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Conserved domains on  [gi|1716574268|ref|XP_030017692|]
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splicing factor 1 isoform X2 [Sphaeramia orbicularis]

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];
113-334 7.68e-66

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: 217.92  E-value: 7.68e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 113 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKIEEERHSLITE 192
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 193 MVGLNPDFKPPADYKPPaTRVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 272
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1716574268 273 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 334
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
113-334 7.68e-66

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 217.92  E-value: 7.68e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 113 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKIEEERHSLITE 192
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 193 MVGLNPDFKPPADYKPPaTRVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 272
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1716574268 273 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 334
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 95-207 2.44e-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: 194.75  E-value: 2.44e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268  95 KKSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 173
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1716574268 174 REYRTRKKIEEERHSLITEMVGLNPDFKPPADYK 207
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 212-304 1.46e-55

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: 184.05  E-value: 1.46e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 291
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1716574268 292 VKKAVEQIRNILK 304
Cdd:cd22382    81 VKKAVDKIKEIIK 93
KH smart00322
K homology RNA-binding domain;
211-303 1.65e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 1.65e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268  211 TRVNDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 290
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1716574268  291 NVKKAVEQIRNIL 303
Cdd:smart00322  56 NVEKAAELILEIL 68
 
Name Accession Description Interval E-value
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
113-334 7.68e-66

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 217.92  E-value: 7.68e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 113 MPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDlGIPVNPEDRSPSPEPIYNSEGKRLNTREYRTRKKIEEERHSLITE 192
Cdd:COG5176    50 LPSKISGALTREQIYSYQVMMRPFEITEKLRTPD-GVPSKRELRSPSPPPRYDEIGRRLNTREARYNKKLEDERLWLKER 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 193 MVGLNPDFKPPADYKPPaTRVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQM 272
Cdd:COG5176   129 AQKILPRFVLPNDYIRP-SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPES 207

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1716574268 273 LPGEDEPLHALVTANTMENVKKAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLRED 334
Cdd:COG5176   208 LKNAEAVLHCLIEADSEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNGTLRAD 269
SF1-HH pfam16275
Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is ...
 95-207 2.44e-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: 194.75  E-value: 2.44e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268  95 KKSRWSSETPD-QKTVIPGMPTVIPPGLTRDQERAYIVQLQIEDLTRKLRTGDLGIPVNPEDRSPSPEPIYNSEGKRLNT 173
Cdd:pfam16275   1 RKSRWGGEPEKtDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLGVPPSPEERSPSPPPIYDANGKRTNT 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1716574268 174 REYRTRKKIEEERHSLITEMVGLNPDFKPPADYK 207
Cdd:pfam16275  81 REVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 212-304 1.46e-55

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: 184.05  E-value: 1.46e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 291
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1716574268 292 VKKAVEQIRNILK 304
Cdd:cd22382    81 VKKAVDKIKEIIK 93
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 212-303 6.42e-38

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: 135.81  E-value: 6.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKvGRKDGQMLPGEDEPLHALVTANTMEN 291
Cdd:cd02395     1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGK-GRSDPQPDPDEEEDLHVLITADTEEK 79

                          90
                  ....*....|..
gi 1716574268 292 VKKAVEQIRNIL 303
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 ...
 213-304 9.37e-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: 101.66  E-value: 9.37e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 213 VNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEG-KVGRKDGQmlPGE---DEPLHALVTANT 288
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKkKEEANRGK--PNWehlNDDLHVLITVED 79

                          90       100
                  ....*....|....*....|.
gi 1716574268 289 MEN-----VKKAVEQIRNILK 304
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 ...
 209-303 1.52e-18

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: 81.51  E-value: 1.52e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 209 PATRVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHAL 283
Cdd:cd22466     2 PSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKedlnrGKPNWEHL---NDELHVL 78

                          90       100
                  ....*....|....*....|....*
gi 1716574268 284 VTANTMEN-----VKKAVEQIRNIL 303
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; ...
 212-303 5.66e-17

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: 76.90  E-value: 5.66e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHALVTA 286
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeqnrGKPNWEHL---NEDLHVLITV 77

                          90       100
                  ....*....|....*....|..
gi 1716574268 287 NTMEN-----VKKAVEQIRNIL 303
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, ...
 212-286 4.36e-16

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: 74.24  E-value: 4.36e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSV----KEGKVGRKDGQMLPGEDEPLHALVTA 286
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 ...
 219-304 7.61e-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: 73.68  E-value: 7.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 219 IPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE-GKVGRKDGQmlPGED---EPLHALVTANTMENV-- 292
Cdd:cd22467     8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDtAKEEKLRDK--PGYEhlnEPLHVLIEAELPANIid 85

                          90
                  ....*....|....*
gi 1716574268 293 ---KKAVEQIRNILK 304
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 ...
 215-304 7.97e-13

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: 64.88  E-value: 7.97e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 215 DKVMIPQDEYPE-INFVGLLIGPRGNTLKNIEKECCAKIMIRGKGS-VKEGKVGRKDgqmlpgeDEPLHALVTANTMENV 292
Cdd:cd22386     5 EKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSgFIEPASGREA-------DEPLHLLISHPDPEGL 77

                          90
                  ....*....|..
gi 1716574268 293 KKAVEQIRNILK 304
Cdd:cd22386    78 QQAKKLCEDLLQ 89
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 212-320 1.72e-11

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: 61.68  E-value: 1.72e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGS----VKEGKVGRKDGQMLPGEDEPLHALVT-- 285
Cdd:cd22469     6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkAKEEELRKSGEAKYAHLSDELHVLIEvf 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1716574268 286 ---ANTMENVKKAVEQIRNILkqgieTPEDQNDLRKMQ 320
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 ...
 212-294 4.24e-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: 60.03  E-value: 4.24e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKEGKvgrKDGQMLPGEDEP-------LHALV 284
Cdd:cd22468     4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKA---KEEELRKGGDPKyahlnmdLHVFI 80

                          90       100
                  ....*....|....*....|..
gi 1716574268 285 ------------TANTMENVKK 294
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 ...
 212-262 1.67e-09

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: 55.83  E-value: 1.67e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1716574268 212 RVNDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKE 262
Cdd:cd22470     8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRD 58
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 215-300 1.15e-07

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: 48.83  E-value: 1.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 215 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 294
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57


                  ....*.
gi 1716574268 295 AVEQIR 300
Cdd:cd00105    58 AKELIE 63
KH smart00322
K homology RNA-binding domain;
211-303 1.65e-07

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 1.65e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268  211 TRVNDKVMIPQdeypeiNFVGLLIGPRGNTLKNIEKECCAKIMIrgkgsvkegkvgrkdgqmlPGEDEPLHALVTANTME 290
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDI-------------------PGPGSEERVVEITGPPE 55

                           90
                   ....*....|...
gi 1716574268  291 NVKKAVEQIRNIL 303
Cdd:smart00322  56 NVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 216-301 1.12e-05

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: 43.42  E-value: 1.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 216 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENVKK 294
Cdd:pfam00013   3 EILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAVEA 58


                  ....*..
gi 1716574268 295 AVEQIRN 301
Cdd:pfam00013  59 AKALIEE 65
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 237-303 5.22e-05

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: 42.19  E-value: 5.22e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1716574268 237 RGNTLKNIEKECCAKIMIRGKGSVKEGKVGRKDGqmlpgeDEPLHALVTANTMENVKKAVEQIRNIL 303
Cdd:cd22385    24 KGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPG------ERPLYLHVQAPTKEAVDRAVNKINEII 84
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 216-304 8.66e-05

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: 40.92  E-value: 8.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1716574268 216 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECCAKIMIRGKGSVKegkvgrkdgqmlpgedeplhalVTANTMENVKKA 295
Cdd:cd02393     7 TIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVT----------------------IFATDKESAEAA 58


                  ....*....
gi 1716574268 296 VEQIRNILK 304
Cdd:cd02393    59 KAMIEDIVA 67
KH-I_Dim2p_like_rpt1 cd22389
first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and ...
 217-257 1.14e-03

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: 37.95  E-value: 1.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1716574268 217 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECCAKIMIRGK 257
Cdd:cd22389     3 VKIPKER------IGVLIGKKGETKREIEERTGVKITVDSE 37
 
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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