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Conserved domains on  [gi|6319439|ref|NP_009521|]
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Hek2p [Saccharomyces cerevisiae S288C]

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 44-113 1.77e-26

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


:

Pssm-ID: 411883  Cd Length: 70  Bit Score: 100.45  E-value: 1.77e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439   44 INHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAIGDIVDVLNK 113
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 158-226 9.56e-26

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 98.52  E-value: 9.56e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319439  158 YVRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNATLEIGKTLL 69
KH smart00322
K homology RNA-binding domain;
257-330 1.39e-06

K homology RNA-binding domain;


:

Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.36  E-value: 1.39e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439     257 SNTRIELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddddKDENFRKFIITSKfPKNVKLAESMLLKNL 330
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGP-PENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 44-113 1.77e-26

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 100.45  E-value: 1.77e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439   44 INHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAIGDIVDVLNK 113
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 158-226 9.56e-26

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 98.52  E-value: 9.56e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319439  158 YVRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNATLEIGKTLL 69
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 159-223 5.61e-08

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: 49.20  E-value: 5.61e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319439    159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDfLPASDERIIEIQGFPGSITNVLIEISE 223
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGTPEAVEAAKALIEE 65
KH smart00322
K homology RNA-binding domain;
159-225 9.49e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 9.49e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439     159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKdflPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEKAAELILEIL 68
KH smart00322
K homology RNA-binding domain;
257-330 1.39e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.36  E-value: 1.39e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439     257 SNTRIELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddddKDENFRKFIITSKfPKNVKLAESMLLKNL 330
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGP-PENVEKAAELILEIL 68
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 46-109 1.17e-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: 42.65  E-value: 1.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439     46 HRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAIGDIVD 109
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 261-328 1.20e-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: 42.65  E-value: 1.20e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439    261 IELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddDDKDENFRKFIITSKfPKNVKLAESMLLK 328
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPP---SESEGNERIVTITGT-PEAVEAAKALIEE 65
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 261-327 1.50e-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: 42.29  E-value: 1.50e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439  261 IELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddDDKDENFRKFIITSKfPKNVKLAESMLL 327
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPK---EGEGSGERVVTITGT-PEAVEKAKELIE 63
KH smart00322
K homology RNA-binding domain;
44-111 8.80e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 8.80e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439      44 INHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEkvPGCSDRILSCAGNVINVANAIGDIVDVL 111
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPENVEKAAELILEIL 68
 
Name Accession Description Interval E-value
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 44-113 1.77e-26

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411883  Cd Length: 70  Bit Score: 100.45  E-value: 1.77e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439   44 INHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAIGDIVDVLNK 113
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 158-226 9.56e-26

second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411884 [Multi-domain]  Cd Length: 69  Bit Score: 98.52  E-value: 9.56e-26
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319439  158 YVRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQGTPDAIHNATLEIGKTLL 69
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 158-225 3.02e-10

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411863 [Multi-domain]  Cd Length: 73  Bit Score: 56.01  E-value: 3.02e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439  158 YVRLIVANSHISSIIGKAGATIKSLINKHGVKIVASK--DFLPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:cd22435   3 SLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKnnDFYPGTTERVCLIQGEVEAVNAVLDFILEKI 72
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 47-111 1.57e-09

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 53.80  E-value: 1.57e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319439   47 RLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKvpGCSDRILSCAGNVINVANAIGDIVDVL 111
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINISDG--SCPERIVTVTGTTDAVFKAFELICRKL 64
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 159-223 2.39e-09

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 53.39  E-value: 2.39e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKI-VASKDFLPA---SDERIIEIQGFPGSITNVLIEISE 223
Cdd:cd22460   2 ARLLVASSQAGSLIGKGGAIIKQIREESGASVrILPEEELPPcasPDDRVVQISGEAQAVKKALELVSS 70
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 159-225 3.14e-09

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 53.03  E-value: 3.14e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:cd22433   4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQIGGKPDKVVECIREILELL 70
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 159-226 3.77e-09

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411948 [Multi-domain]  Cd Length: 72  Bit Score: 52.72  E-value: 3.77e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTVSGVPDAIIQCVRQICAVIL 71
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 160-226 3.90e-09

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411806 [Multi-domain]  Cd Length: 72  Bit Score: 52.66  E-value: 3.90e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439  160 RLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd02396   5 RLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTISGSPEAITKCVEQICCVML 71
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 159-226 3.42e-08

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411946 [Multi-domain]  Cd Length: 78  Bit Score: 50.12  E-value: 3.42e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22518   9 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGIPQSIIECVKQICVVML 76
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 159-209 4.55e-08

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 49.52  E-value: 4.55e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHG--VKIVASKDFLPASDERIIEIQG 209
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNanIKISPKDQLLPGSSERIVTITG 53
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 159-223 5.61e-08

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: 49.20  E-value: 5.61e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319439    159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDfLPASDERIIEIQGFPGSITNVLIEISE 223
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGTPEAVEAAKALIEE 65
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 159-226 7.93e-08

second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411947 [Multi-domain]  Cd Length: 79  Bit Score: 49.40  E-value: 7.93e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEIIL 226
Cdd:cd22519   8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTISGTPDAIIQCVKQICVVML 75
KH smart00322
K homology RNA-binding domain;
159-225 9.49e-08

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 48.83  E-value: 9.49e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439     159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKdflPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEKAAELILEIL 68
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 47-111 1.08e-07

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411861 [Multi-domain]  Cd Length: 70  Bit Score: 48.40  E-value: 1.08e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6319439   47 RLLLSLKEAAKIIGTKGSTISRIRAANAVKIGI-SEKVPGCSDRILSCAGNVINVANAIGDIVDVL 111
Cdd:cd22433   5 RLLVHQSQAGCIIGRAGFKIKELREKTGATIKVySECCPRSTDRVVQIGGKPDKVVECIREILELL 70
KH smart00322
K homology RNA-binding domain;
257-330 1.39e-06

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 45.36  E-value: 1.39e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439     257 SNTRIELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddddKDENFRKFIITSKfPKNVKLAESMLLKNL 330
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGP-PENVEKAAELILEIL 68
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 160-207 1.47e-06

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 45.29  E-value: 1.47e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 6319439  160 RLIVANSHISSIIGKAGATIKSLINKHGVKIVASkDFLPASDERIIEI 207
Cdd:cd22459   5 RLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVE-DGVPGTEERVITI 51
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 158-218 1.50e-06

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411941 [Multi-domain]  Cd Length: 73  Bit Score: 45.51  E-value: 1.50e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319439  158 YVRLIVANSHISSIIGKAGATIKSLINKHGVKIVASK--DFLPASDERIIEIQGFPGSITNVL 218
Cdd:cd22513   3 VAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRaqEFFPGTTDRVLLVSGSLNEVLTAL 65
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 43-113 2.27e-06

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411943  Cd Length: 70  Bit Score: 45.00  E-value: 2.27e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319439   43 TINHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKvpGCSDRILSCAGNVINVANAIGDIVDVLNK 113
Cdd:cd22515   1 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTNAIFKAFAMIIDKLEE 69
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 43-107 4.69e-06

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411945  Cd Length: 70  Bit Score: 43.86  E-value: 4.69e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6319439   43 TINHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKvpGCSDRILSCAGNVINVANAIGDI 107
Cdd:cd22517   1 TLTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEG--SCPERITTITGSTDAVFRAFSMI 63
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 159-221 5.24e-06

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: 43.44  E-value: 5.24e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFlPASDERIIEIQGFPGSITNVLIEI 221
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEG-EGSGERVVTITGTPEAVEKAKELI 62
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 46-109 1.17e-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: 42.65  E-value: 1.17e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439     46 HRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAIGDIVD 109
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 261-328 1.20e-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: 42.65  E-value: 1.20e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439    261 IELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddDDKDENFRKFIITSKfPKNVKLAESMLLK 328
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPP---SESEGNERIVTITGT-PEAVEAAKALIEE 65
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 46-96 1.47e-05

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.


Pssm-ID: 411887 [Multi-domain]  Cd Length: 69  Bit Score: 42.60  E-value: 1.47e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 6319439   46 HRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGN 96
Cdd:cd22459   4 FRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSS 54
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 261-327 1.50e-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: 42.29  E-value: 1.50e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6319439  261 IELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddDDKDENFRKFIITSKfPKNVKLAESMLL 327
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPK---EGEGSGERVVTITGT-PEAVEKAKELIE 63
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 43-108 1.72e-05

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 42.17  E-value: 1.72e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439   43 TINHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIgiseKVPGCS--DRILSCAGNVINVANAIGDIV 108
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASV----SVPDSSgpERILTISADRETVLGILTEIL 64
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 159-214 1.90e-05

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411807 [Multi-domain]  Cd Length: 71  Bit Score: 42.18  E-value: 1.90e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASK--DFLPASDERIIEIQGFPGSI 214
Cdd:cd09031   3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISKkgEFVPGTRNRKVTITGTPAAV 60
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 38-103 2.47e-05

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 41.92  E-value: 2.47e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6319439   38 TTAQPTINHRLllslkeAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANA 103
Cdd:cd22434   2 TTTQVTIPKDL------AGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNA 61
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 159-211 3.13e-05

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411864 [Multi-domain]  Cd Length: 70  Bit Score: 41.45  E-value: 3.13e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKI-VASKDFLPASDERIIEIQGFP 211
Cdd:cd22436   3 VKILVPNSTAGMIIGKGGATIKAIMEQSGARVqISQKPESINLQERVVTVTGEP 56
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 255-328 5.46e-05

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


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 41.17  E-value: 5.46e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6319439  255 TSSNTRIELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERKDDDDKDEnFRKFIItSKFPKNVKLAESMLLK 328
Cdd:cd22428   1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELP-ERVLLI-QGNPVQAQRAEEAIHQ 72
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 47-104 6.42e-05

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.


Pssm-ID: 411888 [Multi-domain]  Cd Length: 73  Bit Score: 40.68  E-value: 6.42e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319439   47 RLLLSLKEAAKIIGTKGSTISRIR--AANAVKIGISEKVPGC---SDRILSCAGNVINVANAI 104
Cdd:cd22460   3 RLLVASSQAGSLIGKGGAIIKQIReeSGASVRILPEEELPPCaspDDRVVQISGEAQAVKKAL 65
KH-I_BTR1_rpt1 cd22513
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 47-111 6.47e-05

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411941 [Multi-domain]  Cd Length: 73  Bit Score: 40.88  E-value: 6.47e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439   47 RLLLSLKEAAKIIGTKGSTISRIRAANAVKIGIS---EKVPGCSDRILSCAGNVINVANAIGDIVDVL 111
Cdd:cd22513   5 KLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSraqEFFPGTTDRVLLVSGSLNEVLTALNLILEKL 72
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 159-209 1.15e-04

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411866 [Multi-domain]  Cd Length: 67  Bit Score: 39.93  E-value: 1.15e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPasdERIIEIQG 209
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCP---ERIVTVTG 48
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 159-224 1.29e-04

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain 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 first one.


Pssm-ID: 411828 [Multi-domain]  Cd Length: 68  Bit Score: 39.95  E-value: 1.29e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDERIIEIQGFPGSITNVLIEISEI 224
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAITIYGTPEGCSSACKQILEI 67
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 43-95 2.26e-04

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411944  Cd Length: 77  Bit Score: 39.32  E-value: 2.26e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6319439   43 TINHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKvpGCSDRILSCAG 95
Cdd:cd22516   8 TLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITG 58
KH-I_Vigilin_rpt14 cd22417
fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 159-225 4.69e-04

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


Pssm-ID: 411845 [Multi-domain]  Cd Length: 72  Bit Score: 38.34  E-value: 4.69e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKI-VASKDflpASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:cd22417   3 LTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIqFPDKG---DENDDEITITGYEKNAEAAKDAILKIV 67
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 263-312 4.94e-04

third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain 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 third one.


Pssm-ID: 411830 [Multi-domain]  Cd Length: 66  Bit Score: 38.00  E-value: 4.94e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 6319439  263 LKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERKDDDDKDEnfRKFIIT 312
Cdd:cd22402   5 LYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPE--RKVTIT 52
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 166-225 5.02e-04

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


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 37.94  E-value: 5.02e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439  166 SHISSIIGKAGATIKSLINKHGVKIVASKDFLPASDeriIEIQGFPGSITNVLIEISEII 225
Cdd:cd02394  11 KFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDE---IRIEGSPEGVKKAKAEILELV 67
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 46-104 5.69e-04

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: 37.66  E-value: 5.69e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 6319439   46 HRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILSCAGNVINVANAI 104
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAK 59
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 170-216 6.48e-04

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411862 [Multi-domain]  Cd Length: 74  Bit Score: 38.07  E-value: 6.48e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 6319439  170 SIIGKAGATIKSLINKHGVKIVASkDFLPASDERIIEIQGFPGSITN 216
Cdd:cd22434  15 SIIGKGGQRIRQIRHESGASIKID-EPLPGSEDRIITITGTQDQIQN 60
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 159-209 7.55e-04

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411942 [Multi-domain]  Cd Length: 71  Bit Score: 37.79  E-value: 7.55e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASK--DFLPASDERIIEIQG 209
Cdd:cd22514   3 VTIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDrgDFVSGTRNRKVTITG 55
KH smart00322
K homology RNA-binding domain;
44-111 8.80e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 8.80e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6319439      44 INHRLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEkvPGCSDRILSCAGNVINVANAIGDIVDVL 111
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPENVEKAAELILEIL 68
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 165-223 2.41e-03

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain 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: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 36.44  E-value: 2.41e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319439  165 NSHISSIIGKAGATIKSLINKHGVKIVASK--DFLPASDERIIEIQGFPGSITNVLIEISE 223
Cdd:cd22401   8 NNLCGRLIGKDGRNIKKIMEDTNTKITISSlqDLTSYNPERTITIKGSLEAMSEAESLISE 68
KH-I_ScSCP160_rpt4 cd22449
fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 166-225 3.91e-03

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


Pssm-ID: 411877 [Multi-domain]  Cd Length: 70  Bit Score: 35.71  E-value: 3.91e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439  166 SHISSIIGKAGATIKSLINKHGVKIvaskDFLPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:cd22449  13 KYVPHIIGKKGANINKLREEYGVKI----DFEDKTGEGNVEIKGSKKNVEEAKKRILSQI 68
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 159-221 4.48e-03

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.


Pssm-ID: 411860 [Multi-domain]  Cd Length: 64  Bit Score: 35.23  E-value: 4.48e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319439  159 VRLIVANSHISSIIGKAGATIKSLINKHGVKIVASKDFLPasdERIIEIQGFPGSITNVLIEI 221
Cdd:cd22432   4 LRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGP---ERILTISADRETVLGILTEI 63
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 258-327 5.37e-03

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.


Pssm-ID: 411882 [Multi-domain]  Cd Length: 71  Bit Score: 35.37  E-value: 5.37e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6319439  258 NTRIELKIPELYVGAIIGRGMNRIKNLKTFTKTNIVVERkddDDKDENFRKFIITSKfPKNVKLAESMLL 327
Cdd:cd22454   3 QTTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFER---VNGGSPNREVQITGS-PDNVAAAKRLIE 68
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 47-104 6.61e-03

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411865 [Multi-domain]  Cd Length: 69  Bit Score: 34.89  E-value: 6.61e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6319439   47 RLLLSLKEAAKIIGTKGSTISRIRAANAVKIGISEK---VPGCSDRILSCAGNVINVANAI 104
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKdqlLPGSSERIVTITGSFDQVVKAV 62
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 154-225 6.64e-03

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


Pssm-ID: 411856 [Multi-domain]  Cd Length: 74  Bit Score: 35.00  E-value: 6.64e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6319439  154 EDIGYVRLIVANSHISSIIGKAGATIKSLINKHGVKI-VASKDFLPASDERIIEIQGFPGSITNVLIEISEII 225
Cdd:cd22428   2 SRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIdFKDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 53-107 8.78e-03

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


Pssm-ID: 411804 [Multi-domain]  Cd Length: 68  Bit Score: 34.47  E-value: 8.78e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6319439   53 KEAAKIIGTKGSTISRIRAANAVKIGISEKVPGCSDRILScaGNVINVANAIGDI 107
Cdd:cd02394  11 KFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIE--GSPEGVKKAKAEI 63
 
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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