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Conserved domains on  [gi|45752620|gb|AAS76208|]
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At2g03110 [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 74-147 1.54e-21

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: 82.28  E-value: 1.54e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVR-NDNLPMCALAlsHDELLQIIGDPSAVREALYQVAFLLY 147
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILpEEELPPCASP--DDRVVQISGEAQAVKKALELVSSRLR 73
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 1-43 7.37e-07

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


The actual alignment was detected with superfamily member cd22459:

Pssm-ID: 469614 [Multi-domain]  Cd Length: 69  Bit Score: 44.14  E-value: 7.37e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45752620   1 MRVNEALPGCDERVVTIYSNseernrieDDNEDFVCPAFDALF 43
Cdd:cd22459  35 IKVEDGVPGTEERVITISSS--------EAPEAPVSPAQEALL 69
 
Name Accession Description Interval E-value
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 74-147 1.54e-21

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: 82.28  E-value: 1.54e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVR-NDNLPMCALAlsHDELLQIIGDPSAVREALYQVAFLLY 147
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILpEEELPPCASP--DDRVVQISGEAQAVKKALELVSSRLR 73
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 74-142 3.34e-15

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: 65.77  E-value: 3.34e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620    74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESE------GNERIVTITGTPEAVEAAKALI 63
KH smart00322
K homology RNA-binding domain;
71-143 6.90e-13

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 60.00  E-value: 6.90e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620     71 TVVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalalSHDELLQIIGDPSAVREALYQVA 143
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--------SEERVVEITGPPENVEKAAELIL 65
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 1-43 7.37e-07

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: 44.14  E-value: 7.37e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45752620   1 MRVNEALPGCDERVVTIYSNseernrieDDNEDFVCPAFDALF 43
Cdd:cd22459  35 IKVEDGVPGTEERVITISSS--------EAPEAPVSPAQEALL 69
 
Name Accession Description Interval E-value
KH-I_PEPPER_rpt2_like cd22460
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 74-147 1.54e-21

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: 82.28  E-value: 1.54e-21
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVR-NDNLPMCALAlsHDELLQIIGDPSAVREALYQVAFLLY 147
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILpEEELPPCASP--DDRVVQISGEAQAVKKALELVSSRLR 73
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 74-142 3.34e-15

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: 65.77  E-value: 3.34e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620    74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESE------GNERIVTITGTPEAVEAAKALI 63
KH-I_PCBP_rpt2 cd02396
second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 73-142 3.90e-13

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: 60.75  E-value: 3.90e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPN-----STERAVTISGSPEAITKCVEQI 66
KH smart00322
K homology RNA-binding domain;
71-143 6.90e-13

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 60.00  E-value: 6.90e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620     71 TVVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalalSHDELLQIIGDPSAVREALYQVA 143
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--------SEERVVEITGPPENVEKAAELIL 65
KH-I_PCBP3_rpt2 cd22519
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 73-150 1.27e-11

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: 57.10  E-value: 1.27e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQVAFLLYNNP 150
Cdd:cd22519   6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPN-----STERAVTISGTPDAIIQCVKQICVVMLESP 78
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 75-142 1.30e-11

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: 56.54  E-value: 1.30e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEG------SGERVVTITGTPEAVEKAKELI 62
KH-I_PCBP1_2_rpt2 cd22518
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 73-146 9.62e-11

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: 54.74  E-value: 9.62e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22518   7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN-----STERAITIAGIPQSIIECVKQICVVM 75
KH-I_PCBP4_rpt2 cd22520
second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 73-142 4.75e-10

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: 4.75e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPN-----STERAVTVSGVPDAIIQCVRQI 66
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 73-117 9.00e-10

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: 51.84  E-value: 9.00e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVrNDNLPMCA 117
Cdd:cd22459   2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV-EDGVPGTE 45
KH-I_HNRNPK_rpt2 cd22433
second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 75-146 3.19e-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: 50.33  E-value: 3.19e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22433   4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPR-----STDRVVQIGGKPDKVVECIREILELL 70
KH-I_IGF2BP_rpt1 cd22400
first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 75-142 1.19e-08

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: 48.81  E-value: 1.19e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV-RNDNLPmcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIhRKENAG------AAEKAITIYGTPEGCSSACKQI 64
KH-I_Rnc1_rpt2 cd22456
second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe ...
 74-143 5.21e-08

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: 47.29  E-value: 5.21e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalaLSHDELLQIIGDPSAVREALYQVA 143
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLP-----LSTERILEVQGTPDAIHNATLEIG 65
KH-I_HNRNPK_rpt1 cd22432
first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 72-114 4.01e-07

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: 44.86  E-value: 4.01e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45752620  72 VVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLP 114
Cdd:cd22432   1 VVELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSSGP 43
KH-I_BTR1_rpt2 cd22437
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 ...
 75-111 5.81e-07

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: 44.52  E-value: 5.81e-07
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRND 111
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPK 37
KH-I_PEPPER_rpt1_like cd22459
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH ...
 1-43 7.37e-07

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: 44.14  E-value: 7.37e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 45752620   1 MRVNEALPGCDERVVTIYSNseernrieDDNEDFVCPAFDALF 43
Cdd:cd22459  35 IKVEDGVPGTEERVITISSS--------EAPEAPVSPAQEALL 69
KH-I_NOVA_rpt1 cd22435
first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 75-139 7.95e-07

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: 44.07  E-value: 7.95e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV--RNDNLPMcalalSHDELLQIIGDPSAVREAL 139
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLskNNDFYPG-----TTERVCLIQGEVEAVNAVL 65
KH-I_HNRNPK_rpt3 cd22434
third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ...
 72-140 9.62e-07

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: 43.85  E-value: 9.62e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  72 VVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVrNDNLPMcalalSHDELLQIIGDPSAVREALY 140
Cdd:cd22434   1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKI-DEPLPG-----SEDRIITITGTQDQIQNAQY 63
KH-I_Vigilin_rpt6 cd02394
sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...
 79-138 8.04e-06

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: 41.40  E-value: 8.04e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalalSHDELLQIIGDPSAVREA 138
Cdd:cd02394   8 IDPKFHGHIIGKGGANIKRIREESGVSIRIPDDE--------ANSDEIRIEGSPEGVKKA 59
KH-I_NOVA_rpt2 cd22436
second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 74-138 9.39e-06

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: 41.07  E-value: 9.39e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV----RNDNLPmcalalshDELLQIIGDPSAVREA 138
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQIsqkpESINLQ--------ERVVTVTGEPEANRKA 62
KH-I_PCBP3_rpt1 cd22516
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 73-144 1.12e-05

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: 41.24  E-value: 1.12e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalalshDELLQIIGDPSAVREALYQVAF 144
Cdd:cd22516   9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGNCP--------ERIVTITGPTDAIFKAFAMIAY 72
KH-I_Mextli_like cd22454
type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic ...
 73-138 1.15e-05

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: 41.15  E-value: 1.15e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalALSHDELLQIIGDPSAVREA 138
Cdd:cd22454   4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVN------GGSPNREVQITGSPDNVAAA 63
KH-I_PCBP_rpt1 cd22438
first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 75-114 1.97e-05

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: 40.32  E-value: 1.97e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 45752620  75 VRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLP 114
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSCP 40
KH-I_FUBP3_rpt2 cd22483
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 77-138 2.53e-05

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; 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. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411911 [Multi-domain]  Cd Length: 83  Bit Score: 40.66  E-value: 2.53e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620  77 MLVPSDQIGYLIGKGGPIIQTLRNDTNAQ-IRVRNDNLPMCAlalshDELLQIIGDPSAVREA 138
Cdd:cd22483   9 ILIPASKVGLVIGKGGETIKQLQERTGVKmIMIQDGPLPTGA-----DKPLRITGDPFKVQQA 66
KH-I_AKAP1 cd22395
type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 ...
 79-131 2.64e-05

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


Pssm-ID: 411823 [Multi-domain]  Cd Length: 68  Bit Score: 39.81  E-value: 2.64e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRN----DNLPMCALALSHDEL---LQIIGD 131
Cdd:cd22395   6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPhpytQNFQICSIEGTQQQIdkaLKLIRK 65
KH-I_FUBP_rpt1 cd22396
first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 73-138 2.84e-05

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: 39.93  E-value: 2.84e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalsHDELLQIIGDPSAVREA 138
Cdd:cd22396   1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGL------PERPCTLTGTPDAIETA 60
KH-I_TDRKH_rpt1 cd22428
first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing ...
 68-142 3.43e-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: 40.01  E-value: 3.43e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45752620  68 EGQTVVTVRmlVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMCAlalsHDELLQIIGDPSAV---REALYQV 142
Cdd:cd22428   2 SRQIEIEMK--VPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGEL----PERVLLIQGNPVQAqraEEAIHQI 73
KH-I_PCBP_rpt3 cd22439
third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding ...
 74-140 3.95e-05

third 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 third one.


Pssm-ID: 411867 [Multi-domain]  Cd Length: 68  Bit Score: 39.52  E-value: 3.95e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRN--DNlpmcalalSHDELLQIIGDPSAVREALY 140
Cdd:cd22439   3 TQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANseDG--------STERSVTITGTPEAVSLAQY 63
KH-I_ScSCP160_rpt2 cd22447
second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein ...
 71-138 4.72e-05

second 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 second one.


Pssm-ID: 411875 [Multi-domain]  Cd Length: 80  Bit Score: 39.71  E-value: 4.72e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  71 TVVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMCALALSHDELLQ--IIGDPSAVREA 138
Cdd:cd22447   2 PKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPADEDDDTMVEvtITGDEFNVQHA 71
KH-I_FUBP_rpt2 cd22397
second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 74-146 5.64e-05

second 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 second one.


Pssm-ID: 411825 [Multi-domain]  Cd Length: 69  Bit Score: 39.15  E-value: 5.64e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcALALSHDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22397   1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDG----PQPTGQDKPLRITGDPQKVQRAKELVMELI 69
KH-I_PNPase cd02393
type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...
 76-111 1.48e-04

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


Pssm-ID: 411803 [Multi-domain]  Cd Length: 70  Bit Score: 37.84  E-value: 1.48e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 45752620  76 RMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRND 111
Cdd:cd02393   7 TIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDD 42
KH-I_BTR1_rpt3 cd22514
third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and ...
 74-140 1.74e-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: 1.74e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV--RNDNLPMcalalSHDELLQIIGDPSAVREALY 140
Cdd:cd22514   2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKIsdRGDFVSG-----TRNRKVTITGPQDAVQMAQY 65
KH-I_Rnc1_rpt1 cd22455
first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 73-148 1.79e-04

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: 37.66  E-value: 1.79e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVrNDNLPMCalalsHDELLQIIGDPSAVREALYQVAFLLYN 148
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGV-SKVVPGV-----HDRVLTVSGPLEGVAKAFGLIARTLNE 70
KH-I_PCBP4_rpt1 cd22517
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 73-146 1.83e-04

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: 38.09  E-value: 1.83e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalalshDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22517   2 LTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGSCP--------ERITTITGSTDAVFRAFSMIAFKL 67
KH-I_IGF2BP_rpt3 cd22402
third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 74-142 1.86e-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: 37.62  E-value: 1.86e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMcalalSHDELLQIIGDPSAVREALYQV 142
Cdd:cd22402   2 TTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPD-----APERKVTITGPPEAQWKAQLCI 65
KH-I_NOVA_rpt3 cd09031
third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ...
 73-140 1.98e-04

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: 37.56  E-value: 1.98e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV--RNDNLPMcalalSHDELLQIIGDPSAVREALY 140
Cdd:cd09031   1 TVIELEVPENLVGAILGKGGKTLVEIQELTGARIQIskKGEFVPG-----TRNRKVTITGTPAAVQAAQY 65
KH-I_PCBP3_rpt3 cd22522
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) ...
 74-142 2.64e-04

third 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 third one.


Pssm-ID: 411950 [Multi-domain]  Cd Length: 75  Bit Score: 37.79  E-value: 2.64e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNdnlpmcALALSHDELLQIIGDPSAVREALYQV 142
Cdd:cd22522  10 THELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIAN------ATEGSSERQITITGSPANISLAQYLI 72
KH-I_MER1_like cd22458
type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic ...
 73-139 3.54e-04

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.


Pssm-ID: 411886 [Multi-domain]  Cd Length: 65  Bit Score: 37.04  E-value: 3.54e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 45752620  73 VTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVrndnlpmCALALSHDELLQIIGDPSAVREAL 139
Cdd:cd22458   1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRL-------IPISNSSQQTIHLSGTDKQIALAI 60
KH-I_FUBP_rpt3 cd22398
third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding ...
 77-138 4.05e-04

third 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 third one.


Pssm-ID: 411826 [Multi-domain]  Cd Length: 67  Bit Score: 36.85  E-value: 4.05e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45752620  77 MLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRND--NLPmcalalshDELLQIIGDPSAVREA 138
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDdgNSP--------DRICVITGPPDQVQHA 59
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 76-138 4.06e-04

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: 36.82  E-value: 4.06e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620  76 RMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcaLALSHDELLQIIGDPSAVREA 138
Cdd:cd22401   3 KILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDL---TSYNPERTITIKGSLEAMSEA 62
KH-I_PCBP1_2_rpt1 cd22515
first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 72-121 4.68e-04

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: 36.91  E-value: 4.68e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 45752620  72 VVTVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPMCALALS 121
Cdd:cd22515   1 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLA 50
KH-I_IGF2BP2_rpt4 cd22500
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 79-142 5.02e-04

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), 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 also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. 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 fourth one.


Pssm-ID: 411928  Cd Length: 78  Bit Score: 37.03  E-value: 5.02e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLPmcalALSHDELLQIIGDPSA-------VREALYQV 142
Cdd:cd22500   8 VPSSAAGRVIGKGGKTVNELQNLTSAEVIVPRDQTP----DENEEVIVKIIGHFFAsqtaqrkIREIVQQV 74
KH-I_FUBP1_rpt2 cd22481
second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 77-138 5.77e-04

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; 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. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411909 [Multi-domain]  Cd Length: 71  Bit Score: 36.52  E-value: 5.77e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45752620  77 MLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlPMCALAlshDELLQIIGDPSAVREA 138
Cdd:cd22481   6 IMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDG-PQNTGA---DKPLRITGDPYKVQQA 63
KH-I_FUBP3_rpt3 cd22486
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 74-146 9.53e-04

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; 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. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411914  Cd Length: 70  Bit Score: 36.08  E-value: 9.53e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalALSHDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22486   4 SIEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDD------GISPERVAQVMGPPDRCQHAAHIINELI 70
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 74-108 1.01e-03

fourth 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 fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 35.68  E-value: 1.01e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 45752620  74 TVRMLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRV 108
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKL 35
KH-I_Rnc1_rpt3 cd22457
third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding ...
 79-147 1.01e-03

third 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 third one.


Pssm-ID: 411885 [Multi-domain]  Cd Length: 64  Bit Score: 35.51  E-value: 1.01e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalalsHDE----LLQIIGDPSAVREALYqvafLLY 147
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAP---------HDEtgerMFTITGTPEANDRALR----LLY 64
KH-I_ASCC1 cd22419
type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex ...
 79-108 1.09e-03

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.


Pssm-ID: 411847 [Multi-domain]  Cd Length: 66  Bit Score: 35.63  E-value: 1.09e-03
                        10        20        30
                ....*....|....*....|....*....|
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRV 108
Cdd:cd22419   7 VPSALFKFIIGKKGETKKRLESETKTQIRI 36
KH-I_IGF2BP3_rpt4 cd22501
fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 79-114 1.15e-03

fourth 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 fourth one.


Pssm-ID: 411929  Cd Length: 66  Bit Score: 35.82  E-value: 1.15e-03
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNLP 114
Cdd:cd22501   6 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTP 41
KH-I_PCBP1_2_rpt3 cd22521
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) ...
 77-140 1.37e-03

third 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 third one.


Pssm-ID: 411949  Cd Length: 76  Bit Score: 35.80  E-value: 1.37e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45752620  77 MLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNdnlpmcALALSHDELLQIIGDPSAVREALY 140
Cdd:cd22521   9 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN------PVEGSTDRQVTITGSAASISLAQY 66
KH-I_PCBP4_rpt3 cd22523
third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) ...
 77-140 1.77e-03

third 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 third one.


Pssm-ID: 411951  Cd Length: 68  Bit Score: 35.26  E-value: 1.77e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 45752620  77 MLVPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDnlpmcaLALSHDELLQIIGDPSAVREALY 140
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQ------TEGTSERHVTITGSPVSITLAQY 63
KH-I_Vigilin_rpt8 cd22411
eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; ...
 79-138 3.17e-03

eighth 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 eighth one.


Pssm-ID: 411839 [Multi-domain]  Cd Length: 62  Bit Score: 34.10  E-value: 3.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalalSHDELLQIIGDPSAVREA 138
Cdd:cd22411   6 IFKQFHKNIIGKGGATIKKIREETNTRIDLPEEN--------SDSDVITITGKKEDVEKA 57
KH-I_FUBP2_rpt3 cd22485
third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein ...
 79-146 3.88e-03

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; 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. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.


Pssm-ID: 411913  Cd Length: 68  Bit Score: 34.16  E-value: 3.88e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 45752620  79 VPSDQIGYLIGKGGPIIQTLRNDTNAQIRVRNDNlpmcalALSHDELLQIIGDPSAVREALYQVAFLL 146
Cdd:cd22485   7 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD------GTGPEKIAHIMGPPDRCEHAARIINDLL 68
 
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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