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Conserved domains on  [gi|17647843|ref|NP_523772|]
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quaking related 54B, isoform B [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 117-218 8.60e-63

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: 197.51  E-value: 8.60e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22384   1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                        90       100
                ....*....|....*....|..
gi 17647843 197 STIAPPAEAYARIAYAMAELRK 218
Cdd:cd22384  81 EAFAPPAEAYARLAHALAELRK 102
Qua1 super family cl24747
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 68-118 1.74e-03

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


The actual alignment was detected with superfamily member pfam16274:

Pssm-ID: 465079  Cd Length: 52  Bit Score: 36.25  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17647843    68 YIRDCMAERNRMDRKFPIAEKLLEGEIEKVQTTGRIPSREQKYADIYREKP 118
Cdd:pfam16274   2 YLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52
 
Name Accession Description Interval E-value
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 117-218 8.60e-63

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: 197.51  E-value: 8.60e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22384   1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                        90       100
                ....*....|....*....|..
gi 17647843 197 STIAPPAEAYARIAYAMAELRK 218
Cdd:cd22384  81 EAFAPPAEAYARLAHALAELRK 102
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
96-193 1.20e-09

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 58.83  E-value: 1.20e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843  96 KVQTTGRipsreQKYADIYReKPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSmrdrVKEE 175
Cdd:COG5176 129 AQKILPR-----FVLPNDYI-RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS----VKEG 198

                        90
                ....*....|....*...
gi 17647843 176 ELRSSKDPKYAHLNSDLH 193
Cdd:COG5176 199 KISSDTPESLKNAEAVLH 216
KH smart00322
K homology RNA-binding domain;
120-172 3.15e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 38.82  E-value: 3.15e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17647843    120 RISQRVLVPIrehpkfNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRV 172
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVV 48
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 122-167 1.64e-03

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: 36.88  E-value: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 17647843   122 SQRVLVPirehpkFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNS 167
Cdd:pfam00013   1 TVEILVP------SSLVGLIIGKGGSNIKEIREETGAKIQIPPSES 40
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 68-118 1.74e-03

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 36.25  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17647843    68 YIRDCMAERNRMDRKFPIAEKLLEGEIEKVQTTGRIPSREQKYADIYREKP 118
Cdd:pfam16274   2 YLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52
 
Name Accession Description Interval E-value
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 117-218 8.60e-63

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: 197.51  E-value: 8.60e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22384   1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                        90       100
                ....*....|....*....|..
gi 17647843 197 STIAPPAEAYARIAYAMAELRK 218
Cdd:cd22384  81 EAFAPPAEAYARLAHALAELRK 102
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 117-232 1.98e-47

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: 158.36  E-value: 1.98e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22469   3 KNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHVLI 82

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 17647843 197 STIAPPAEAYARIAYAMAELRKYLIPDSNDIIRQEQ 232
Cdd:cd22469  83 EVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 118
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 117-222 2.96e-47

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: 157.49  E-value: 2.96e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22468   1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                        90       100
                ....*....|....*....|....*.
gi 17647843 197 STIAPPAEAYARIAYAMAELRKYLIP 222
Cdd:cd22468  81 EVFGPPCEAYARMAHAMEEVKKFLVP 106
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 117-225 1.52e-44

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: 150.97  E-value: 1.52e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 117 KPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSKDPKYAHLNSDLHVEI 196
Cdd:cd22470   5 KNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLI 84

                        90       100
                ....*....|....*....|....*....
gi 17647843 197 STIAPPAEAYARIAYAMAELRKYLIPDSN 225
Cdd:cd22470  85 EVFAPPAEAYARMGHALEEIKKFLIPDYN 113
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 121-222 1.99e-31

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: 115.53  E-value: 1.99e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 121 ISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRssKDPKYAHLNSDLHVEISTIA 200
Cdd:cd22383   2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANR--GKPNWEHLNDDLHVLITVED 79

                        90       100
                ....*....|....*....|..
gi 17647843 201 PPAEAYARIAYAMAELRKYLIP 222
Cdd:cd22383  80 TENRAHIKLAKAVEEVKKLLIP 101
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 118-222 6.01e-29

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: 109.24  E-value: 6.01e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 118 PLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSkdPKYAHLNSDLHVEIS 197
Cdd:cd22466   3 SVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNRGK--PNWEHLNDELHVLIT 80

                        90       100
                ....*....|....*....|....*
gi 17647843 198 TIAPPAEAYARIAYAMAELRKYLIP 222
Cdd:cd22466  81 VEDTENRAKVKLQRAVEEVRKLLVP 105
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 120-222 9.45e-27

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: 103.09  E-value: 9.45e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 120 RISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSkdPKYAHLNSDLHVEISTI 199
Cdd:cd22465   1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGK--PNWEHLNEDLHVLITVE 78

                        90       100
                ....*....|....*....|...
gi 17647843 200 APPAEAYARIAYAMAELRKYLIP 222
Cdd:cd22465  79 DAQNRAEIKLKRAVEEVKKLLVP 101
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 123-222 2.51e-21

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: 88.32  E-value: 2.51e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 123 QRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRVKEEELRSSkdPKYAHLNSDLHVEISTIAPP 202
Cdd:cd22467   4 LRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDK--PGYEHLNEPLHVLIEAELPA 81

                        90       100
                ....*....|....*....|
gi 17647843 203 AEAYARIAYAMAELRKYLIP 222
Cdd:cd22467  82 NIIDARLQHAQEIIEDLLKP 101
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 120-196 2.73e-14

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: 68.01  E-value: 2.73e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17647843 120 RISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSmrdrVKEEelRSSKDPKYA-HLNSDLHVEI 196
Cdd:cd02395   1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGS----VKEG--KGRSDPQPDpDEEEDLHVLI 72
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 120-205 4.16e-14

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: 67.72  E-value: 4.16e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 120 RISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSmrdrVKEEELRSSKDPKYAHLNSDLHVEISti 199
Cdd:cd22382   1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGS----VKEGKVGRKDGQPLPGEDEPLHALVT-- 74


                ....*.
gi 17647843 200 APPAEA 205
Cdd:cd22382  75 ANTAES 80
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
96-193 1.20e-09

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 58.83  E-value: 1.20e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843  96 KVQTTGRipsreQKYADIYReKPLRISQRVLVPIREHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSmrdrVKEE 175
Cdd:COG5176 129 AQKILPR-----FVLPNDYI-RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGS----VKEG 198

                        90
                ....*....|....*...
gi 17647843 176 ELRSSKDPKYAHLNSDLH 193
Cdd:COG5176 199 KISSDTPESLKNAEAVLH 216
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 124-215 8.42e-07

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: 47.17  E-value: 8.42e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17647843 124 RVLVPI-REHPKFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSmrDRVKEEELRSSKDPkyahlnsdLHVEIStiAPP 202
Cdd:cd22386   6 KVFVGLeHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS--GFIEPASGREADEP--------LHLLIS--HPD 73

                        90
                ....*....|...
gi 17647843 203 AEAYARiAYAMAE 215
Cdd:cd22386  74 PEGLQQ-AKKLCE 85
KH smart00322
K homology RNA-binding domain;
120-172 3.15e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 38.82  E-value: 3.15e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 17647843    120 RISQRVLVPIrehpkfNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNSMRDRV 172
Cdd:smart00322   2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVV 48
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 122-167 1.64e-03

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: 36.88  E-value: 1.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 17647843   122 SQRVLVPirehpkFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNS 167
Cdd:pfam00013   1 TVEILVP------SSLVGLIIGKGGSNIKEIREETGAKIQIPPSES 40
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 124-167 1.69e-03

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: 36.51  E-value: 1.69e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 17647843 124 RVLVPirehpkFNFVGKLLGPKGNSLRRLQEETLCKMTVLGRNS 167
Cdd:cd00105   2 EIEVP------SELVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 68-118 1.74e-03

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 36.25  E-value: 1.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17647843    68 YIRDCMAERNRMDRKFPIAEKLLEGEIEKVQTTGRIPSREQKYADIYREKP 118
Cdd:pfam16274   2 YLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52
 
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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