C2HC-type zinc finger protein similar to caulimoviridae capsid protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MSL5 super family cl34926
Splicing factor (branch point binding protein) [RNA processing and modification];
17-257 4.96e-70

Splicing factor (branch point binding protein) [RNA processing and modification];


The actual alignment was detected with superfamily member COG5176:

Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 227.55  E-value: 4.96e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  17 RKRSRWNQDTMEQktVIP---GMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDlGIPPNPEDRSPSPEPIYNSEGKR 93
Cdd:COG5176    30 VNLSLWRKNTVES--DVHrfnSLPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRR 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  94 LNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNA 173
Cdd:COG5176   107 LNTREARYNKKLEDERLWLKERAQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA 185

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 174 KIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253
Cdd:COG5176   186 KIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265


                  ....
gi 1075637951 254 LRED 257
Cdd:COG5176   266 LRAD 269
ZnF_C2HC smart00343
zinc finger;
278-293 4.22e-03

zinc finger;


:

Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.73  E-value: 4.22e-03
                           10
                   ....*....|....*.
gi 1075637951  278 VCTKCGGAGHIASDCK 293
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
17-257 4.96e-70

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 227.55  E-value: 4.96e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  17 RKRSRWNQDTMEQktVIP---GMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDlGIPPNPEDRSPSPEPIYNSEGKR 93
Cdd:COG5176    30 VNLSLWRKNTVES--DVHrfnSLPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRR 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  94 LNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNA 173
Cdd:COG5176   107 LNTREARYNKKLEDERLWLKERAQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA 185

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 174 KIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253
Cdd:COG5176   186 KIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265


                  ....
gi 1075637951 254 LRED 257
Cdd:COG5176   266 LRAD 269
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 135-227 2.79e-59

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 192.52  E-value: 2.79e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1075637951 215 VKKAVEQIRNILK 227
Cdd:cd22382    81 VKKAVDKIKEIIK 93
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 18-130 4.03e-59

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.


Pssm-ID: 465080  Cd Length: 114  Bit Score: 192.82  E-value: 4.03e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  18 KRSRWNQDTME-QKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNT 96
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1075637951  97 REFRTRKKLEEERHNLITEMVALNPDFKPPADYK 130
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH smart00322
K homology RNA-binding domain;
134-226 1.99e-09

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 53.84  E-value: 1.99e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  134 TRVSDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECNAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 213
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1075637951  214 NVKKAVEQIRNIL 226
Cdd:smart00322  56 NVEKAAELILEIL 68
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 124-225 1.63e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 41.57  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 124 KPPADYKPPATRVsDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedepl 203
Cdd:PRK11824  543 EPRAELSPYAPRI-ETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIEDDGTVK------------------- 596

                          90       100
                  ....*....|....*....|..
gi 1075637951 204 halVTANTMENVKKAVEQIRNI 225
Cdd:PRK11824  597 ---IAATDGEAAEAAKERIEGI 615
ZnF_C2HC smart00343
zinc finger;
278-293 4.22e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.73  E-value: 4.22e-03
                           10
                   ....*....|....*.
gi 1075637951  278 VCTKCGGAGHIASDCK 293
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 278-293 7.22e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.04  E-value: 7.22e-03
                          10
                  ....*....|....*.
gi 1075637951 278 VCTKCGGAGHIASDCK 293
Cdd:pfam00098   2 KCYNCGEPGHIARDCP 17
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 140-225 8.15e-03

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 37.54  E-value: 8.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 140 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVKegkvgrkdgqMLPGEDEPLHALvtantmenvkKA 218
Cdd:TIGR03665   2 VKIPKDR------IGVLIGKGGETKKEIEERTGVKLDIDSEtGEVK----------IEPEDEDPLAVM----------KA 55


                  ....*..
gi 1075637951 219 VEQIRNI 225
Cdd:TIGR03665  56 REVVKAI 62
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
17-257 4.96e-70

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 227.55  E-value: 4.96e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  17 RKRSRWNQDTMEQktVIP---GMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDlGIPPNPEDRSPSPEPIYNSEGKR 93
Cdd:COG5176    30 VNLSLWRKNTVES--DVHrfnSLPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRR 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  94 LNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPaTRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNA 173
Cdd:COG5176   107 LNTREARYNKKLEDERLWLKERAQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRA 185

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 174 KIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGT 253
Cdd:COG5176   186 KIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGT 265


                  ....
gi 1075637951 254 LRED 257
Cdd:COG5176   266 LRAD 269
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 135-227 2.79e-59

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 192.52  E-value: 2.79e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1075637951 215 VKKAVEQIRNILK 227
Cdd:cd22382    81 VKKAVDKIKEIIK 93
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 18-130 4.03e-59

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.


Pssm-ID: 465080  Cd Length: 114  Bit Score: 192.82  E-value: 4.03e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  18 KRSRWNQDTME-QKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNT 96
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1075637951  97 REFRTRKKLEEERHNLITEMVALNPDFKPPADYK 130
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 135-226 6.91e-40

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 140.43  E-value: 6.91e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKvGRKDGQMLPGEDEPLHALVTANTMEN 214
Cdd:cd02395     1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGK-GRSDPQPDPDEEEDLHVLITADTEEK 79

                          90
                  ....*....|..
gi 1075637951 215 VKKAVEQIRNIL 226
Cdd:cd02395    80 VDKAAKLIEKLL 91
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 136-227 2.04e-26

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 103.59  E-value: 2.04e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 136 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEG-KVGRKDGQmlPGE---DEPLHALVTANT 211
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKkKEEANRGK--PNWehlNDDLHVLITVED 79

                          90       100
                  ....*....|....*....|.
gi 1075637951 212 MEN-----VKKAVEQIRNILK 227
Cdd:cd22383    80 TENrahikLAKAVEEVKKLLI 100
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 132-226 4.32e-19

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411894 [Multi-domain]  Cd Length: 105  Bit Score: 82.66  E-value: 4.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 132 PATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHAL 206
Cdd:cd22466     2 PSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKedlnrGKPNWEHL---NDELHVL 78

                          90       100
                  ....*....|....*....|....*
gi 1075637951 207 VTANTMEN-----VKKAVEQIRNIL 226
Cdd:cd22466    79 ITVEDTENrakvkLQRAVEEVRKLL 103
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 135-226 8.55e-18

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.


Pssm-ID: 411893 [Multi-domain]  Cd Length: 103  Bit Score: 78.83  E-value: 8.55e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHALVTA 209
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeqnrGKPNWEHL---NEDLHVLITV 77

                          90       100
                  ....*....|....*....|..
gi 1075637951 210 NTMEN-----VKKAVEQIRNIL 226
Cdd:cd22465    78 EDAQNraeikLKRAVEEVKKLL 99
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 135-209 1.70e-17

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411812 [Multi-domain]  Cd Length: 102  Bit Score: 78.09  E-value: 1.70e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSV----KEGKVGRKDGQMLPGEDEPLHALVTA 209
Cdd:cd22384     4 KLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMrdkaKEEELRKSGDPKYAHLNEDLHVLIEA 82
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 142-227 4.58e-16

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.


Pssm-ID: 411895  Cd Length: 101  Bit Score: 74.06  E-value: 4.58e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 142 IPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE-GKVGRKDGQmlPGED---EPLHALVTANTMENV-- 215
Cdd:cd22467     8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDtAKEEKLRDK--PGYEhlnEPLHVLIEAELPANIid 85

                          90
                  ....*....|....*
gi 1075637951 216 ---KKAVEQIRNILK 227
Cdd:cd22467    86 arlQHAQEIIEDLLK 100
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 136-227 4.09e-14

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 68.35  E-value: 4.09e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 136 VSDKVMIPQDEYPE-INFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS-VKEGKVGRKDgqmlpgeDEPLHALVTANTME 213
Cdd:cd22386     3 YQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSgFIEPASGREA-------DEPLHLLISHPDPE 75

                          90
                  ....*....|....
gi 1075637951 214 NVKKAVEQIRNILK 227
Cdd:cd22386    76 GLQQAKKLCEDLLQ 89
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-243 1.98e-12

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.


Pssm-ID: 411897 [Multi-domain]  Cd Length: 118  Bit Score: 64.37  E-value: 1.98e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS----VKEGKVGRKDGQMLPGEDEPLHALVT-- 208
Cdd:cd22469     6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkAKEEELRKSGEAKYAHLSDELHVLIEvf 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1075637951 209 ---ANTMENVKKAVEQIRNILkqgieTPEDQNDLRKMQ 243
Cdd:cd22469    86 appGEAYSRMSHALEEIKKFL-----VPDYNDEIRQEQ 118
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-217 1.05e-11

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.


Pssm-ID: 411896 [Multi-domain]  Cd Length: 106  Bit Score: 61.57  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKvgrKDGQMLPGEDEP-------LHALV 207
Cdd:cd22468     4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKA---KEEELRKGGDPKyahlnmdLHVFI 80

                          90       100
                  ....*....|....*....|..
gi 1075637951 208 ------------TANTMENVKK 217
Cdd:cd22468    81 evfgppceayarMAHAMEEVKK 102
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 135-185 7.41e-10

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 56.60  E-value: 7.41e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1075637951 135 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE 185
Cdd:cd22470     8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRD 58
KH smart00322
K homology RNA-binding domain;
134-226 1.99e-09

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 53.84  E-value: 1.99e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951  134 TRVSDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECNAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 213
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1075637951  214 NVKKAVEQIRNIL 226
Cdd:smart00322  56 NVEKAAELILEIL 68
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 138-223 2.52e-08

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 50.76  E-value: 2.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 138 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 217
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57


                  ....*.
gi 1075637951 218 AVEQIR 223
Cdd:cd00105    58 AKELIE 63
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 137-224 8.78e-07

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 46.51  E-value: 8.78e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 137 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 215
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56


                  ....*....
gi 1075637951 216 KKAVEQIRN 224
Cdd:pfam00013  57 EAAKALIEE 65
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 139-227 2.20e-06

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 45.55  E-value: 2.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 139 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedeplhalVTANTMENVKKA 218
Cdd:cd02393     7 TIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVT----------------------IFATDKESAEAA 58


                  ....*....
gi 1075637951 219 VEQIRNILK 227
Cdd:cd02393    59 KAMIEDIVA 67
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 160-226 4.07e-06

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411813  Cd Length: 84  Bit Score: 45.28  E-value: 4.07e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1075637951 160 RGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGqmlpgeDEPLHALVTANTMENVKKAVEQIRNIL 226
Cdd:cd22385    24 KGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPG------ERPLYLHVQAPTKEAVDRAVNKINEII 84
KH-I_Dim2p_like_rpt1 cd22389
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 140-184 4.02e-05

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411817 [Multi-domain]  Cd Length: 70  Bit Score: 41.80  E-value: 4.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1075637951 140 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVK 184
Cdd:cd22389     3 VKIPKER------IGVLIGKKGETKREIEERTGVKITVDSEtGEVI 42
KH-I_ScSCP160_rpt6 cd22451
sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 136-228 1.43e-04

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.


Pssm-ID: 411879 [Multi-domain]  Cd Length: 69  Bit Score: 40.13  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 136 VSDKVMIPQDEYpeinfvGLLIGPRGNTLKNIEKECNAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTMENV 215
Cdd:cd22451     1 ASIDIDIPKEYH------RAIIGKGGAVLRELEAETGCRIQV-------------------PKKDDPSGKIRITGARDGV 55

                          90
                  ....*....|...
gi 1075637951 216 KKAVEQIRNILKQ 228
Cdd:cd22451    56 EAATAKILNISDE 68
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 124-225 1.63e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 41.57  E-value: 1.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 124 KPPADYKPPATRVsDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedepl 203
Cdd:PRK11824  543 EPRAELSPYAPRI-ETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIEDDGTVK------------------- 596

                          90       100
                  ....*....|....*....|..
gi 1075637951 204 halVTANTMENVKKAVEQIRNI 225
Cdd:PRK11824  597 ---IAATDGEAAEAAKERIEGI 615
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 140-184 3.51e-03

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 38.70  E-value: 3.51e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1075637951 140 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVK 184
Cdd:PRK13763    7 VKIPKDR------IGVLIGKKGETKKEIEERTGVKLEIDSEtGEVI 46
KH-I_DDX46_like cd22387
type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); ...
 163-226 3.53e-03

type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); The DDX46 family includes DEAD box protein 46 (DDX46), fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5, Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this family contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411815  Cd Length: 82  Bit Score: 36.87  E-value: 3.53e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1075637951 163 TLKNIEKECNAKIMIRGKGSVKEGKVgrkdgqmLPGEdEPLHALVTANTMENVKKAVEQIRNIL 226
Cdd:cd22387    27 VLNSIMEETGATITIKGQYYPPGKKP-------KPGE-RKLYLLIEGATEESVQSARNEIKRVL 82
ZnF_C2HC smart00343
zinc finger;
278-293 4.22e-03

zinc finger;


Pssm-ID: 197667 [Multi-domain]  Cd Length: 17  Bit Score: 34.73  E-value: 4.22e-03
                           10
                   ....*....|....*.
gi 1075637951  278 VCTKCGGAGHIASDCK 293
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 153-226 4.87e-03

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 36.16  E-value: 4.87e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1075637951 153 VGLLIGPRGNTLKNIEKECNAKIMIRGKGSvkegkvgrkdgqmlpGEDEPLHALVTANTMENVKKAVEQIRNIL 226
Cdd:cd22428    16 VGLIIGRQGATIKQIQKETGARIDFKDEGS---------------GGELPERVLLIQGNPVQAQRAEEAIHQII 74
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 151-178 5.82e-03

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.


Pssm-ID: 411823 [Multi-domain]  Cd Length: 68  Bit Score: 35.58  E-value: 5.82e-03
                          10        20
                  ....*....|....*....|....*...
gi 1075637951 151 NFVGLLIGPRGNTLKNIEKECNAKIMIR 178
Cdd:cd22395     9 ELVGRLIGKQGRNVKQLKQKSGAKIYIK 36
zf-CCHC pfam00098
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 278-293 7.22e-03

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 395050 [Multi-domain]  Cd Length: 18  Bit Score: 34.04  E-value: 7.22e-03
                          10
                  ....*....|....*.
gi 1075637951 278 VCTKCGGAGHIASDCK 293
Cdd:pfam00098   2 KCYNCGEPGHIARDCP 17
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 140-225 8.15e-03

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 37.54  E-value: 8.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 140 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVKegkvgrkdgqMLPGEDEPLHALvtantmenvkKA 218
Cdd:TIGR03665   2 VKIPKDR------IGVLIGKGGETKKEIEERTGVKLDIDSEtGEVK----------IEPEDEDPLAVM----------KA 55


                  ....*..
gi 1075637951 219 VEQIRNI 225
Cdd:TIGR03665  56 REVVKAI 62
KH-I_Vigilin_rpt2 cd22406
second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 133-225 9.14e-03

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.


Pssm-ID: 411834 [Multi-domain]  Cd Length: 75  Bit Score: 35.36  E-value: 9.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1075637951 133 ATRVSDKVMIPQDEYpeinfvGLLIGPRGNTLKNIEKECNAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTM 212
Cdd:cd22406     2 QTQASVTVNIPKEHH------RFILGKKGKKLQELELKTATKIVI-------------------PRQEDNSDEIKITGTK 56

                          90
                  ....*....|...
gi 1075637951 213 ENVKKAVEQIRNI 225
Cdd:cd22406    57 EGIEKARHEIQLI 69
 
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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