NCBI Conserved Domain Search

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: 112.33 E-value: 7.36e-30

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 149 LCRMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISSTDQIPPCAFPGDVVIQMNGKFSSVKKALLLVTNCLQ 221
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCASPDDRVVQISGEAQAVKKALELVSSRLR 73

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: 106.15 E-value: 9.57e-28

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 275 EVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLERRHSLAQDGVM 343
Cdd:cd22459   1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSSEAPEAPVSPAQEALL 69

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; 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. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 80.76 E-value: 7.09e-19

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLIEAFI 66

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: 75.35 E-value: 7.16e-17

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 361 VARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRLR 433
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCASPDDRVVQISGEAQAVKKALELVSSRLR 73

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: 67.25 E-value: 3.96e-14

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15217969  21 FRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDdiPVP-SEERVVLIiapSGKKKDESNVC 83
Cdd:cd22459   4 FRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVED--GVPgTEERVITI---SSSEAPEAPVS 62

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: 62.68 E-value: 1.87e-12

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 15217969   279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:pfam00013   3 EILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTIT 50

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: 61.55 E-value: 3.99e-12

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISA-RENLER 333
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGtPEAVEK 57

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: 61.40 E-value: 6.04e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSdPTHD----SEERIIVISAREnlerrhslaqDGVMRVHNRIVE 351
Cdd:cd22435   2 CSLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLS-KNNDfypgTTERVCLIQGEV----------EAVNAVLDFILE 70

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: 59.64 E-value: 2.41e-11

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISAREN 330
Cdd:cd22434   9 PKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQD 56

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 57.31 E-value: 1.38e-10

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969    279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPthDSEERIIVISA-RENLER 333
Cdd:smart00322   6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--GSEERVVEITGpPENVEK 59

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; 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. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 56.87 E-value: 1.96e-10

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:cd22462   2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLIS 49

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: 55.75 E-value: 4.92e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969   361 VARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDqatkyESQHDEIVQVIGNLKTVQDALFQIL 429
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSE-----SEGNERIVTITGTPEAVEAAKALIE 64

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: 53.82 E-value: 2.07e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15217969    22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDiPVPSEERVVLIIAP 72
Cdd:pfam00013   3 EILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPS-ESEGNERIVTITGT 52

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: 52.67 E-value: 5.96e-09

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15217969   551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHA 614
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

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: 52.62 E-value: 6.17e-09

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 278 FRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSD-----PTHDSEERIIVIS 326
Cdd:cd22460   2 ARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPeeelpPCASPDDRVVQIS 55

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: 52.27 E-value: 8.11e-09

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKV-SDPTHDSEERIIVIS 326
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVaSEMLPNSTERAVTIS 53

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 51.14 E-value: 2.23e-08

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969     17 ESVHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDipvPSEERVVLIIAP 72
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP---GSEERVVEITGP 53

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: 50.37 E-value: 3.29e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRvIDDIPVPSEERVVLIIAP 72
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQ-IPKEGEGSGERVVTITGT 51

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: 49.54 E-value: 6.73e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 552 EIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHA 614
Cdd:cd22439   5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLAQYLINA 67

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: 49.56 E-value: 7.04e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15217969 361 VARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAK--DQATkyesqhDEIVQVIGNLKTVQDALFQIL 429
Cdd:cd22433   3 ELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSEccPRST------DRVVQIGGKPDKVVECIREIL 67

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: 8.63e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESqhDEIVQVIGNLKTVQDALFQILCRL 432
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSS--ERIVTITGSFDQVVKAVALILEKL 69

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: 49.46 E-value: 9.00e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969  19 VHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVI---DDIPvPSEERVVLI 69
Cdd:cd22435   2 CSLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSknnDFYP-GTTERVCLI 54

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: 48.75 E-value: 1.30e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSE---ERIIVIS 326
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPgssERIVTIT 52

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: 48.82 E-value: 1.44e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969   150 CRMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRIsstdqIPPCAFPGDVVIQMNGKFSSVKKALLLVTN 218
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQI-----PPSESEGNERIVTITGTPEAVEAAKALIEE 65

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: 48.79 E-value: 1.48e-07

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPThdSEERIIVIS 326
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINISDGS--CPERIVTVT 47

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: 48.42 E-value: 2.11e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969  18 SVHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd02396   1 PITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTERAVTI 52

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: 47.98 E-value: 2.54e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 150 CRMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISSTDQIPPCAFpgDVVIQMNGKFSSVKKALLLVTN 218
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSS--ERIVTITGSFDQVVKAVALILE 67

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: 47.68 E-value: 2.68e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLL 612
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELI 62

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: 47.61 E-value: 3.88e-07

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:cd22439   9 PNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTIT 52

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: 47.71 E-value: 4.21e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  19 VHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTERAVTV 52

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: 46.79 E-value: 6.40e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDipvPSEERVVLIIA 71
Cdd:cd22432   5 RLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS---SGPERILTISA 51

third 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 and flowering locus K homology domain protein (FLK). 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. The model corresponds to the KH3 domain of PEPPER and FLK.

Pssm-ID: 411889 Cd Length: 69 Bit Score: 46.39 E-value: 9.09e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 555 IPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd22461   8 IPLSYADAIIGTAGANISYIRRTSGATITIQETRGAPGEMTVEIHGTQSQVQTAQQLIQNFM 69

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: 46.70 E-value: 9.64e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969  14 TAAESVHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd22519   1 TSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTERAVTI 56

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: 46.55 E-value: 9.78e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVS-DPTHDSEERIIVIS 326
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAgDLLPNSTERAVTVS 53

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: 46.64 E-value: 9.91e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 552 EIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHA 614
Cdd:cd22522  12 ELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGSPANISLAQYLINA 74

second 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 second one.

Pssm-ID: 411857 [Multi-domain] Cd Length: 82 Bit Score: 46.17 E-value: 1.56e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 270 PVVEEevafrLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPT--HDSEERIIVIS-ARENLERRHSLAQDGV 342
Cdd:cd22429   1 IITEE-----LHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESddTLDLVRLITITgTKKEVDAAKSLILEKV 71

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: 45.31 E-value: 1.98e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15217969 364 LLVHSPYIGRLLGKGGHLISEMRRATGASIRVfAKDQATKYESqhDEIVQVIGNLKTVQDALFQI 428
Cdd:cd22403   4 IRVPSSMVGRIIGKGGQNVRELQRLTGAIIKL-PRDQTPDEGD--EVPVEIIGNFYATQSAQRRI 65

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: 45.31 E-value: 2.49e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 15217969  23 LLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEE 64
Cdd:cd22397   4 IMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQ 45

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: 45.43 E-value: 2.58e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 552 EIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHA 614
Cdd:cd22521   8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINA 70

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: 45.16 E-value: 3.16e-06

                        10        20        30
                ....*....|....*....|....*....|.
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSD 313
Cdd:cd02393  11 PPDKIGDVIGPGGKTIRAIIEETGAKIDIED 41

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: 45.00 E-value: 3.31e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 15217969  18 SVHfRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPS 62
Cdd:cd22481   2 AVQ-EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT 45

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: 44.90 E-value: 3.54e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRV--IDDIPVPSEERVVLI 69
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKIspKDQLLPGSSERIVTI 51

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: 44.21 E-value: 4.55e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKyesqhDEIVQVIGNLKTVQDALFQIL 429
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG-----ERVVTITGTPEAVEKAKELIE 63

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: 44.15 E-value: 5.12e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969  26 PATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDI-PVPSEERVVLIIAP 72
Cdd:cd22403   7 PSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQtPDEGDEVPVEIIGN 54

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: 44.16 E-value: 5.34e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDP-THDSEERIIVIS 326
Cdd:cd22402   4 YLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPAdSPDAPERKVTIT 52

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 44.21 E-value: 5.83e-06

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969    360 VVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfakdqatKYESQHDEIVQVIGNLKTVQDALFQIL 429
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI-------PGPGSEERVVEITGPPENVEKAAELIL 65

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: 44.39 E-value: 7.17e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVS-DPTHDSEERIIVISA 327
Cdd:cd22519   6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAgDMLPNSTERAVTISG 58

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: 43.76 E-value: 7.56e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHD--SEERIIVIS 326
Cdd:cd22436   4 KILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESinLQERVVTVT 53

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: 44.34 E-value: 8.14e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969  13 ATAAESVHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd22518   1 AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI 57

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: 44.13 E-value: 8.55e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15217969  23 LLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPS 62
Cdd:cd22483   9 ILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLPT 48

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: 43.60 E-value: 8.81e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 282 CPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDS--EERIIVISARENLER 333
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDEtgERMFTITGTPEANDR 58

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: 43.44 E-value: 9.76e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969 277 AFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSD---PThdSEERIIVI 325
Cdd:cd22456   1 PIRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKeflPL--STERILEV 50

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: 43.32 E-value: 1.11e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPThdSEERIIVISA-RENL 331
Cdd:cd22432   5 RLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDSS--GPERILTISAdRETV 56

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: 43.42 E-value: 1.14e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969  21 FRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAAEKAITI 50

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: 43.39 E-value: 1.22e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIIAP 72
Cdd:cd22402   4 YLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADSPDAPERKVTITGP 54

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: 43.46 E-value: 1.37e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDptHDSEERIIVISAREN 330
Cdd:cd22515   2 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTN 54

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: 43.03 E-value: 1.61e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969 278 FRLLCPADKVGSLIGKGGAVVRALQNESGASIKVS-DPTHDSEERIIVI 325
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHrKENAGAAEKAITI 50

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 43.04 E-value: 1.64e-05

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 15217969 285 DKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERI 322
Cdd:cd22430   9 SLVGAVIGRGGSKIRELEESTGSKIKIIKGGQEAEVKI 46

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: 42.85 E-value: 1.76e-05

                        10        20
                ....*....|....*....|....*..
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIRVIDD 57
Cdd:cd02393  16 GDVIGPGGKTIRAIIEETGAKIDIEDD 42

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: 2.00e-05

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 15217969 360 VVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRV 395
Cdd:cd22459   2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV 37

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: 42.69 E-value: 2.01e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969 275 EVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISAR-ENLER 333
Cdd:cd22454   3 QTTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSpDNVAA 62

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: 42.61 E-value: 2.14e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKV-SDPTHDSEERIIV 324
Cdd:cd22403   7 PSSMVGRIIGKGGQNVRELQRLTGAIIKLpRDQTPDEGDEVPV 49

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: 42.56 E-value: 2.19e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 285 DKVGSLIGKGGAVVRALQNESGASIKVSDP-THDSEERII-----VISARENLE 332
Cdd:cd02394  11 KFHGHIIGKGGANIKRIREESGVSIRIPDDeANSDEIRIEgspegVKKAKAEIL 64

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: 42.42 E-value: 2.67e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15217969 359 AVVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfAKDQATkYESQHDEIVQVIGNLKTVQDALFQILCRL 432
Cdd:cd22513   1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQL-SRAQEF-FPGTTDRVLLVSGSLNEVLTALNLILEKL 72

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: 42.80 E-value: 2.85e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVS-DPTHDSEERIIVISA 327
Cdd:cd22518   7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAgDMLPNSTERAITIAG 59

sixth 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 sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 42.44 E-value: 2.98e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 280 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDpTHDSEERIIVISARENLER 333
Cdd:cd22451   5 IDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPK-KDDPSGKIRITGARDGVEA 57

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: 41.86 E-value: 3.58e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 287 VGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS-ARENLER 333
Cdd:cd22396  12 VGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTgTPDAIET 59

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: 41.83 E-value: 3.84e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  21 FRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRV--IDDIPVPSEERVVLI 69
Cdd:cd22401   2 LKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITIssLQDLTSYNPERTITI 52

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: 41.67 E-value: 4.29e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15217969 287 VGSLIGKGGAVVRALQNESGASIKVSdPTHDSEERIIVIS 326
Cdd:cd22458  12 CGRLIGAKGKNIKALSEKSGASIRLI-PISNSSQQTIHLS 50

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

Pssm-ID: 411924 Cd Length: 76 Bit Score: 41.93 E-value: 4.53e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969 274 EEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDP-THDSEERIIVIS 326
Cdd:cd22496   1 EQETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPeTPDSKVRMVIIT 54

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: 41.83 E-value: 5.06e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969 278 FRLLCPADKVGSLIGKGGAVVRALQNESGASIKVS---DPTHDSEERIIVI 325
Cdd:cd22401   2 LKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISslqDLTSYNPERTITI 52

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: 41.51 E-value: 5.07e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLII 70
Cdd:cd22456   3 RLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLSTERILEVQ 51

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: 41.54 E-value: 5.29e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLL 612
Cdd:cd22434   4 TQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNAQYLL 65

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: 41.55 E-value: 5.60e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIRVIDDIP-VPSEERVVLI 69
Cdd:cd22428  17 GLIIGRQGATIKQIQKETGARIDFKDEGSgGELPERVLLI 56

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: 41.47 E-value: 5.74e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANV-VVHDPKAGTTEGLVVVSGTSDQAHFAQ 609
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIkIAPADSPDAPERKVTITGPPEAQWKAQ 62

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: 41.64 E-value: 6.20e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 280 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISA 327
Cdd:cd22522  13 LTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITG 60

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: 41.02 E-value: 8.49e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSD-----P-THDseeRIIVISA-RENLERRHSLAQ 339
Cdd:cd09031   8 PENLVGAILGKGGKTLVEIQELTGARIQISKkgefvPgTRN---RKVTITGtPAAVQAAQYLIE 68

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: 40.78 E-value: 1.00e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASI--KVSDPTHDSEERIIVIS 326
Cdd:cd22428  12 PREAVGLIIGRQGATIKQIQKETGARIdfKDEGSGGELPERVLLIQ 57

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: 40.70 E-value: 1.01e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKV-SDPTHDSEERIIVIS 326
Cdd:cd22433   5 RLLVHQSQAGCIIGRAGFKIKELREKTGATIKVySECCPRSTDRVVQIG 53

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: 40.64 E-value: 1.11e-04

                        10        20
                ....*....|....*....|....*....
gi 15217969  26 PATRTGAIIGKGGSVIRHLQSVTGSKIRV 54
Cdd:cd09031   8 PENLVGAILGKGGKTLVEIQELTGARIQI 36

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: 40.65 E-value: 1.11e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969 548 SANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHA 614
Cdd:cd22523   1 TSSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLITT 67

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: 40.86 E-value: 1.12e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDptHDSEERIIVISA 327
Cdd:cd22516   9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITG 58

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 40.35 E-value: 1.15e-04

                        10        20
                ....*....|....*....|....*..
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIRVIDD 57
Cdd:cd22430  12 GAVIGRGGSKIRELEESTGSKIKIIKG 38

third 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 third one.

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 40.83 E-value: 1.19e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969  16 AESVHfrLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIIAP 72
Cdd:cd22498   4 SETVH--LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGPDAKLRMVIITGP 58

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: 40.32 E-value: 1.27e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISArenlerrhslAQDGVMRVHNRIVEI 352
Cdd:cd22398   7 PRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITG----------PPDQVQHAARMIQEL 66

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: 40.81 E-value: 1.30e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15217969 280 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:cd22521   9 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTIT 55

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: 40.14 E-value: 1.31e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969  25 CPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIIAPS 73
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDETGERMFTITGTP 53

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: 40.38 E-value: 1.34e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 151 RMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISSTDqippCAfpgDVVIQMNGKFSSVKKALLLVTNCLQE 222
Cdd:cd22515   5 RLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN----CP---ERIITLAGPTNAIFKAFAMIIDKLEE 69

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: 40.40 E-value: 1.36e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPThdSEERIIVIS 326
Cdd:cd22517   2 LTLRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGS--CPERITTIT 50

second 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 second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 40.78 E-value: 1.37e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESQHDEIVQviGNLKTVQDALFQILCRLREA 435
Cdd:cd22494   3 KILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDLTIYNPERTITVK--GSIEACSSAEVEIMKKLREA 73

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: 40.25 E-value: 1.40e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTteGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd02394   4 TTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANS--DEIRIEGSPEGVKKAKAEILELV 67

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: 40.33 E-value: 1.62e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15217969 360 VVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfAKDqatKYESQHDEIVQVIGNLKTVQDALFQILCRLRE 434
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQV-ASE---MLPNSTERAVTISGSPEAITKCVEQICCVMLE 72

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 39.97 E-value: 1.69e-04

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969    547 TSANVEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVhdPKAGTTEGLVVVSGTSDQAHFAQSLL 612
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI--PGPGSEERVVEITGPPENVEKAAELI 64

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; 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. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 39.93 E-value: 1.98e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIdDIPVPSEERVVLI 69
Cdd:cd22462   2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVL-KPDSATGERIVLI 48

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 39.89 E-value: 2.15e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15217969 552 EIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLINALI 68

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: 2.17e-04

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSdPTHDSEE 320
Cdd:cd22395   7 PSELVGRLIGKQGRNVKQLKQKSGAKIYIK-PHPYTQN 43

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: 39.73 E-value: 2.24e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 276 VAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDpTHD----SEERIIVISAREN 330
Cdd:cd22513   2 VVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSR-AQEffpgTTDRVLLVSGSLN 59

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: 39.59 E-value: 2.27e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 151 RMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISstdqiPPCAFPGDVVIQMNGKFSSVKKALLLV 216
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIP-----KEGEGSGERVVTITGTPEAVEKAKELI 62

fourth 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 fourth one.

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 39.51 E-value: 2.42e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVS-DPTHDSEERIIVI 325
Cdd:cd22399   7 PANKCGLVIGKGGETIRQINQQSGAHVELDrNPPPNPNEKLFII 50

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: 39.13 E-value: 3.57e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESqhDEIVQVIGNLKTVQDALFQILCRLRE 434
Cdd:cd22401   3 KILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYNP--ERTITIKGSLEAMSEAESLISEKLRE 72

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; 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 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 38.95 E-value: 4.34e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANV-VVHD-PKAGTTEGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd22463   4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVaIVQDrYPLEETQKILRISGTEEQLKRAQSLVEGLI 71

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; 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 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 38.95 E-value: 4.43e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  26 PATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDipVPSEERVVLIIAPSGKK 76
Cdd:cd22463   9 PEAVVGLIIGKSGNTIKQISERSGAFVAIVQD--RYPLEETQKILRISGTE 57

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 43.11 E-value: 4.75e-04

                         10        20        30
                 ....*....|....*....|....*....|.
gi 15217969  283 PADKVGSLIGKGGAVVRALQNESGASIKVSD 313
Cdd:PRK11824 561 PPDKIRDVIGPGGKTIREITEETGAKIDIED 591

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: 38.34 E-value: 5.35e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIrvidDIPVPSEERVVLIIapSGKKKD 78
Cdd:cd22411  12 KNIIGKGGATIKKIREETNTRI----DLPEENSDSDVITI--TGKKED 53

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: 38.56 E-value: 5.70e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 15217969  26 PATRTGAIIGKGGSVIRHLQSVTGSKIRVID--DIPVPSEERVVLIIAP 72
Cdd:cd22514   8 PDEHIGAILGRGGRTINEIQQHSGARIKISDrgDFVSGTRNRKVTITGP 56

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

Pssm-ID: 411927 Cd Length: 76 Bit Score: 38.47 E-value: 7.15e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKV-SDPTHDSEERIIV 324
Cdd:cd22499   9 PASAAGRVIGKGGKTVNELQNLTAAEVVVpRDQTPDENDQVIV 51

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: 38.27 E-value: 7.32e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 370 YIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYesqhdEIVQVIGNLKTVQDAL 425
Cdd:cd22395  10 LVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNF-----QICSIEGTQQQIDKAL 60

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: 38.32 E-value: 7.58e-04

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVV 67
Cdd:cd02394  14 GHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIE 50

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: 7.85e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVISARENLE 332
Cdd:cd22417   8 DPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDDEITITGYEKNAE 57

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

Pssm-ID: 411918 Cd Length: 76 Bit Score: 38.53 E-value: 7.96e-04

                        10        20        30
                ....*....|....*....|....*....|....
gi 15217969  21 FRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRV 54
Cdd:cd22490   2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDV 35

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: 8.84e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIrVIDDiPVP-SEERVVLI 69
Cdd:cd22434  14 GSIIGKGGQRIRQIRHESGASI-KIDE-PLPgSEDRIITI 51

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: 38.29 E-value: 9.13e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfAKDQATkYESQHDEIVQVIGNLKTVQDALFQILCRLR 433
Cdd:cd22435   5 KLLVPNYAAGSIIGKGGQTIAQLQKETGARIKL-SKNNDF-YPGTTERVCLIQGEVEAVNAVLDFILEKIR 73

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: 37.98 E-value: 9.56e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVI---DDIPVPseERVVLIIAP 72
Cdd:cd22436   4 KILVPNSTAGMIIGKGGATIKAIMEQSGARVQISqkpESINLQ--ERVVTVTGE 55

third 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 third one.

Pssm-ID: 411925 Cd Length: 77 Bit Score: 38.15 E-value: 1.01e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 273 EEEVAFrLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDP-THDSEERIIVISA 327
Cdd:cd22497   1 EQEVVY-LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAeGPDVSERMVIITG 55

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: 38.01 E-value: 1.03e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRvIDDIPVPseERVVLIIAP 72
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARIN-ISDGSCP--ERIVTVTGT 49

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: 37.95 E-value: 1.07e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 15217969 280 LLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTIT 52

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: 1.07e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 364 LLVHSPYIGRLLGKGGHLISEMRRATGASIRVfaKDQATKYESQHDEIVQVIGNLKTVQDALFQILCRL 432
Cdd:cd22514   5 IGVPDEHIGAILGRGGRTINEIQQHSGARIKI--SDRGDFVSGTRNRKVTITGPQDAVQMAQYLLEQKL 71

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: 38.04 E-value: 1.08e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVIS 326
Cdd:cd22455   4 RALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVS 51

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411817 [Multi-domain] Cd Length: 70 Bit Score: 37.95 E-value: 1.17e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVsdpthDSEERIIVISAREN 330
Cdd:cd22389   2 YVKIPKERIGVLIGKKGETKREIEERTGVKITV-----DSETGEVIIEPEDE 48

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 37.66 E-value: 1.26e-03

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969    151 RMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISSTDqippcafPGDVVIQMNGKFSSVKKALLLVTNCL 220
Cdd:smart00322   6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPENVEKAAELILEIL 68

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: 37.62 E-value: 1.27e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 15217969  30 TGAIIGKGGSVIRHLQSVTGSKIRVIDDiPVPSEERVVLI 69
Cdd:cd22396  12 VGLIIGRGGEQINRLQAESGAKIQIAPD-SGGLPERPCTL 50

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

Pssm-ID: 411924 Cd Length: 76 Bit Score: 37.69 E-value: 1.31e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15217969  17 ESVHfrLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIIA-PSGKKKDESNVC 83
Cdd:cd22496   3 ETVH--VFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGpPEAQFKAQGRIY 68

third 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 third one.

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 38.13 E-value: 1.31e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15217969 274 EEVAFRLLCPADKVGSLIGKGGAVVRALQNESGASIKVSdPTH--DSEERIIVISA 327
Cdd:cd22498   3 ESETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEgpDAKLRMVIITG 57

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: 37.59 E-value: 1.33e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969 553 IVIPQAYLGHVYGENCSNLNYIKQVSGANVVVHDPKAGTTEGLVVVSGTSD 603
Cdd:cd22459   6 LLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSSEA 56

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: 1.35e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 15217969  19 VHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPvPSEERVVLI 69
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVP-GVHDRVLTV 50

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: 37.62 E-value: 1.39e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15217969 151 RMIVRGNQVDYLMSKGGKMIQKIREDSGAivRISSTDQIPPcafpgDVVIQMNGKFSSVKKALLLVTNCLQE 222
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGA--RINISDGSCP-----ERIVTVTGTTDAVFKAFELICRKLEE 66

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: 37.62 E-value: 1.41e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 15217969  31 GAIIGKGGSVIRHLQSVTGSKIRVIDDIPVpSEERVVLIIAP 72
Cdd:cd22398  12 GVVIGKGGEMIKKIQNETGARVQFKPDDGN-SPDRICVITGP 52

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: 37.23 E-value: 1.70e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969  22 RLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIiapSGKKKD 78
Cdd:cd22433   5 RLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCPRSTDRVVQI---GGKPDK 58

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: 37.42 E-value: 1.96e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15217969  18 SVHFRLLCPATRTGAIIGKGGSVIRHLQSVTGSKI---RVIDDIPvPSEERVVLIIAP 72
Cdd:cd22513   1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIqlsRAQEFFP-GTTDRVLLVSGS 57

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; 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 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 37.03 E-value: 2.13e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEE--RIIVISAREN-LERRHSLAQD 340
Cdd:cd22463   9 PEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEEtqKILRISGTEEqLKRAQSLVEG 69

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: 36.79 E-value: 2.28e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 551 VEIVIPQAYLGHVYGENCSNLNYIKQVSGANVVVH---DPKAGTTEGLVVVSGTSDQAHFAQSLLHAFI 616
Cdd:cd09031   3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISkkgEFVPGTRNRKVTITGTPAAVQAAQYLIEQRI 71

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

Pssm-ID: 411923 Cd Length: 77 Bit Score: 37.33 E-value: 2.29e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVFAKDQATKYESQhdEIVQVIGNLKTVQDALFQILCRLREA 435
Cdd:cd22495   3 KILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPE--RTITVKGSIETCAKAEEEIMKKIRES 73

first 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 first one.

Pssm-ID: 411920 Cd Length: 76 Bit Score: 37.10 E-value: 2.31e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15217969  21 FRLLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLIIA-PSG 74
Cdd:cd22492   2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENAGAAEKSITILStPEG 56

first 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 first one.

Pssm-ID: 411920 Cd Length: 76 Bit Score: 37.10 E-value: 2.52e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 278 FRLLCPADKVGSLIGKGGAVVRALQNESGASIKV--SDPTHDSEERIIVISAREN--------LERRHSLAQD 340
Cdd:cd22492   2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVhrKENAGAAEKSITILSTPEGtsaacksiLEIMHKEAQD 74

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: 36.79 E-value: 2.70e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15217969 371 IGRLLGKGGHLISEMRRATGASIRVFAKDQ---ATKyesqhDEIVQVIGNLKTVQDALFQILCRL 432
Cdd:cd09031  12 VGAILGKGGKTLVEIQELTGARIQISKKGEfvpGTR-----NRKVTITGTPAAVQAAQYLIEQRI 71

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: 36.47 E-value: 2.84e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfaKDQATKyesqhDEIVQVIGNLKTVQDAlFQILCR 431
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINI--SDGSCP-----ERIVTVTGTTDAVFKA-FELICR 62

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: 36.86 E-value: 2.98e-03

                        10        20        30
                ....*....|....*....|....*....|....*
gi 15217969 151 RMIVRGNQVDYLMSKGGKMIQKIREDSGAIVRISS 185
Cdd:cd02396   5 RLLVPASQCGSLIGKGGSKIKEIRESTGASVQVAS 39

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: 36.45 E-value: 2.99e-03

                        10        20
                ....*....|....*....|....*...
gi 15217969 280 LLCPADKVGSLIGKGGAVVRALQNESGA 307
Cdd:cd22397   4 IMIPGNKVGLIIGKGGETIKQLQERAGV 31

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 36.42 E-value: 3.18e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVI 325
Cdd:cd22404   8 PNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITI 50

fourth 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 fourth one.

Pssm-ID: 411917 [Multi-domain] Cd Length: 69 Bit Score: 36.45 E-value: 3.61e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVS---DPTHDSEERIIVI 325
Cdd:cd22489   7 PADKCGLVIGKGGENIKSINQQSGAHVELQrnpPPNTDPNVRIFTI 52

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: 36.69 E-value: 3.73e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15217969 360 VVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVF------AKDQATKYESQHDEIVQVIGNLKTV 421
Cdd:cd22519   6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAgdmlpnSTERAVTISGTPDAIIQCVKQICVV 73

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: 36.54 E-value: 4.02e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15217969 360 VVARLLVHSPYIGRLLGKGGHLISEMRRATGASIRVF------AKDQATKYESQHDEIVQVIGNLKTV 421
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAgdllpnSTERAVTVSGVPDAIIQCVRQICAV 69

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: 36.24 E-value: 4.45e-03

                        10        20        30
                ....*....|....*....|....*....|.
gi 15217969 283 PADKVGSLIGKGGAVVRALQNESGASIKVSD 313
Cdd:cd22514   8 PDEHIGAILGRGGRTINEIQQHSGARIKISD 38

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.

Pssm-ID: 411931 Cd Length: 83 Bit Score: 36.26 E-value: 5.27e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15217969 279 RLLCPADKVGSLIGKGGAVVRALQNESGASIKVSDPTHDSEERIIVI-----SARENLERRHSLAQD 340
Cdd:cd22503   4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNGERMITIrggteSTRYAVQLINALIQD 70

second 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 second one.

Pssm-ID: 411910 [Multi-domain] Cd Length: 73 Bit Score: 36.04 E-value: 5.31e-03

                        10        20        30
                ....*....|....*....|....*....|....*
gi 15217969  23 LLCPATRTGAIIGKGGSVIRHLQSVTGSKIRVIDD 57
Cdd:cd22482   6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQD 40

fourth 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 fourth one.

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 35.66 E-value: 5.69e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 15217969  26 PATRTGAIIGKGGSVIRHLQSVTGSKIRVIDDIPVPSEERVVLI 69
Cdd:cd22399   7 PANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNEKLFII 50

first 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 first one.

Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 36.23 E-value: 5.74e-03

                        10        20        30
                ....*....|....*....|....*....|
gi 15217969  25 CPATRTGAIIGKGGSVIRHLQSVTGSKIRV 54
Cdd:cd22446  13 VPSSVRGAIIGSRGKNLKSIQDKTGTKIQI 42

ATPase; Provisional

Pssm-ID: 184311 [Multi-domain] Cd Length: 602 Bit Score: 39.05 E-value: 8.21e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15217969  319 EERIIV-ISARENLERRHSLAQDGVMRVHNRIVEIGFE-----PSAAVVArllVHSPYIGRLLGKGGHLISEMRRATGAS 392
Cdd:PRK13764 437 EQTVVVpVEEEEEKSPVWRLAEKEIEREIKRYLPGPVEvevvsDNKAVVY---VPEKDIPKVIGKGGKRIKKIEKKLGID 513

                         90       100
                 ....*....|....*....|...
gi 15217969  393 IRVFAKDQATKYESQHDEIVQVI 415
Cdd:PRK13764 514 IDVRPLDEEPGEEAEEGEEVTVE 536

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: 35.35 E-value: 8.80e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15217969 363 RLLVHSPYIGRLLGKGGHLISEMRRATGASIRVfakdqaTKY-ESQHDEIVQVIGNLKTVQDA 424
Cdd:cd22455   4 RALVSSKEAAVIIGKGGENIARLRATTGVKAGV------SKVvPGVHDRVLTVSGPLEGVAKA 60

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: 34.87 E-value: 9.39e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 15217969 287 VGSLIGKGGAVVRALQNESGASIKVsdPTHDSEERIIVISAR-ENLER 333
Cdd:cd22411  11 HKNIIGKGGATIKKIREETNTRIDL--PEENSDSDVITITGKkEDVEK 56