NCBI Conserved Domain Search

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: 98.45 E-value: 3.31e-25

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269  49 DTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPsdetnafGDGEKVLSPAQDALF 124
Cdd:cd22459   1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSS-------EAPEAPVSPAQEALL 69

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: 93.45 E-value: 2.57e-23

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPKVASDDDEMVQISGELDVAKEALIQITSRLR 443
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: 92.67 E-value: 3.79e-23

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 283 EFFIRLVSPVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITISAREVFEDAYSPTIEAVM 351
Cdd:cd22459   1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSSEAPEAPVSPAQEALL 69

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: 92.30 E-value: 6.03e-23

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLCALNSDELIQISGEVLIVKKALLQIASRL 219
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCASPDDRVVQISGEAQAVKKALELVSSRL 72

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 65.77 E-value: 1.07e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269   148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPlcalnSDELIQISGEVLIVKKALLQI 215
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEG-----NERIVTITGTPEAVEAAKALI 63

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: 63.07 E-value: 1.03e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269   371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlpkvaSDDDEMVQISGELDVAKEALIQI 438
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES-----EGNERIVTITGTPEAVEAAKALI 63

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 58.46 E-value: 5.50e-11

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269    145 KQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRnmplcalNSDELIQISGEVLIVKKALLQIASRL 219
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-------SEERVVEITGPPENVEKAAELILEIL 68

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 54.22 E-value: 1.72e-09

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269    371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlpkvasdDDEMVQISGELDVAKEALIQITSRL 442
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-------EERVVEITGPPENVEKAAELILEIL 68

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: 53.44 E-value: 2.75e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 30685269    51 VFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSD 104
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPE 54

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: 53.05 E-value: 3.51e-09

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 30685269   286 IRLVSPVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITIS 334
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTIT 50

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: 51.94 E-value: 1.23e-08

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITI 99
Cdd:cd22434   9 PKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITI 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: 51.53 E-value: 1.35e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNmplcaLNSDELIQISGEVLIVKKALLQI 215
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE-----GSGERVVTITGTPEAVEKAKELI 62

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: 50.76 E-value: 2.50e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSD 104
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPE 53

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: 50.72 E-value: 2.58e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAipGCDERVITIYSPSDET-NAFG 110
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINISDG--SCPERIVTVTGTTDAVfKAFE 58

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 49.99 E-value: 4.60e-08

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269     48 DDTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEaiPGCDERVITIYSPSDE 105
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG--PGSEERVVEITGPPEN 56

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: 5.94e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPkvASDDDEMVQISGELD 429
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLL--PGSSERIVTITGSFD 56

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: 48.77 E-value: 1.17e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlpkvaSDDDEMVQISGELDVAKEALIQITSR 441
Cdd:cd22439   3 TQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED-----GSTERSVTITGTPEAVSLAQYLINAR 68

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: 48.45 E-value: 1.40e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlpkvaSDDDEMVQISGELDVAKEALIQI 438
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE-----GSGERVVTITGTPEAVEKAKELI 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: 48.03 E-value: 2.27e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRnMPlcalNSDE-LIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEM-LP----NSTErAVTISGSPEAITKCVEQICCVMLE 72

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: 48.08 E-value: 2.36e-07

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 30685269 291 PVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITIS 334
Cdd:cd22434   9 PKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITIT 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: 48.02 E-value: 2.79e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 149 AKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDrnmplCALNS-DELIQISGEVLIVKKALLQIASRL 219
Cdd:cd22433   4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSE-----CCPRStDRVVQIGGKPDKVVECIREILELL 70

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: 47.60 E-value: 3.09e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269 370 FTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlgkenLPKVASDDDEMVQISGE 427
Cdd:cd22459   2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV-----EDGVPGTEERVITISSS 54

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: 47.41 E-value: 4.97e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAipGCDERVITIYSPSD 104
Cdd:cd22516  12 RLLMHGKEVGSIIGKKGETVKKMREESGARINISEG--NCPERIVTITGPTD 61

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: 47.23 E-value: 5.66e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30685269  51 VFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI--GEAIPGC---DERVITI 99
Cdd:cd22460   1 SARLLVASSQAGSLIGKGGAIIKQIREESGASVRIlpEEELPPCaspDDRVVQI 54

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: 46.14 E-value: 1.04e-06

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 30685269 291 PVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITISARE 337
Cdd:cd00105   6 PSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTP 52

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

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 45.68 E-value: 1.36e-06

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRI 182
Cdd:cd22459   2 VVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKV 37

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: 45.73 E-value: 1.45e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLcalnSDELIQISGE 204
Cdd:cd22400   3 RILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGA----AEKAITIYGT 53

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: 45.68 E-value: 1.51e-06

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 30685269 146 QVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRI 182
Cdd:cd22439   1 QTTQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKI 37

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

Pssm-ID: 411943 Cd Length: 70 Bit Score: 45.77 E-value: 1.80e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAipGCDERVITIYSPSD 104
Cdd:cd22515   5 RLLMHGKEVGSIIGKKGESVKKMREESGARINISEG--NCPERIITLAGPTN 54

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: 45.33 E-value: 2.14e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIvKDRNMPlcalnsDELIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINI-SDGSCP------ERIVTVTGTTDAVFKAFELICRKLEE 66

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: 45.34 E-value: 2.20e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLPKVasddDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd22400   3 RILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAA----EKAITIYGTPEGCSSACKQILEIM 68

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: 45.10 E-value: 3.10e-06

                        10        20        30
                ....*....|....*....|....*....|....*
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRI 182
Cdd:cd22522  10 THELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKI 44

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: 44.88 E-value: 3.43e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLpkVASDDDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd09031   2 VIELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEF--VPGTRNRKVTITGTPAAVQAAQYLIEQRI 71

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: 44.55 E-value: 3.82e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIrilgkenlpKVASD-----DDEMVQISGELDVAKEALIQI 438
Cdd:cd22433   5 RLLVHQSQAGCIIGRAGFKIKELREKTGATI---------KVYSEccprsTDRVVQIGGKPDKVVECIREI 66

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: 44.62 E-value: 4.04e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 146 QVTakllVPSDQIGCILGRGGQIVQNIRSETGAQIRIvkDRNMPlcalNSDE-LIQISG 203
Cdd:cd22434   5 QVT----IPKDLAGSIIGKGGQRIRQIRHESGASIKI--DEPLP----GSEDrIITITG 53

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: 44.78 E-value: 5.12e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDrnmpLCALNSDELIQISGEVLIVKKALLQIASRLHENP 223
Cdd:cd22519   6 VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGD----MLPNSTERAVTISGTPDAIIQCVKQICVVMLESP 78

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: 44.28 E-value: 5.41e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 145 KQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKdrnmPLCAlNSDELIQISGEVLIVKKALLQIASRL 219
Cdd:cd22521   3 QTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN----PVEG-STDRQVTITGSAASISLAQYLINARL 72

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: 6.17e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGkENLPkvaSDDDEMVQISGELDVAKEALIQI 438
Cdd:cd22519   7 TLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAG-DMLP---NSTERAVTISGTPDAIIQCVKQI 70

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: 43.77 E-value: 6.79e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlgKENlPKVASDDDEMVQISGELDVAKEALIQI 438
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKL--PRD-QTPDEGDEVPVEIIGNFYATQSAQRRI 65

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: 43.86 E-value: 6.99e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDrnmpLCALNSDELIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd22520   2 VTLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGD----LLPNSTERAVTVSGVPDAIIQCVRQICAVILE 72

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: 43.82 E-value: 7.25e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIrILGKENLPkvaSDDDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd22456   3 RLLIPHSLIGSIIGKGGARIKEIQDGSGARL-VASKEFLP---LSTERILEVQGTPDAIHNATLEIGKTL 68

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: 8.08e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNmplcALNSDE-LIQISGEVLIVKKA 211
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPE----SINLQErVVTVTGEPEANRKA 62

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

Pssm-ID: 411945 Cd Length: 70 Bit Score: 43.86 E-value: 8.45e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30685269  52 FRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAipGCDERVITIYSPSD 104
Cdd:cd22517   4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITISEG--SCPERITTITGSTD 54

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: 43.41 E-value: 1.07e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269  50 TVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITIYSPSD 104
Cdd:cd02396   2 ITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVaSEMLPNSTERAVTISGSPE 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: 43.40 E-value: 1.13e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITI 99
Cdd:cd22396   4 EYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTL 50

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: 43.36 E-value: 1.20e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 30685269  61 IGSVIGRGGDIVKQLRNDTRSKIRIG---EAIPGCDERVITI 99
Cdd:cd22437  10 CGLIIGKGGSTIKELREDSNANIKISpkdQLLPGSSERIVTI 51

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: 42.98 E-value: 1.24e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIV-KDRNMPLCalnSDELIQISGEVLIVKKALLQIASRL 219
Cdd:cd22437   2 RLLVPNSSCGLIIGKGGSTIKELREDSNANIKISpKDQLLPGS---SERIVTITGSFDQVVKAVALILEKL 69

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: 1.35e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269  52 FRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITIY-SPSDETNA 108
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIhRKENAGAAEKAITIYgTPEGCSSA 60

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: 42.83 E-value: 1.42e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNmplcALNSDELIQISGEVLIVKKAL 212
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPH----DETGERMFTITGTPEANDRAL 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: 42.94 E-value: 1.52e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIvKDRNmplcaLNSDElIQISGEVLIVKKALLQI 215
Cdd:cd02394   2 AFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRI-PDDE-----ANSDE-IRIEGSPEGVKKAKAEI 63

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: 43.08 E-value: 1.54e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIvKDRNMPlcalnsDELIQISGEVLIVKKALLQIASRLHEN 222
Cdd:cd22515   2 LTIRLLMHGKEVGSIIGKKGESVKKMREESGARINI-SEGNCP------ERIITLAGPTNAIFKAFAMIIDKLEED 70

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: 42.96 E-value: 1.57e-05

                        10        20        30
                ....*....|....*....|....*....|...
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRI 182
Cdd:cd22523   5 EFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKI 37

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: 43.09 E-value: 1.69e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGkENLPkvaSDDDEMVQISGELDVAKEALIQITS 440
Cdd:cd22520   3 TLRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAG-DLLP---NSTERAVTVSGVPDAIIQCVRQICA 68

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: 42.64 E-value: 1.75e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30685269 369 SFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGkENLPkvaSDDDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd02396   1 PITLRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVAS-EMLP---NSTERAVTISGSPEAITKCVEQICCVM 70

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: 42.67 E-value: 2.01e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDE-TNAFGDGEKVL 116
Cdd:cd22455   4 RALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGvAKAFGLIARTL 68

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: 42.26 E-value: 2.18e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRAtiKVDSSRTEGN---DCLITI 333
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGA--RIDIHRKENAgaaEKAITI 50

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 42.28 E-value: 2.28e-05

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 30685269    291 PVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLIT 332
Cdd:smart00322  10 PADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEIT 51

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: 41.84 E-value: 3.02e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPlcalNSDE-LIQISGEVLIVKKALLQI 215
Cdd:cd22403   1 RTEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPD----EGDEvPVEIIGNFYATQSAQRRI 65

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: 41.83 E-value: 3.81e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 30685269 291 PVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITIS 334
Cdd:cd22439   9 PNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTIT 52

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: 41.96 E-value: 3.84e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGkenlpKVASDDDEMVQISGELDVAKEALIQITSRLRA 444
Cdd:cd22521   6 SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIAN-----PVEGSTDRQVTITGSAASISLAQYLINARLSS 74

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: 41.47 E-value: 4.57e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 372 TRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGkenlPKVASdDDEMVQISGELDVAKEA 434
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLK----PDSAT-GERIVLISGTPDQARHA 58

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: 41.41 E-value: 4.70e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRI---GEAIPGCDERVITI 99
Cdd:cd09031   8 PENLVGAILGKGGKTLVEIQELTGARIQIskkGEFVPGTRNRKVTI 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: 41.65 E-value: 4.87e-05

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKD 185
Cdd:cd22518   7 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGD 45

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: 41.55 E-value: 4.87e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30685269  52 FRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITIYSPSD 104
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVaGDLLPNSTERAVTVSGVPD 57

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: 41.31 E-value: 6.73e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30685269  52 FRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITI 99
Cdd:cd22519   8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVaGDMLPNSTERAVTI 56

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: 40.92 E-value: 7.14e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRIGeaipgcDERVITIYSPSDE 105
Cdd:cd02393  11 PPDKIGDVIGPGGKTIRAIIEETGAKIDIE------DDGTVTIFATDKE 53

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

Pssm-ID: 411944 Cd Length: 77 Bit Score: 41.24 E-value: 7.64e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIvKDRNMPlcalnsDELIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd22516   9 LTIRLLMHGKEVGSIIGKKGETVKKMREESGARINI-SEGNCP------ERIVTITGPTDAIFKAFAMIAYKFEE 76

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

Pssm-ID: 411941 [Multi-domain] Cd Length: 73 Bit Score: 40.88 E-value: 9.23e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 146 QVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIvkDRNMPLCALNSDELIQISGEVLIVKKALLQIASRLH 220
Cdd:cd22513   1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQL--SRAQEFFPGTTDRVLLVSGSLNEVLTALNLILEKLL 73

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: 40.88 E-value: 9.30e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 30685269  47 RDDTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITI 99
Cdd:cd22518   4 RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVaGDMLPNSTERAITI 57

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: 40.87 E-value: 1.04e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 30685269 364 DSGLVSFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRI 405
Cdd:cd22522   3 DASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKI 44

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: 1.14e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCD--ERVITI 99
Cdd:cd22428  12 PREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGElpERVLLI 56

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: 40.31 E-value: 1.17e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 149 AKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPlcalnSDELIQISG 203
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSAT-----GERIVLISG 50

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: 40.27 E-value: 1.28e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 30685269 291 PVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITI 333
Cdd:cd22404   8 PNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITI 50

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: 40.48 E-value: 1.33e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENLpkVASDDDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd22514   2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGDF--VSGTRNRKVTITGPQDAVQMAQYLLEQKL 71

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: 40.26 E-value: 1.36e-04

                        10        20        30
                ....*....|....*....|....*....|..
gi 30685269 374 LLVPSSRIGCILGKGGAIITEMRRMTKANIRI 405
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKI 37

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: 40.21 E-value: 1.38e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 292 VENIA--SVIGKGGALINQLRQETRATIKVDSSR-----TEGNDCLITISAREVFE 340
Cdd:cd22435   8 VPNYAagSIIGKGGQTIAQLQKETGARIKLSKNNdfypgTTERVCLIQGEVEAVNA 63

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: 40.21 E-value: 1.60e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30685269  52 FRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI---GEAIPGCDERVITI 99
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLsknNDFYPGTTERVCLI 54

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

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 40.48 E-value: 1.61e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 145 KQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIV-KDRNMPLCALNSDELIQ--ISGEVLIVKKALLQIAS 217
Cdd:cd22447   2 PKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPpRDADAAPADEDDDTMVEvtITGDEFNVQHAKQRIEE 77

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: 39.87 E-value: 1.64e-04

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVK 184
Cdd:cd09031   1 TVIELEVPENLVGAILGKGGKTLVEIQELTGARIQISK 38

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: 1.64e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDCLITIS 334
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLIS 49

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: 40.07 E-value: 1.84e-04

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKEN 410
Cdd:cd22490   3 RLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKEN 40

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

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 40.01 E-value: 1.85e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 143 GEKQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRiVKDRNMPlcALNSDELIQISGEVLIVKKALLQI 215
Cdd:cd22428   1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARID-FKDEGSG--GELPERVLLIQGNPVQAQRAEEAI 70

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: 39.61 E-value: 2.10e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSD 104
Cdd:cd22454  11 PNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSPD 58

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: 39.83 E-value: 2.32e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRiLGKEN--LPKVAsddDEMVQISGELDVAKEALIQITSRLR 443
Cdd:cd22435   5 KLLVPNYAAGSIIGKGGQTIAQLQKETGARIK-LSKNNdfYPGTT---ERVCLIQGEVEAVNAVLDFILEKIR 73

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: 39.52 E-value: 2.67e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30685269  51 VFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIG---EAIPGCDERVITIY 100
Cdd:cd22401   1 PLKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISslqDLTSYNPERTITIK 53

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: 39.48 E-value: 2.78e-04

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30685269 296 ASVIGKGGALINQLRQETRATIKVDSSrtEGNDCLITIS 334
Cdd:cd02394  14 GHIIGKGGANIKRIREESGVSIRIPDD--EANSDEIRIE 50

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: 39.89 E-value: 2.91e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPlcaLNSDELIQISGEVLIVKKA 211
Cdd:cd22483   8 EILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLP---TGADKPLRITGDPFKVQQA 66

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

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 39.71 E-value: 3.02e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30685269 374 LLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKEN-LPKVASDDDEMVQIS 425
Cdd:cd22447   8 VPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDAdAAPADEDDDTMVEVT 60

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: 39.16 E-value: 3.23e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlgkenLPKVASDDDE-MVQISGELD 429
Cdd:cd22402   2 TTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKI-----APADSPDAPErKVTITGPPE 56

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: 38.97 E-value: 3.55e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNmplcalNSDELIQISGEVLIVKKALLQI 215
Cdd:cd22458   1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISN------SSQQTIHLSGTDKQIALAISSI 63

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: 38.94 E-value: 3.62e-04

                        10        20        30
                ....*....|....*....|....*....|....*
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRI 182
Cdd:cd22514   2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKI 36

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: 39.06 E-value: 3.76e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNM-PlcaLNSDELIQISGEVLIVKKALLQIASRLH 220
Cdd:cd22435   5 KLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFyP---GTTERVCLIQGEVEAVNAVLDFILEKIR 73

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: 38.74 E-value: 3.93e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRATIKVDSSRTEGNDC---LITIS 334
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSserIVTIT 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: 38.43 E-value: 5.73e-04

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30685269  53 RYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIG-EAIPGCDERVITIY 100
Cdd:cd22456   3 RLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASkEFLPLSTERILEVQ 51

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: 38.57 E-value: 6.55e-04

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRILG 407
Cdd:cd22518   8 TLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG 44

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: 38.40 E-value: 7.35e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRATIKVDS----SRTEgndCLITIS 334
Cdd:cd02396   4 LRLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASemlpNSTE---RAVTIS 53

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: 38.00 E-value: 9.69e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269  49 DTVFRYLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRI-GEAIPGCDERVITIY-SPSDETNAFGD 111
Cdd:cd22433   1 DCELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVySECCPRSTDRVVQIGgKPDKVVECIRE 65

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: 37.57 E-value: 1.06e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 30685269  54 YLCPVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITI 99
Cdd:cd22523   6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTI 51

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: 37.87 E-value: 1.12e-03

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKEN 410
Cdd:cd22492   3 RLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKEN 40

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: 37.44 E-value: 1.19e-03

                        10        20        30
                ....*....|....*....|....*....|
gi 30685269 376 VPSSRIGCILGKGGAIITEMRRMTKANIRI 405
Cdd:cd22457   5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISI 34

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: 37.68 E-value: 1.21e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30685269 371 TTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlgKENLPKVasdDDEMVQISGELDVAKEA--LIQ 437
Cdd:cd22434   3 TTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKI--DEPLPGS---EDRIITITGTQDQIQNAqyLLQ 66

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: 37.58 E-value: 1.22e-03

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRN 187
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKG 41

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: 37.59 E-value: 1.24e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 150 KLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPLCalNSDELIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd22401   3 KILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSY--NPERTITIKGSLEAMSEAESLISEKLRE 72

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: 37.84 E-value: 1.41e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 30685269 279 PPATeffIRLVSPVENIASVIGKGGALINQLRQETRATIKV 319
Cdd:cd22519   4 PPVT---LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQV 41

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: 37.21 E-value: 1.44e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKenlPKVASDDDEMVQISGELDVAKEA 434
Cdd:cd22436   4 KILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQK---PESINLQERVVTVTGEPEANRKA 62

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: 37.24 E-value: 1.68e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 30685269  57 PVKK--IGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSD 104
Cdd:cd22398   5 PVPRfaVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPD 54

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

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 37.07 E-value: 1.96e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIVKD 185
Cdd:cd02393  10 IPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDD 42

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: 36.93 E-value: 2.11e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 30685269 280 PATEFFIRLVSPVENIASVIGKGGALINQLRQETRATIKVD 320
Cdd:cd22428   1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFK 41

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: 37.03 E-value: 2.16e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 369 SFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRI-LGKENLPKVAsddDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd22513   1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLsRAQEFFPGTT---DRVLLVSGSLNEVLTALNLILEKL 72

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: 36.77 E-value: 2.22e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 30685269 287 RLVSPVENIASVIGKGGALINQLRQETRATIKVDSSrtEGNDCLITISA 335
Cdd:cd22432   5 RLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS--SGPERILTISA 51

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: 36.99 E-value: 2.46e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30685269 374 LLVPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlPKVAsddDEMVQISGELDVAKEALIQITSRLRANVF 447
Cdd:cd22497   7 LFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEG-PDVS---ERMVIITGPPEAQFKAQGRIFGKLKEENF 76

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: 36.83 E-value: 2.46e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIvkDRNMPlcaLNSDELIQIsgevLIVKKALLQI 215
Cdd:cd22489   6 IPADKCGLVIGKGGENIKSINQQSGAHVEL--QRNPP---PNTDPNVRI----FTIRGVPQQI 59

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: 36.80 E-value: 2.55e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRI 405
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEI 36

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: 37.00 E-value: 2.93e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 145 KQVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVK--DRNMPLCALNsDELIQISGE-----VLIVKKALLQIAS 217
Cdd:cd22446   5 PKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKrnEEGNYDEDDD-DETVEISIEgdaegVELAKKEIEAIVK 83

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: 36.54 E-value: 3.07e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30685269 376 VPSSRIGCILGKGGAIITEMRRMTKANIRILGKENlpkVASDDDEMVQISGELD---VAKEALIQI 438
Cdd:cd22428  11 VPREAVGLIIGRQGATIKQIQKETGARIDFKDEGS---GGELPERVLLIQGNPVqaqRAEEAIHQI 73

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

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 36.46 E-value: 3.28e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIVKD 185
Cdd:cd22396   7 VPDKMVGLIIGRGGEQINRLQAESGAKIQIAPD 39

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: 36.54 E-value: 3.35e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 30685269 146 QVTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMplcALNSDELIQISG 203
Cdd:cd22429   1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDD---TLDLVRLITITG 55

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: 36.25 E-value: 4.10e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 30685269 279 PPATeffIRLVSPVENIASVIGKGGALINQLRQETRATIKV 319
Cdd:cd22518   5 PPVT---LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV 42

first 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 first one.

Pssm-ID: 411908 [Multi-domain] Cd Length: 71 Bit Score: 36.03 E-value: 4.53e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRN-MP 189
Cdd:cd22480   1 ITEEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGgMP 44

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: 35.87 E-value: 4.67e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNmplcalNSDE---LIQISGevlivKKALLQIASRL 219
Cdd:cd22463   8 IPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRY------PLEEtqkILRISG-----TEEQLKRAQSL 66

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: 35.92 E-value: 4.79e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 30685269 291 PVENIASVIGKGGALINQLRQETRATIKVDssrtegNDCLITISA 335
Cdd:cd02393  11 PPDKIGDVIGPGGKTIRAIIEETGAKIDIE------DDGTVTIFA 49

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: 35.77 E-value: 5.03e-03

                        10        20        30
                ....*....|....*....|....*....|....
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRATIKV 319
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQV 37

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: 35.73 E-value: 5.26e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKdrNMPLCalnSDELIQISGEVLIVKKALLQIASRLHE 221
Cdd:cd22455   1 LTLRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSK--VVPGV---HDRVLTVSGPLEGVAKAFGLIARTLNE 70

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 39.26 E-value: 6.26e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 30685269  291 PVENIASVIGKGGALINQLRQETRATIKVDssrtegNDCLITISA 335
Cdd:PRK11824 561 PPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAA 599

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: 35.85 E-value: 6.45e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30685269 368 VSFTTRLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlGKENLPkvasddDEMVQISGELDVAKEALIQITSRL 442
Cdd:cd22516   7 VTLTIRLLMHGKEVGSIIGKKGETVKKMREESGARINI-SEGNCP------ERIVTITGPTDAIFKAFAMIAYKF 74

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: 35.31 E-value: 6.88e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 30685269 286 IRLVSPVENIASVIGKGGALINQLRQETRATIKV-DSSRTE 325
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINIsDGSCPE 41

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: 35.47 E-value: 6.98e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRI---GEAIPGCDERVITIYSPSD 104
Cdd:cd22514   8 PDEHIGAILGRGGRTINEIQQHSGARIKIsdrGDFVSGTRNRKVTITGPQD 58

tenth 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 tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 35.31 E-value: 7.33e-03

                        10        20        30
                ....*....|....*....|....*....|....*
gi 30685269 299 IGKGGALINQLRQETRATIKVDSSRTEGNDcLITI 333
Cdd:cd22413  18 IGRGGANIRKIRDNTGARIIFPTARDEDQE-LITI 51

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: 35.30 E-value: 7.60e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30685269 148 TAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKDRNMPlcaLNSDELIQISGEVLIVKKA 211
Cdd:cd22397   1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQP---TGQDKPLRITGDPQKVQRA 61

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: 35.30 E-value: 7.61e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 30685269  57 PVKKIGSVIGRGGDIVKQLRNDTRSKIRIGEAIPGCDERVITIYSPSDETNA 108
Cdd:cd22462   6 PAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARH 57

first 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 first one.

Pssm-ID: 411906 [Multi-domain] Cd Length: 75 Bit Score: 35.38 E-value: 7.76e-03

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRIVKD 185
Cdd:cd22478   4 MTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPD 42

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: 35.28 E-value: 8.09e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRIlgkENLPKVAS-DDDEMVQISGELDVAKEALIQITSRLRA 444
Cdd:cd22401   3 KILAHNNLCGRLIGKDGRNIKKIMEDTNTKITI---SSLQDLTSyNPERTITIKGSLEAMSEAESLISEKLRE 72

fourth 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 fourth one.

Pssm-ID: 411915 Cd Length: 72 Bit Score: 35.32 E-value: 9.30e-03

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 30685269 153 VPSDQIGCILGRGGQIVQNIRSETGAQIRIvkDRNMP 189
Cdd:cd22487   8 VPTGKTGLIIGKGGETIKSISQQSGARIEL--QRNPP 42

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: 34.93 E-value: 9.62e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 30685269 373 RLLVPSSRIGCILGKGGAIITEMRRMTKANIRI 405
Cdd:cd22438   2 RMLMQGKEVGSIIGKKGETIKKFREESGARINI 34

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: 34.85 E-value: 9.72e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 30685269 147 VTAKLLVPSDQIGCILGRGGQIVQNIRSETGAQIRiVKDRNMP 189
Cdd:cd22432   2 VELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVS-VPDSSGP 43