NCBI Conserved Domain Search

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: 136.13 E-value: 3.83e-39

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651  49 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIR 121
Cdd:cd22435   1 QCSLKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFYPGTTERVCLIQGEVEAVNAVLDFILEKIR 73

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: 134.24 E-value: 1.78e-38

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 398 DVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd09031   1 TVIELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEFVPGTRNRKVTITGTPAAVQAAQYLIEQRI 71

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: 125.81 E-value: 2.69e-35

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 148 KQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22436   1 KQVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLQERVVTVTGEPEANRKAVSLILQKI 70

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: 98.65 E-value: 2.63e-25

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22514   3 VTIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGDFVSGTRNRKVTITGPQDAVQMAQYLLEQKL 71

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: 76.71 E-value: 1.56e-17

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651  49 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22513   1 PVVAKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQEFFPGTTDRVLLVSGSLNEVLTALNLILEKL 72

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: 74.56 E-value: 7.87e-17

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD-GINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQlLPGSSERIVTITGSFDQVVKAVALILEKL 69

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: 70.00 E-value: 3.32e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651   150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELIIQ 215
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGN--ERIVTITGTPEAVEAAKALIEE 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: 69.18 E-value: 6.89e-15

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQR 467
Cdd:cd22439   5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED---GSTERSVTITGTPEAVSLAQYLINAR 68

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: 67.95 E-value: 2.20e-14

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGI-NLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFYpGTTERVCLIQGEVEAVNAVLDFILEKI 72

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: 67.95 E-value: 2.27e-14

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22435   4 LKLLVPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFYPGTTERVCLIQGEVEAVNAVLDFILEKI 72

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: 66.17 E-value: 7.17e-14

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGinLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEG--SGERVVTITGTPEAVEKAKELI 62

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: 66.06 E-value: 9.14e-14

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd09031   3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEFVPGTRNRKVTITGTPAAVQAAQYLIEQRI 71

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: 65.40 E-value: 1.28e-13

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLI 464
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE---GSGERVVTITGTPEAVEKAKELI 62

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 65.39 E-value: 1.70e-13

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651    148 KQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP----GSEERVVEITGPPENVEKAAELILEIL 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: 65.00 E-value: 1.99e-13

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651   399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQ 466
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES---EGNERIVTITGTPEAVEAAKALIEE 65

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 64.24 E-value: 3.44e-13

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651    396 SKDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpgtRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-----EERVVEITGPPENVEKAAELILEIL 68

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

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 63.40 E-value: 7.39e-13

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDgINLQERVVTVSGEPEQNRKAVELIIQK 216
Cdd:cd22399   1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPP-PNPNEKLFIIRGNPQQIEHAKQLIREK 67

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

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 61.85 E-value: 2.60e-12

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69

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: 61.97 E-value: 2.79e-12

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 144 PDRIKQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22428   1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74

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: 61.89 E-value: 2.97e-12

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPgtrNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22396   3 EEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLP---ERPCTLTGTPDAIETAKRLIDQIV 68

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: 61.50 E-value: 3.04e-12

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 159 AGLIIGKGGATVKAVMEQSGAWVQLSqkpDGiNLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22438  10 VGSIIGKKGETIKKFREESGARINIS---DG-SCPERIVTVTGTTDAVFKAFELICRKLEED 67

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: 61.10 E-value: 5.93e-12

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLS---QKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQ 218
Cdd:cd22460   2 ARLLVASSQAGSLIGKGGAIIKQIREESGASVRILpeeELPPCASPDDRVVQISGEAQAVKKALELVSSRLR 73

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: 60.77 E-value: 6.41e-12

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGAtiKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22456   2 IRLLIPHSLIGSIIGKGGARIKEIQDGSGA--RLVASKEFLPLSTERILEVQGTPDAIHNATLEIGKTL 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: 59.99 E-value: 1.06e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651    52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEALNAVHGFIAE 118
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSES---EGNERIVTITGTPEAVEAAKALIEE 65

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: 59.92 E-value: 1.36e-11

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22437   1 VRLLVPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69

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: 59.76 E-value: 1.63e-11

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 410 GAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22513  14 GSVIGKGGATINDFQAQSGARIQLSRAQEFFPGTTDRVLLVSGSLNEVLTALNLILEKL 72

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: 59.58 E-value: 1.92e-11

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGinLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22396   3 EEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGG--LPERPCTLTGTPDAIETAKRLIDQIV 68

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: 59.16 E-value: 2.40e-11

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD-GINLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22401   1 PLKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDlTSYNPERTITIKGSLEAMSEAESLISEKLRE 72

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: 58.46 E-value: 4.06e-11

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEALNA 111
Cdd:cd00105   1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGE---GSGERVVTITGTPEAVEK 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: 58.59 E-value: 5.03e-11

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQR 467
Cdd:cd22522  12 ELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATE---GSSERQITITGSPANISLAQYLINAR 75

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: 58.14 E-value: 6.05e-11

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKgefVPGTRNRKVTITGTPAATQAAQYLITQRITYE 471
Cdd:cd22521   8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANP---VEGSTDRQVTITGSAASISLAQYLINARLSSE 75

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: 57.62 E-value: 8.88e-11

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22401   2 LKILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYNPERTITIKGSLEAMSEAESLISEKLRE 72

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: 57.71 E-value: 9.70e-11

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgeFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22454   6 IEVVIPNADVGKVIGKGGETIKRIEALTDTVITFER---VNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 57.31 E-value: 1.01e-10

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651     52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKskdfyPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG-----PGSEERVVEITGPPENVEKAAELILEIL 68

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: 56.57 E-value: 3.10e-10

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTeRVCLIQGTVEALNAVHGFIAEKIREM 123
Cdd:cd22429   6 LHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLV-RLITITGTKKEVDAAKSLILEKVSEE 74

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: 55.69 E-value: 3.56e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651  51 FLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfyPGTTERVCLIQGTvEALNAVH 113
Cdd:cd22459   3 VFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGV---PGTEERVITISSS-EAPEAPV 61

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: 55.67 E-value: 3.69e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLIT 465
Cdd:cd22523   5 EFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTE---GTSERHVTITGSPVSITLAQYLIT 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: 55.68 E-value: 4.02e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISK-KGEfvPGTRNrkVTITGTPAATQAAQYLITQRI 468
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKqKGE--QGDRR--ITIKGSADATRQAAQLINALI 68

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: 55.77 E-value: 4.33e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22456   2 IRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASK--EFLPLSTERILEVQGTPDAIHNATLEIGKTL 68

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: 55.34 E-value: 5.08e-10

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSkdfypGTTERVCLIQGTVEALNAVHGFIAEKIREM 123
Cdd:cd22438   1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDG-----SCPERIVTVTGTTDAVFKAFELICRKLEED 67

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: 55.32 E-value: 5.27e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRK--VTITGTPAATQAAQ 461
Cdd:cd22403   2 TEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQT---PDEGDEvpVEIIGNFYATQSAQ 62

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: 55.50 E-value: 5.45e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22514   4 TIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGDFVSGTRNRKVTITGPQDAVQMAQYLLEQKL 71

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: 54.97 E-value: 6.86e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDgINLQERVVTVSGEPEQNRKAVELIIQ 215
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKEN-AGAAEKAITIYGTPEGCSSACKQILE 66

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: 55.13 E-value: 7.18e-10

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 148 KQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELII 214
Cdd:cd22463   2 SKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQKILRISGTEEQLKRAQSLVE 68

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: 54.88 E-value: 7.64e-10

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSkdfypGTTERVCLIQGTVEAL 109
Cdd:cd22432   4 LRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS-----SGPERILTISADRETV 56

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: 54.63 E-value: 1.17e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfyPGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22434   6 VTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPL---PGSEDRIITITGTQDQIQNAQYLLQNSVKQ 71

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: 54.65 E-value: 1.35e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 152 IIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22429   6 LHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEE 74

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: 54.36 E-value: 1.52e-09

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD---GINlqERVVTVSGEPEQNRKAVELIIQKIQ 218
Cdd:cd22513   4 AKLLVSNAAAGSVIGKGGATINDFQAQSGARIQLSRAQEffpGTT--DRVLLVSGSLNEVLTALNLILEKLL 73

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: 54.25 E-value: 1.60e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGefvPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22434   4 TQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPL---PGSEDRIITITGTQDQIQNAQYLLQNSV 69

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: 53.62 E-value: 1.76e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgefVPG--TRNRKVTITGTPAATQAAQYLIT 465
Cdd:cd22457   3 ISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAK----APHdeTGERMFTITGTPEANDRALRLLY 64

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: 54.26 E-value: 1.83e-09

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTrNRKVTITGTPAATQAAQYLITQRITYEQGVRA 476
Cdd:cd22429   5 ELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDL-VRLITITGTKKEVDAAKSLILEKVSEEEEFRQ 79

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: 53.43 E-value: 2.72e-09

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK--PdgiNLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd02396   5 RLLVPASQCGSLIGKGGSKIKEIRESTGASVQVASEmlP---NSTERAVTISGSPEAITKCVEQICCVMLE 72

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

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 53.29 E-value: 3.11e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 152 IIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQerVVTVSGEPEQNRKAVELIIQK 216
Cdd:cd22395   4 FEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQ--ICSIEGTQQQIDKALKLIRKK 66

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: 53.01 E-value: 3.37e-09

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVpGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22436   2 QVKILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESI-NLQERVVTVTGEPEANRKAVSLILQKI 70

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: 53.11 E-value: 4.20e-09

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGefvPGTRN--RKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22428   6 EIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEG---SGGELpeRVLLIQGNPVQAQRAEEAIHQII 74

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

Pssm-ID: 411806 [Multi-domain] Cd Length: 72 Bit Score: 52.66 E-value: 4.43e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 404 VPENLVGAILGKGGKTLVEYQELTGARIQISkkGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd02396   8 VPASQCGSLIGKGGSKIKEIRESTGASVQVA--SEMLPNSTERAVTISGSPEAITKCVEQICCVM 70

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: 51.88 E-value: 7.34e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLsKSKDfyPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGARVQF-KPDD--GNSPDRICVITGPPDQVQHAARMIQELI 67

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: 51.86 E-value: 7.97e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22397   2 IEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQDKPLRITGDPQKVQRAKELVMELI 69

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: 51.49 E-value: 1.05e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 152 IIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsqKPDGINLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETGARVQF--KPDDGNSPDRICVITGPPDQVQHAARMI 63

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: 51.88 E-value: 1.08e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 147 IKQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK-PDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22487   1 LQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNpPPNADPNMKLFTIRGSPQQIDYARQLIEEKI 72

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: 51.50 E-value: 1.17e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCLIQGTVEALNA 111
Cdd:cd02396   4 LRLLVPASQCGSLIGKGGSKIKEIRESTGASVQV--ASEMLPNSTERAVTISGSPEAITK 61

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: 51.49 E-value: 1.18e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCLIQGTVE 107
Cdd:cd22433   4 LRLLVHQSQAGCIIGRAGFKIKELREKTGATIKV--YSECCPRSTDRVVQIGGKPD 57

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: 51.47 E-value: 1.19e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD--FYPGTTERVCLIQGTVEA 108
Cdd:cd22460   3 RLLVASSQAGSLIGKGGAIIKQIREESGASVRILPEEElpPCASPDDRVVQISGEAQA 60

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: 51.44 E-value: 1.44e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 148 KQVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsQKPDGINlQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22404   1 KSKKVTVPNSAISRVIGRGGCNINAIREVSGAHIEI-DKQKGEQ-GDRRITIKGSADATRQAAQLINALIKD 70

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: 51.10 E-value: 1.70e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfyPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPD---SATGERIVLISGTPDQARHAQNLIEAFI 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: 51.12 E-value: 1.87e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLITQR 467
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKEN--AGAAEKAITIYGTPEGCSSACKQILEI 67

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: 51.17 E-value: 2.03e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 149 QVKIivPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKA 209
Cdd:cd22434   5 QVTI--PKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSE--DRIITITGTQDQIQNA 61

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: 51.04 E-value: 2.14e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGI-NLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd09031   3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEFVpGTRNRKVTITGTPAAVQAAQYLIEQRI 71

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: 50.69 E-value: 2.66e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPE 204
Cdd:cd22459   5 RLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTE--ERVITISSSEA 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: 50.33 E-value: 2.67e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATG--ERIVLISGTPDQARHAQNLIEAFI 66

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: 50.33 E-value: 2.75e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDS---ATGERIVLISGTPDQARHAQNLIEAFI 66

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: 50.39 E-value: 3.26e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22454   6 IEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSP--NREVQITGSPDNVAAAKRLIEDTI 71

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: 50.40 E-value: 3.45e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22515   4 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEG----NCPERIITLAGPTNAIFKAFAMIIDKLEED 70

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: 49.94 E-value: 3.73e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLI 464
Cdd:cd22402   2 TTYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPADS--PDAPERKVTITGPPEAQWKAQLCI 65

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: 50.30 E-value: 3.97e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22401   4 ILAHNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYNPERTITIKGSLEAMSEAESLISEKL 70

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: 49.54 E-value: 5.82e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK-PDGINLQERVVTVSGEPEQNRKAVELIIQK 216
Cdd:cd22489   1 EITYTIPADKCGLVIGKGGENIKSINQQSGAHVELQRNpPPNTDPNVRIFTIRGVPQQIEHARQLIDEK 69

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: 49.60 E-value: 6.28e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSkdfYPGTTERVCLIQGTVEALNAVHGFIA 117
Cdd:cd22455   3 LRALVSSKEAAVIIGKGGENIARLRATTGVKAGVSKV---VPGVHDRVLTVSGPLEGVAKAFGLIA 65

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: 49.56 E-value: 6.51e-08

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPgttERVCLIQGTVEALNA 111
Cdd:cd22396   7 VPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLP---ERPCTLTGTPDAIET 59

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: 49.64 E-value: 7.00e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPgtrNRKVTITGTPAATQAAQYLITQ 466
Cdd:cd22478   7 EYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP---ERSCMLTGTPESVQSAKRLLDQ 69

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: 49.72 E-value: 7.96e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 395 GSKDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGT-----RNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22447   1 SPKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPAdedddTMVEVTITGDEFNVQHAKQRIEEII 79

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: 48.72 E-value: 9.06e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGepeqNRKAVELIIQKI 217
Cdd:cd22432   3 ELRLLIPSKAAGAIIGKGGENIKRLRTEYNASVSVPDS----SGPERILTISA----DRETVLGILTEI 63

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: 49.25 E-value: 9.25e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651  47 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLsksKDFYPGTT--ERVCLIQGTVEA 108
Cdd:cd22428   2 SRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDF---KDEGSGGElpERVLLIQGNPVQ 62

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: 49.16 E-value: 9.48e-08

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22397   1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGP-QPTGQDKPLRITGDPQKVQRAKELVMELI 69

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: 48.79 E-value: 9.73e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqKPDGINLQERVVTVSGEPEQNRKA 209
Cdd:cd22402   3 TYLYIPNKAVGAIIGTKGSHIRYIKRFSGASIKIA-PADSPDAPERKVTITGPPEAQWKA 61

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 49.26 E-value: 1.05e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQN 126
Cdd:cd22494   2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDLTIYNPERTITVKGSIEACSSAEVEIMKKLREAYEN 76

fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411916 Cd Length: 69 Bit Score: 48.56 E-value: 1.64e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLS-QKPDGINLQERVVTVSGEPEQNRKAVELIIQK 216
Cdd:cd22488   6 IPTHKCGLVIGRGGENVKAINQQTGAFVEISrQPPPNGDPNFKLFIIRGSPQQIDHAKQLIEEK 69

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: 48.55 E-value: 1.71e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651  49 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22497   2 QEVVYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEG--PDVSERMVIITGPPEAQFKAQGRIFGKLKE 73

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411907 [Multi-domain] Cd Length: 71 Bit Score: 48.01 E-value: 2.13e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqkPDGINLQERVVTVSGEPEQNRKA 209
Cdd:cd22479   7 VPDGMVGLIIGRGGEQINKIQQDSGCKVQIS--PDSGGLPERSVSLTGSPEAVQKA 60

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

Pssm-ID: 411867 [Multi-domain] Cd Length: 68 Bit Score: 47.61 E-value: 2.56e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEALNA 111
Cdd:cd22439   5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSED---GSTERSVTITGTPEAVSL 60

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

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 47.37 E-value: 4.38e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22498   9 LFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDAKLRMVIITGPPEAQFKAQGRIYGKLKE 75

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

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 47.06 E-value: 4.63e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTrnrKVTITGTPAATQAAQYLItQRITYEQ 472
Cdd:cd22451   2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDD--PSG---KIRITGARDGVEAATAKI-LNISDEE 69

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

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 46.75 E-value: 5.86e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFvpgTRNRKVTITGTPAATQAAQYLITQR 467
Cdd:cd22395   3 EFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYT---QNFQICSIEGTQQQIDKALKLIRKK 66

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: 46.66 E-value: 6.91e-07

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRnRKVTITGTPAATQAAQYLI 464
Cdd:cd22463   4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQ-KILRISGTEEQLKRAQSLV 67

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

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 46.55 E-value: 8.96e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISkkGEFVPGTRNRKVTITGTPAA 456
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVA--GDLLPNSTERAVTVSGVPDA 58

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: 46.05 E-value: 9.33e-07

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPgttERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22404   4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQG---DRRITIKGSADATRQAAQLINALIKD 70

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

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 46.70 E-value: 9.44e-07

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISkkGEFVPGTRNRKVTITGTPAA 456
Cdd:cd22519   8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVA--GDMLPNSTERAVTISGTPDA 62

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

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 46.17 E-value: 1.03e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK--PdgiNLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDllP---NSTERAVTVSGVPDAIIQCVRQICAVILE 72

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

Pssm-ID: 411924 Cd Length: 76 Bit Score: 46.17 E-value: 1.03e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651  49 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22496   2 QETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIITGPPEAQFKAQGRIYGKLKE 73

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: 46.09 E-value: 1.13e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPdGINLQERVVTVSGEPEQNRKAVELIIQ 215
Cdd:cd22433   3 ELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSEC-CPRSTDRVVQIGGKPDKVVECIREILE 68

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: 46.44 E-value: 1.14e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 394 DGSKDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22483   1 DGNSTIQEILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGP-LPTGADKPLRITGDPFKVQQAREMVLEII 74

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: 45.71 E-value: 1.18e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQIsKKGEfvPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22398   3 EVPVPRFAVGVVIGKGGEMIKKIQNETGARVQF-KPDD--GNSPDRICVITGPPDQVQHAARMIQELI 67

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411907 [Multi-domain] Cd Length: 71 Bit Score: 46.09 E-value: 1.25e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPgtrNRKVTITGTPAATQAAQYLI 464
Cdd:cd22479   4 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGSPEAVQKAKMML 64

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

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 45.74 E-value: 1.30e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 407 NLVGAILGKGGKTLVEYQELTGARIQISKkgefvpGTRNRKVTITGTPAATQAAQYLI 464
Cdd:cd22430   9 SLVGAVIGRGGSKIRELEESTGSKIKIIK------GGQEAEVKIFGSDEAQQKAKELI 60

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: 45.78 E-value: 1.57e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCLIQGTVEAL 109
Cdd:cd22520   4 LRLVIPASQCGSLIGKAGSKIKEIRESTGAQVQV--AGDLLPNSTERAVTVSGVPDAI 59

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: 45.27 E-value: 1.93e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPgtrNRKVTITGTPAATQAAQYLITQ 466
Cdd:cd22480   4 EYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMP---ERPCVLTGTPESIEQAKRLLGQ 66

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411909 [Multi-domain] Cd Length: 71 Bit Score: 45.38 E-value: 1.95e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22481   5 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELI 71

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

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 44.91 E-value: 2.29e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651  55 LIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGttERVCLIQGTVEALNAVHGFIAEK 119
Cdd:cd22399   5 LVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPN--EKLFIIRGNPQQIEHAKQLIREK 67

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

Pssm-ID: 411830 [Multi-domain] Cd Length: 66 Bit Score: 44.55 E-value: 2.81e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfYPGTTERVCLIQGTVEA 108
Cdd:cd22402   7 IPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPAD--SPDAPERKVTITGPPEA 57

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: 44.96 E-value: 2.82e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEA 108
Cdd:cd22400   2 LRILVPSEFVGAIIGKGGATIRQITQQTGARIDIHRKEN--AGAAEKAITIYGTPEG 56

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: 44.73 E-value: 2.92e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfYPGTTERVCLIQGTVEALN 110
Cdd:cd22463   4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRY-PLEETQKILRISGTEEQLK 61

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: 45.01 E-value: 3.16e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqkPDGINLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22478  10 VPDGMVGFIIGRGGEQISRIQQESGCKIQIA--PDSGGLPERSCMLTGTPESVQSAKRLLDQIVEK 73

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: 45.16 E-value: 3.37e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCLIQGTVEAL 109
Cdd:cd22519   8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQV--AGDMLPNSTERAVTISGTPDAI 63

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: 44.53 E-value: 3.45e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 404 VPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPG--TRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22460   6 VASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPCasPDDRVVQISGEAQAVKKALELVSSRL 72

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: 44.61 E-value: 3.85e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651  48 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKskdFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22454   2 GQTTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFER---VNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

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: 44.25 E-value: 4.72e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22517   4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITISEG----SCPERITTITGSTDAVFRAFSMIAFKLEED 70

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: 44.14 E-value: 4.74e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELI 213
Cdd:cd22439   5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGST--ERSVTITGTPEAVSLAQYLI 65

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: 5.29e-06

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSG 201
Cdd:cd22403   2 TEIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEVPVEIIG 53

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411911 [Multi-domain] Cd Length: 83 Bit Score: 44.51 E-value: 5.43e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQEDPQS 223
Cdd:cd22483   8 EILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLPTGADKPLRITGDPFKVQQAREMVLEIIREKDQA 80

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: 5.78e-06

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKD 90
Cdd:cd22403   4 IRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQT 40

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

Pssm-ID: 411931 Cd Length: 83 Bit Score: 43.97 E-value: 8.11e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELIIQKIQeDP 221
Cdd:cd22503   4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNG--ERMITIRGGTESTRYAVQLINALIQ-DP 71

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

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 42.96 E-value: 9.21e-06

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpgtRNRKVTITGTPAATQAAQYLI 464
Cdd:cd22411   2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENS-----DSDVITITGKKEDVEKARERI 61

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: 43.62 E-value: 9.33e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK--PdgiNLQERVVTVSGEPEQNRKAVELIIQKIQEDP 221
Cdd:cd22519   8 LRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDmlP---NSTERAVTISGTPDAIIQCVKQICVVMLESP 78

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: 43.55 E-value: 1.18e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22516  11 IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEG----NCPERIVTITGPTDAIFKAFAMIAYKFEED 77

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

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 42.98 E-value: 1.26e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISkkgEFVPGTRNRKVTITGTPAA 456
Cdd:cd22459   3 VFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVE---DGVPGTEERVITISSSEAP 57

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

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 42.89 E-value: 1.38e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFypgTTERVCLIQGTVEALNA 111
Cdd:cd22395   6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYT---QNFQICSIEGTQQQIDK 58

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: 42.45 E-value: 1.52e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22457   2 NISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHDET-GERMFTITGTPEANDRALRLL 63

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

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 43.14 E-value: 1.61e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22498   7 VHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIA-PAEGPDAKLRMVIITGPPEAQFKAQGRIYGKLKEE 76

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: 42.79 E-value: 1.68e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGIN-LQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22514   3 VTIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDRGDFVSgTRNRKVTITGPQDAVQMAQYLLEQKL 71

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

Pssm-ID: 411923 Cd Length: 77 Bit Score: 42.72 E-value: 1.73e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQN 126
Cdd:cd22495   2 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTLYNPERTITVKGSIETCAKAEEEIMKKIRESYEN 76

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: 42.63 E-value: 1.79e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 409 VGAILGKGGKTLVEYQELTGARIQISKKGefVPgtrNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22438  10 VGSIIGKKGETIKKFREESGARINISDGS--CP---ERIVTVTGTTDAVFKAFELICRKL 64

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411910 [Multi-domain] Cd Length: 73 Bit Score: 42.59 E-value: 1.88e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22482   5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 73

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

Pssm-ID: 411827 [Multi-domain] Cd Length: 67 Bit Score: 42.21 E-value: 2.54e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTrnRKVTITGTPAATQAAQYLITQR 467
Cdd:cd22399   2 VTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPNE--KLFIIRGNPQQIEHAKQLIREK 67

first 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 first one.

Pssm-ID: 411919 Cd Length: 74 Bit Score: 42.36 E-value: 2.59e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGiNLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22491   2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKENA-GAAEKPITIHATPEGCSAACRMILEIMQKE 71

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; 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: 411930 [Multi-domain] Cd Length: 71 Bit Score: 42.05 E-value: 2.64e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22502   4 KVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTG--DRIITIRGGTESTRQATQLINALIKD 70

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: 42.78 E-value: 2.65e-05

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 56549651 395 GSKDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGE 438
Cdd:cd22446   4 SPKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNE 47

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411909 [Multi-domain] Cd Length: 71 Bit Score: 41.92 E-value: 3.70e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTrNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22481   3 VQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA-DKPLRITGDPYKVQQAKEMVLELI 71

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: 42.00 E-value: 3.81e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22497   5 VYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKIA-PAEGPDVSERMVIITGPPEAQFKAQGRIFGKLKEE 74

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411914 Cd Length: 70 Bit Score: 41.47 E-value: 4.07e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsqKPDGINLQERVVTVSGEPEQNRKAVELIIQKI 217
Cdd:cd22486   5 IEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQF--KPDDGISPERVAQVMGPPDRCQHAAHIINELI 70

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 41.55 E-value: 4.71e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD-GINLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22494   2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDlTIYNPERTITVKGSIEACSSAEVEIMKKLRE 72

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: 41.13 E-value: 5.65e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 153 IVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGInlQERVVTVSGEPEQNRKAVELIIQ 215
Cdd:cd22455   6 LVSSKEAAVIIGKGGENIARLRATTGVKAGVSKVVPGV--HDRVLTVSGPLEGVAKAFGLIAR 66

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: 41.04 E-value: 5.97e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqkPDGINLQERVVTVSGEPEQNRKAVELIIQ 215
Cdd:cd22480   7 VPDKMVGFIIGRGGEQISRIQLESGCKIQIA--PDSGGMPERPCVLTGTPESIEQAKRLLGQ 66

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: 41.26 E-value: 6.89e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISkkGEFVPGTRNRKVTITGTPAA 456
Cdd:cd22518   9 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVA--GDMLPNSTERAITIAGIPQS 63

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: 41.16 E-value: 7.49e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEALNA 111
Cdd:cd22478  10 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG---GLPERSCMLTGTPESVQS 62

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: 40.84 E-value: 8.84e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGiNLQERVVTVSGEPEQNRKAVELIIQKIQEDPQS 223
Cdd:cd22490   2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKENA-GAAEKAISIHSTPEGCSAACKMILEIMQKEAKD 74

type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins; MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C.

Pssm-ID: 411881 [Multi-domain] Cd Length: 72 Bit Score: 40.81 E-value: 9.31e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDF-YPGTTERVCLI 102
Cdd:cd22453   4 ISFYVPEKYHKRIIGKGGQNIQRIMKKYNVFIKFSNANDRaDNYYPDNVVIR 55

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

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 40.26 E-value: 9.45e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22411   1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEE----NSDSDVITITGKKEDVEKARERI 61

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: 40.54 E-value: 1.01e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 399 VVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGefvpgtrnrKVTITGT-PAATQAAQYLItQRITYE 471
Cdd:cd02393   5 ITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDDG---------TVTIFATdKESAEAAKAMI-EDIVAE 68

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

Pssm-ID: 411924 Cd Length: 76 Bit Score: 40.77 E-value: 1.04e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 397 KDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGefVPGTRNRKVTITGTPAATQAAQ 461
Cdd:cd22496   2 QETVHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPE--TPDSKVRMVIITGPPEAQFKAQ 64

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

Pssm-ID: 411885 [Multi-domain] Cd Length: 64 Bit Score: 40.14 E-value: 1.08e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEA 108
Cdd:cd22457   2 NISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPH--DETGERMFTITGTPEA 55

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

Pssm-ID: 411921 Cd Length: 97 Bit Score: 41.20 E-value: 1.12e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQN 126
Cdd:cd22493   7 LKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTLYNPERTITVKGSIEACCRAEQEIMKKVREAYEN 81

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

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 40.27 E-value: 1.18e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGinlQERVVTVSGePEQNRKAVELIIQKIQEDPQS 223
Cdd:cd22417   2 TLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDE---NDDEITITG-YEKNAEAAKDAILKIVQELES 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: 40.36 E-value: 1.22e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQK--PDGinlQERVVTVSGEPEQNRKAV 210
Cdd:cd22456   2 IRLLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEflPLS---TERILEVQGTPDAIHNAT 61

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: 40.12 E-value: 1.30e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 152 IIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGinlQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22458   5 IKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNS---SQQTIHLSGTDKQIALAISSI 63

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: 39.86 E-value: 1.39e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 56549651 160 GLIIGKGGATVKAVMEQSGAWVQLsqkPDGiNLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd02394  14 GHIIGKGGANIKRIREESGVSIRI---PDD-EANSDEIRIEGSPEGVKKAKAEI 63

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: 40.18 E-value: 1.48e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGiNLQERVVTVSGEPEQNRKAVELIIQKIQEDPQ 222
Cdd:cd22492   2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKENA-GAAEKSITILSTPEGTSAACKSILEIMHKEAQ 73

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

Pssm-ID: 411943 Cd Length: 70 Bit Score: 40.00 E-value: 1.66e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfypgTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22515   4 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN-----CPERIITLAGPTNAIFKAFAMIIDKLEE 69

third 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 third one.

Pssm-ID: 411912 Cd Length: 68 Bit Score: 39.51 E-value: 1.93e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsqKPDGINLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22484   3 IDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQF--KPDDGTTPERIAQITGPPDRCQHAAEII 64

first 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 first one.

Pssm-ID: 411919 Cd Length: 74 Bit Score: 39.66 E-value: 2.05e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLITQRITYE 471
Cdd:cd22491   2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKEN--AGAAEKPITIHATPEGCSAACRMILEIMQKE 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: 39.54 E-value: 2.37e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 398 DVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgEFVPGTRNRKVTITGTPA 455
Cdd:cd22433   2 CELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYS--ECCPRSTDRVVQIGGKPD 57

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; 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: 411930 [Multi-domain] Cd Length: 71 Bit Score: 39.35 E-value: 2.87e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22502   4 KVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKD---KTGDRIITIRGGTESTRQATQLINALI 68

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: 39.41 E-value: 2.91e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAA 460
Cdd:cd22492   2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKEN--AGAAEKSITILSTPEGTSAA 60

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: 39.34 E-value: 2.97e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCLIQGTVEAL 109
Cdd:cd22518   9 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQV--AGDMLPNSTERAITIAGIPQSI 64

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: 39.31 E-value: 3.05e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 397 KDVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLITQRITYE 471
Cdd:cd22497   2 QEVVYLFIPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEG--PDVSERMVIITGPPEAQFKAQGRIFGKLKEE 74

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

Pssm-ID: 411926 [Multi-domain] Cd Length: 78 Bit Score: 39.28 E-value: 3.07e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 398 DVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLITQRITYE 471
Cdd:cd22498   5 ETVHLFIPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEG--PDAKLRMVIITGPPEAQFKAQGRIYGKLKEE 76

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

Pssm-ID: 411944 Cd Length: 77 Bit Score: 39.32 E-value: 3.15e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfypgTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22516  11 IRLLMHGKEVGSIIGKKGETVKKMREESGARINISEGN-----CPERIVTITGPTDAIFKAFAMIAYKFEE 76

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411928 Cd Length: 78 Bit Score: 39.35 E-value: 3.38e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLskSKDFYPGTTERVCL-IQGTVEALNAVHgfiaEKIREMPQNVAKTE 131
Cdd:cd22500   8 VPSSAAGRVIGKGGKTVNELQNLTSAEVIV--PRDQTPDENEEVIVkIIGHFFASQTAQ----RKIREIVQQVKQQE 78

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

Pssm-ID: 411945 Cd Length: 70 Bit Score: 38.86 E-value: 3.76e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfypgTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22517   4 LRLLMHGKEVGSIIGKKGETVKRIREESSARITISEGS-----CPERITTITGSTDAVFRAFSMIAFKLEE 69

second 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 second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 38.83 E-value: 3.84e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpgtRNRKVTITGTPAATQAAQYLItQRITYEQ 472
Cdd:cd22406   7 VTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQED-----NSDEIKITGTKEGIEKARHEI-QLISDEQ 73

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: 38.94 E-value: 4.02e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL-SKSKDFYPGTTERVCLIQGTVEAL 109
Cdd:cd22447   6 LTVPIPASTRARIIGKKGANLKQIREKTGVRIDIpPRDADAAPADEDDDTMVEVTITGD 64

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: 38.95 E-value: 4.02e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQkpDGI-NLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22518   9 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAG--DMLpNSTERAITIAGIPQSIIECVKQI 71

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

Pssm-ID: 411924 Cd Length: 76 Bit Score: 38.85 E-value: 4.41e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSqKPDGINLQERVVTVSGEPEQNRKAVELIIQKIQED 220
Cdd:cd22496   5 VHVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIA-PPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEE 74

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: 38.72 E-value: 4.61e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEAL 109
Cdd:cd22480   7 VPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSG---GMPERPCVLTGTPESI 57

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411914 Cd Length: 70 Bit Score: 38.78 E-value: 4.69e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPgtrNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22486   5 IEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGISP---ERVAQVMGPPDRCQHAAHIINELI 70

seventh 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 seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 38.46 E-value: 4.84e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 152 IIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKpdgiNLQERVVTVSGEPEQNRKAVELII 214
Cdd:cd22452   6 IKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKK----NKESDVITLRGTKEGVEKAEEMIK 64

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: 38.38 E-value: 5.37e-04

                        10        20        30
                ....*....|....*....|....*....|
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGA 81
Cdd:cd22397   2 IEIMIPGNKVGLIIGKGGETIKQLQERAGV 31

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: 38.64 E-value: 5.78e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQNV 127
Cdd:cd22492   2 LRLLVPTQFVGAIIGKEGATIRNITKQTQSKIDVHRKEN--AGAAEKSITILSTPEGTSAACKSILEIMHKEAQDI 75

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

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 38.03 E-value: 6.57e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 156 NSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPdginlQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22430   8 SSLVGAVIGRGGSKIRELEESTGSKIKIIKGG-----QEAEVKIFGSDEAQQKAKELI 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: 37.94 E-value: 7.39e-04

                        10        20        30
                ....*....|....*....|....*....|..
gi 56549651  57 PSYAaGSIIGKGGQTIVQLQKETGATIKLSKS 88
Cdd:cd02394  10 PKFH-GHIIGKGGANIKRIREESGVSIRIPDD 40

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

Pssm-ID: 411918 Cd Length: 76 Bit Score: 38.15 E-value: 7.73e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAE 118
Cdd:cd22490   2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKEN--AGAAEKAISIHSTPEGCSAACKMILE 66

fourth 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 fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 37.54 E-value: 9.46e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINLqervVTVSGEPEQNRKAVELI 213
Cdd:cd22408   6 VPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSET----ITLRGPADKLGAALTLV 61

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: 37.63 E-value: 9.55e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTVEALNAVHGFIAEKI 120
Cdd:cd22487   8 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGSPQQIDYARQLIEEKI 72

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

Pssm-ID: 411929 Cd Length: 66 Bit Score: 37.36 E-value: 1.05e-03

                        10        20        30
                ....*....|....*....|....*....|....
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSK 89
Cdd:cd22501   6 VPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ 39

third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411913 Cd Length: 68 Bit Score: 37.63 E-value: 1.05e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsqKPDGINLQERVVTVSGEPEQNRKAVELI 213
Cdd:cd22485   3 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQF--KQDDGTGPEKIAHIMGPPDRCEHAARII 64

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

Pssm-ID: 411931 Cd Length: 83 Bit Score: 38.19 E-value: 1.07e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvpGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22503   4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKD---KNGERMITIRGGTESTRYAVQLINALI 68

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

Pssm-ID: 411883 Cd Length: 70 Bit Score: 37.66 E-value: 1.09e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 56549651 410 GAILGKGGKTLVEYQELTGARIQISKKgefVPGTRNRKVTITGT 453
Cdd:cd22455  13 AVIIGKGGENIARLRATTGVKAGVSKV---VPGVHDRVLTVSGP 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: 37.16 E-value: 1.21e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 398 DVVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgefvPGTRNRKVTITGTPAATQAAQYLI 464
Cdd:cd02394   2 AFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPD-----DEANSDEIRIEGSPEGVKKAKAEI 63

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: 37.96 E-value: 1.26e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSkDFYPGTTERVCLIQGTVEALNAVHGFIAEKIREMPQ 125
Cdd:cd22483   8 EILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQD-GPLPTGADKPLRITGDPFKVQQAREMVLEIIREKDQ 79

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: 37.18 E-value: 1.32e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEP 203
Cdd:cd22523   5 EFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTS--ERHVTITGSP 55

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: 37.77 E-value: 1.32e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGIN----LQERVVTVS--GEPEqnrkAVELIIQKI 217
Cdd:cd22446   9 ITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNydedDDDETVEISieGDAE----GVELAKKEI 78

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

Pssm-ID: 411923 Cd Length: 77 Bit Score: 37.33 E-value: 1.39e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 150 VKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD-GINLQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22495   2 LKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDlTLYNPERTITVKGSIETCAKAEEEIMKKIRE 72

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 37.31 E-value: 1.55e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22494   2 LKILAHNSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDLTIYNPERTITVKGSIEACSSAEVEIMKKL 70

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

Pssm-ID: 411929 Cd Length: 66 Bit Score: 36.98 E-value: 1.78e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgEFVPGTRNRK-VTITGTPAATQAAQ 461
Cdd:cd22501   4 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPR--DQTPDENDQVvVKITGHFYASQLAQ 62

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins; FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411909 [Multi-domain] Cd Length: 71 Bit Score: 36.91 E-value: 1.87e-03

                        10        20
                ....*....|....*....|....*...
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETG 80
Cdd:cd22481   5 EIMIPASKAGLVIGKGGETIKQLQERAG 32

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

Pssm-ID: 411950 [Multi-domain] Cd Length: 75 Bit Score: 37.01 E-value: 1.98e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDGINlqERVVTVSGEPEQNRKAVELI 213
Cdd:cd22522  12 ELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSS--ERQITITGSPANISLAQYLI 72

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

Pssm-ID: 411927 Cd Length: 76 Bit Score: 36.93 E-value: 2.13e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgEFVPGTRNRK-VTITGTPAATQAAQYLITQRIT 469
Cdd:cd22499   6 IKVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR--DQTPDENDQViVKIIGHFYASQMAQRKIRDILA 72

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: 2.39e-03

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSK 87
Cdd:cd22446   9 ITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPK 44

first 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 first one.

Pssm-ID: 411919 Cd Length: 74 Bit Score: 36.58 E-value: 2.94e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERVCLIQGTVEALNAVHGFIAE 118
Cdd:cd22491   2 LRILVPTQFVGAIIGKEGLTIKNITKQTQSKVDIHRKEN--AGAAEKPITIHATPEGCSAACRMILE 66

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.

Pssm-ID: 411805 [Multi-domain] Cd Length: 92 Bit Score: 36.81 E-value: 3.03e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 56549651 407 NLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRK------------VTITG-TPAATQAAQYLITQ 466
Cdd:cd02395  17 NFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDpqpdpdeeedlhVLITAdTEEKVDKAAKLIEK 89

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

Pssm-ID: 411931 Cd Length: 83 Bit Score: 36.65 E-value: 3.10e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVE----ALNAVHGFIAEKIREMPQNVA 128
Cdd:cd22503   4 KLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKD---KNGERMITIRGGTEstryAVQLINALIQDPAKELEDLIP 80


                .
gi 56549651 129 K 129
Cdd:cd22503  81 R 81

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

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 36.03 E-value: 3.14e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651  52 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSkdfypGTTERVCLIQGTVE 107
Cdd:cd22411   2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEE-----NSDSDVITITGKKE 52

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

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 36.28 E-value: 3.28e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651  54 VLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfyPGTTERvclIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22451   5 IDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDD--PSGKIR---ITGARDGVEAATAKILNISDE 68

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

Pssm-ID: 411921 Cd Length: 97 Bit Score: 36.96 E-value: 3.40e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI--TYEQGVRAA 477
Cdd:cd22493   7 LKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTLYNPERTITVKGSIEACCRAEQEIMKKVreAYENDVAAM 86


                ...
gi 56549651 478 NPQ 480
Cdd:cd22493  87 NLQ 89

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins; FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411940 [Multi-domain] Cd Length: 78 Bit Score: 36.48 E-value: 3.47e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 396 SKDVVEiaVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFVPGTRNRKV--TITGTPAATQAAQYLITQRITY 470
Cdd:cd22512   2 AEDVIQ--VPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKNIPQEEGMVpfVFVGTKDSITNATVLLDYHLNY 77

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411910 [Multi-domain] Cd Length: 73 Bit Score: 36.04 E-value: 3.56e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKL 85
Cdd:cd22482   5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMIL 37

fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411928 Cd Length: 78 Bit Score: 36.26 E-value: 3.74e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 56549651 402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKkgEFVPGTRNRK-VTITGTPAATQAAQYLITQ 466
Cdd:cd22500   6 IKVPSSAAGRVIGKGGKTVNELQNLTSAEVIVPR--DQTPDENEEViVKIIGHFFASQTAQRKIRE 69

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411849 Cd Length: 70 Bit Score: 36.17 E-value: 3.85e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651 151 KIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLsqkPDGI--NLQERV--VTVSGEPEQNRKAVELI 213
Cdd:cd22421   6 KMDVSHTDHSHVIGKGGNNIKKVMEDTGCHIHF---PDSNrtSQAEKSnqVSIAGQPAGVESARAQI 69

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: 36.06 E-value: 4.04e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56549651  56 IPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKdfyPGTTE---RVCLIQGTVEALNAVHGFIAEK 119
Cdd:cd22489   6 IPADKCGLVIGKGGENIKSINQQSGAHVELQRNP---PPNTDpnvRIFTIRGVPQQIEHARQLIDEK 69

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 39.65 E-value: 4.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  116 IAEKIREMPQNVAKTEpvsilqpQTTVNPDRIkqvkiivpnstaGLIIGKGGATVKAVMEQSGAWVQLSQkpDGInlqer 195
Cdd:PRK11824 541 ISEPRAELSPYAPRIE-------TIKIPPDKI------------RDVIGPGGKTIREITEETGAKIDIED--DGT----- 594

                         90       100       110
                 ....*....|....*....|....*....|
gi 56549651  196 vVTVSG-EPEQNRKAVElIIQKIQEDPQSG 224
Cdd:PRK11824 595 -VKIAAtDGEAAEAAKE-RIEGITAEPEVG 622

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: 4.24e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 141 TVNPDRIkqvkiivpnstaGLIIGKGGATVKAVMEQSGAWVQLSQkpDGinlqerVVTVSGepeQNRKAVELIIQKIQE 219
Cdd:cd02393   9 KIPPDKI------------GDVIGPGGKTIRAIIEETGAKIDIED--DG------TVTIFA---TDKESAEAAKAMIED 64

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

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 35.89 E-value: 4.67e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 56549651 149 QVKIIVPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPDginlQERVVTVSGEPEQNRKAVELIIQKIQE 219
Cdd:cd22451   2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDD----PSGKIRITGARDGVEAATAKILNISDE 68

type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins; MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C.

Pssm-ID: 411881 [Multi-domain] Cd Length: 72 Bit Score: 35.81 E-value: 4.93e-03

                        10        20        30
                ....*....|....*....|....*....|....*
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQLSQKPD 188
Cdd:cd22453   8 VPEKYHKRIIGKGGQNIQRIMKKYNVFIKFSNAND 42

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: 35.83 E-value: 5.30e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 400 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEfvPGTRNRKVTITGTPAATQAAQYLI 464
Cdd:cd22490   2 LRLLVPTQYVGAIIGKEGATIRNITKQTQSKIDVHRKEN--AGAAEKAISIHSTPEGCSAACKMI 64

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: 35.70 E-value: 5.89e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56549651 404 VPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFVPGTRNRKVTITGTPAATQAAQYLITQRI 468
Cdd:cd22487   8 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGSPQQIDYARQLIEEKI 72

third type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411855 [Multi-domain] Cd Length: 79 Bit Score: 35.67 E-value: 5.97e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56549651 401 EIAVPENLVGAILGKGGKTLVEYQELTG-ARIQISKKGEFVPGTRNRKV---TITGTPAATQAAQYLI 464
Cdd:cd22427   5 IFQVPRDLVGKVIGKNGRVIQEIVDKSGvVRVKIEGDNEDGPRPREEGLvpfIFVGTREAIANAKLLL 72

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; 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: 411930 [Multi-domain] Cd Length: 71 Bit Score: 35.50 E-value: 7.29e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56549651  53 KVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDfypGTTERVCLIQGTVEALNAVHGFIAEKIRE 122
Cdd:cd22502   4 KVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKD---KTGDRIITIRGGTESTRQATQLINALIKD 70

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: 35.47 E-value: 7.62e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56549651 154 VPNSTAGLIIGKGGATVKAVMEQSGAWVQL----SQKPDGINLQERVVTVSGE-PEQNRKAVELIIQKI 217
Cdd:cd22447  10 IPASTRARIIGKKGANLKQIREKTGVRIDIpprdADAAPADEDDDTMVEVTITgDEFNVQHAKQRIEEI 78

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

Pssm-ID: 411812 [Multi-domain] Cd Length: 102 Bit Score: 36.11 E-value: 7.69e-03

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 56549651 400 VEIAVPE----NLVGAILGKGGKTLVEYQELTGARIQISKKG 437
Cdd:cd22384   9 VLIPVKEfpkfNFVGKLLGPRGNTLKRLQEETGTKMSILGKG 50

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: 35.14 E-value: 8.03e-03

                        10        20
                ....*....|....*....|..
gi 56549651  62 GSIIGKGGQTIVQLQKETGATI 83
Cdd:cd02393  16 GDVIGPGGKTIRAIIEETGAKI 37

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 38.88 E-value: 8.08e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56549651  402 IAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGefvpgtrnrKVTITGT-PAATQAAQYLI 464
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDG---------TVKIAATdGEAAEAAKERI 612

type II K-homology (KH) RNA-binding domain found in GTPase Era and similar proteins; GTPase Era, also called ERA or GTP-binding protein Era, is an essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring in the order of seconds whereas hydrolysis occurs in the order of minutes. It plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing, and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. GTPase Era may also be critical for maintaining cell growth and cell division rates. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).

Pssm-ID: 411791 [Multi-domain] Cd Length: 87 Bit Score: 35.50 E-value: 9.58e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56549651 115 FIAEKI-----REMPQNVAktepVSILQpqTTVNPD---RIKQVkIIVPN-STAGLIIGKGGATVKAVMEQS 177
Cdd:cd22534   3 IIREKLlellrQELPYSVA----VEIEE--WEEREDgslRIEAE-IIVEKeSQKKIIIGKGGATIKKIGIEA 67