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Conserved domains on  [gi|443720779|gb|ELU10377|]
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hypothetical protein CAPTEDRAFT_94427 [Capitella teleta]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 71-173 8.93e-72

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: 214.03  E-value: 8.93e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLITVEDS 150
Cdd:cd22465    1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 80

                         90       100
                 ....*....|....*....|...
gi 443720779 151 KNRASVKLERAKEEVKKLLVPAP 173
Cdd:cd22465   81 QNRAEIKLKRAVEEVKKLLVPAA 103
STAR_dimer pfam16544
Homodimerization region of STAR domain protein; This family is the homodimerization domain of ...
 8-57 1.67e-21

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.


:

Pssm-ID: 435414  Cd Length: 52  Bit Score: 83.92  E-value: 1.67e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 443720779    8 DRNTPEYLAQLLKDKKQIAAFPNVFIHTERLLDEEINKVRGNLFHLSTNK 57
Cdd:pfam16544   2 PRSTPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51
 
Name Accession Description Interval E-value
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 71-173 8.93e-72

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: 214.03  E-value: 8.93e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLITVEDS 150
Cdd:cd22465    1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 80

                         90       100
                 ....*....|....*....|...
gi 443720779 151 KNRASVKLERAKEEVKKLLVPAP 173
Cdd:cd22465   81 QNRAEIKLKRAVEEVKKLLVPAA 103
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
72-196 6.94e-28

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 106.98  E-value: 6.94e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  72 FSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRK-KEEMNRGKPNWEhlnEDLHVLIT--VE 148
Cdd:COG5176  148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKiSSDTPESLKNAE---AVLHCLIEadSE 224

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 443720779 149 DSKNRASVKLERAKEEVKKllvpAPEGEDDLKKRQLMELAIINGTYRD 196
Cdd:COG5176  225 DKICRLIKSQLNAIREARR----NPEGQNDLKRFQLRWLAHLNGTLRA 268
STAR_dimer pfam16544
Homodimerization region of STAR domain protein; This family is the homodimerization domain of ...
 8-57 1.67e-21

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.


Pssm-ID: 435414  Cd Length: 52  Bit Score: 83.92  E-value: 1.67e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 443720779    8 DRNTPEYLAQLLKDKKQIAAFPNVFIHTERLLDEEINKVRGNLFHLSTNK 57
Cdd:pfam16544   2 PRSTPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51
KH smart00322
K homology RNA-binding domain;
70-118 1.43e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 1.43e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 443720779    70 EQFSEKLYVPVkdypefNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 118
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 73-118 8.49e-04

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: 8.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 443720779   73 SEKLYVPVKdypefnFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 118
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40
 
Name Accession Description Interval E-value
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 71-173 8.93e-72

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: 214.03  E-value: 8.93e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLITVEDS 150
Cdd:cd22465    1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 80

                         90       100
                 ....*....|....*....|...
gi 443720779 151 KNRASVKLERAKEEVKKLLVPAP 173
Cdd:cd22465   81 QNRAEIKLKRAVEEVKKLLVPAA 103
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 71-171 4.19e-66

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: 199.50  E-value: 4.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLITVEDS 150
Cdd:cd22383    1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                         90       100
                 ....*....|....*....|.
gi 443720779 151 KNRASVKLERAKEEVKKLLVP 171
Cdd:cd22383   81 ENRAHIKLAKAVEEVKKLLIP 101
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 67-171 1.06e-65

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: 198.61  E-value: 1.06e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  67 GPTEQFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLIT 146
Cdd:cd22466    1 GPSVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNRGKPNWEHLNDELHVLIT 80

                         90       100
                 ....*....|....*....|....*
gi 443720779 147 VEDSKNRASVKLERAKEEVKKLLVP 171
Cdd:cd22466   81 VEDTENRAKVKLQRAVEEVRKLLVP 105
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 73-167 1.73e-34

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: 118.93  E-value: 1.73e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  73 SEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEE--MNRGKPNWEHLNEDLHVLITVEDS 150
Cdd:cd22384    6 SEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEelRKSGDPKYAHLNEDLHVLIEAFAP 85

                         90
                 ....*....|....*..
gi 443720779 151 KNRASVKLERAKEEVKK 167
Cdd:cd22384   86 PAEAYARLAHALAELRK 102
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 75-171 2.70e-32

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: 113.36  E-value: 2.70e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  75 KLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNWEHLNEDLHVLITVEDSKNRA 154
Cdd:cd22467    5 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDKPGYEHLNEPLHVLIEAELPANII 84

                         90
                 ....*....|....*..
gi 443720779 155 SVKLERAKEEVKKLLVP 171
Cdd:cd22467   85 DARLQHAQEIIEDLLKP 101
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 71-171 7.57e-32

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: 112.42  E-value: 7.57e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNR--GKPNWEHLNEDLHVLITVE 148
Cdd:cd22468    4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRkgGDPKYAHLNMDLHVFIEVF 83

                         90       100
                 ....*....|....*....|...
gi 443720779 149 DSKNRASVKLERAKEEVKKLLVP 171
Cdd:cd22468   84 GPPCEAYARMAHAMEEVKKFLVP 106
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 71-170 3.98e-31

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: 110.00  E-value: 3.98e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNRGKPNwehLNEDLHVLITVEDS 150
Cdd:cd02395    1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPD---EEEDLHVLITADTE 77

                         90       100
                 ....*....|....*....|
gi 443720779 151 KnrasvKLERAKEEVKKLLV 170
Cdd:cd02395   78 E-----KVDKAAKLIEKLLI 92
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
72-196 6.94e-28

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


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 106.98  E-value: 6.94e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  72 FSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRK-KEEMNRGKPNWEhlnEDLHVLIT--VE 148
Cdd:COG5176  148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKiSSDTPESLKNAE---AVLHCLIEadSE 224

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 443720779 149 DSKNRASVKLERAKEEVKKllvpAPEGEDDLKKRQLMELAIINGTYRD 196
Cdd:COG5176  225 DKICRLIKSQLNAIREARR----NPEGQNDLKRFQLRWLAHLNGTLRA 268
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 71-183 4.25e-26

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: 98.27  E-value: 4.25e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNR--GKPNWEHLNEDLHVLITVE 148
Cdd:cd22469    6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRksGEAKYAHLSDELHVLIEVF 85

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 443720779 149 DSKNRASVKLERAKEEVKKLLVpaPEGEDDLKKRQ 183
Cdd:cd22469   86 APPGEAYSRMSHALEEIKKFLV--PDYNDEIRQEQ 118
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 71-171 9.28e-25

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: 94.35  E-value: 9.28e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  71 QFSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRDRKKEEMNR--GKPNWEHLNEDLHVLITVE 148
Cdd:cd22470    8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVF 87

                         90       100
                 ....*....|....*....|...
gi 443720779 149 DSKNRASVKLERAKEEVKKLLVP 171
Cdd:cd22470   88 APPAEAYARMGHALEEIKKFLIP 110
STAR_dimer pfam16544
Homodimerization region of STAR domain protein; This family is the homodimerization domain of ...
 8-57 1.67e-21

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.


Pssm-ID: 435414  Cd Length: 52  Bit Score: 83.92  E-value: 1.67e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 443720779    8 DRNTPEYLAQLLKDKKQIAAFPNVFIHTERLLDEEINKVRGNLFHLSTNK 57
Cdd:pfam16544   2 PRSTPDYLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 72-166 7.89e-20

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: 80.82  E-value: 7.89e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  72 FSEKLYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMRD----RKKEEMNRGkpnwehLNEDLHVLITV 147
Cdd:cd22382    2 VSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEgkvgRKDGQPLPG------EDEPLHALVTA 75

                         90       100
                 ....*....|....*....|
gi 443720779 148 EDSKN-RASVklERAKEEVK 166
Cdd:cd22382   76 NTAESvKKAV--DKIKEIIK 93
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 74-169 9.15e-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: 65.27  E-value: 9.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  74 EKLYVPVKDYPE-FNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSmrdRKKEEMNRGKPnwehlNEDLHVLITVEDSKn 152
Cdd:cd22386    5 EKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPASGREA-----DEPLHLLISHPDPE- 75

                         90
                 ....*....|....*..
gi 443720779 153 rasvKLERAKEEVKKLL 169
Cdd:cd22386   76 ----GLQQAKKLCEDLL 88
KH smart00322
K homology RNA-binding domain;
70-118 1.43e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 1.43e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 443720779    70 EQFSEKLYVPVkdypefNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 118
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH-I_RIK_like_rpt2 cd22472
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and ...
 76-169 1.27e-05

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411900  Cd Length: 96  Bit Score: 42.82  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443720779  76 LYVPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMVRGKGSMrdrkkeEMNRGKpnwehlnEDLHVLITVEDSKnras 155
Cdd:cd22472    7 LYVGIEAPPSFNLAGRIRGPNNSYLQHIASATGATVALRGRGSG------GAPEGP-------EPLHLFLSASDPK---- 69

                         90
                 ....*....|....
gi 443720779 156 vKLERAKEEVKKLL 169
Cdd:cd22472   70 -ALEEARGLAENLI 82
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 74-118 1.75e-05

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: 41.52  E-value: 1.75e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 443720779  74 EKLYVPVKdypefnFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 118
Cdd:cd00105    1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 73-118 8.49e-04

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: 8.49e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 443720779   73 SEKLYVPVKdypefnFVGRILGPRGMTAKQLEQDTGCKIMVRGKGS 118
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 78-113 1.11e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 37.34  E-value: 1.11e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 443720779  78 VPVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMV 113
Cdd:cd22493    5 VPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITI 40
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 73-122 1.36e-03

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411824 [Multi-domain]  Cd Length: 68  Bit Score: 36.08  E-value: 1.36e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 443720779  73 SEKLYVPVKdypefnFVGRILGPRGMTAKQLEQDTGCKI-MVRGKGSMRDR 122
Cdd:cd22396    2 TEEYKVPDK------MVGLIIGRGGEQINRLQAESGAKIqIAPDSGGLPER 46
KH-I_KRR1_rpt2 cd22394
second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome ...
 91-116 2.09e-03

second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins; KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411822  Cd Length: 93  Bit Score: 36.39  E-value: 2.09e-03
                         10        20
                 ....*....|....*....|....*.
gi 443720779  91 RILGPRGMTAKQLEQDTGCKIMVRGK 116
Cdd:cd22394   24 RLIGPNGSTLKAIELLTKCYILVQGN 49
KH-I_IGF2BP3_rpt2 cd22495
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 79-113 4.54e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411923  Cd Length: 77  Bit Score: 35.02  E-value: 4.54e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 443720779  79 PVKDYPEFNFVGRILGPRGMTAKQLEQDTGCKIMV 113
Cdd:cd22495    1 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 35
 
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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