NCBI Conserved Domain Search

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: 140.82 E-value: 7.78e-40

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 234 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22482    1 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 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: 135.45 E-value: 5.26e-38

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 146 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRG 216
Cdd:cd22479    1 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGSPEAVQKAKMMLDDIVSRG 71

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: 134.29 E-value: 1.53e-37

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 236 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22397    1 TIEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQDKPLRITGDPQKVQRAKELVMELI 69

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: 132.00 E-value: 9.52e-37

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 324 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22485    1 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 68

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: 131.67 E-value: 1.26e-36

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 234 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22481    1 NAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGDPYKVQQAKEMVLELI 71

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: 130.61 E-value: 3.57e-36

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEK 495
Cdd:cd22488    1 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQPPPNGDPNFKLFIIRGSPQQIDHAKQLIEEK 69

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: 128.99 E-value: 1.44e-35

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 143 RTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSRGR 217
Cdd:cd22478    1 RSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR 75

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: 128.53 E-value: 1.68e-35

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 146 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22396    1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLIDQIV 68

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: 125.83 E-value: 1.30e-34

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 325 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22398    1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPDQVQHAARMIQELI 67

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: 126.18 E-value: 1.83e-34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 233 NGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGF 312
Cdd:cd22483    3 NSTIQEILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPLPTGADKPLRITGDPFKVQQAREMVLEIIREKDQADF 82

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: 122.72 E-value: 1.87e-33

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNgdPNFKLFVIRGSPQQIDHAKQLIEEK 495
Cdd:cd22399    1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPN--PNEKLFIIRGNPQQIEHAKQLIREK 67

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: 121.17 E-value: 5.86e-33

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 324 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22484    1 EGIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRCQHAAEIITDLL 68

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: 117.74 E-value: 9.70e-32

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 323 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22486    2 GGSIEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGISPERVAQVMGPPDRCQHAAHIINELI 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: 110.79 E-value: 2.93e-29

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEK 495
Cdd:cd22489    1 EITYTIPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNTDPNVRIFTIRGVPQQIEHARQLIDEK 69

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: 110.37 E-value: 4.87e-29

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 146 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22480    1 ITEEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMPERPCVLTGTPESIEQAKRLLGQIVDR 70

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: 105.81 E-value: 2.01e-27

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22487    3 EFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGSPQQIDYARQLIEEKI 72

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: 79.23 E-value: 3.14e-18

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 149 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22398    3 EVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPDQVQHAARMIQELI 67

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

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 79.26 E-value: 3.18e-18

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 148 EEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLD 210
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

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

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 78.09 E-value: 6.71e-18

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948  147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDD 211
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 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: 73.06 E-value: 5.09e-16

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22396    5 YKVPDKMVGLIIGRGGEQINRLQAESGAKIQIA---PDSGGLPERPCTLTGTPDAIETAKRLIDQIV 68

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

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 72.75 E-value: 6.70e-16

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 148 EEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGG--LPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22428    7 IEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGgeLPERVLLIQGNPVQAQRAEEAIHQII 74

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: 71.16 E-value: 2.37e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948  427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqLPPNGDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQI---PPSESEGNERIVTITGTPEAVEAAKALIEE 65

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 70.40 E-value: 3.95e-15

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948   144 TSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDsgGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGP--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: 69.23 E-value: 8.44e-15

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948  236 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVQQACEMVMD 302
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGN--ERIVTITGTPEAVEAAKALIEE 65

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: 69.09 E-value: 1.12e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQlppNGDPNFKLFVIRGSPQQIDHAKQLIEEK 495
Cdd:cd22395    4 FEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPH---PYTQNFQICSIEGTQQQIDKALKLIRKK 66

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: 68.85 E-value: 1.14e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948  326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIND 389
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

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: 69.27 E-value: 1.21e-14

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 143 RTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22454    1 TGQTTIEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

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: 1.26e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22439    3 TQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLAQYLINA 67

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 68.09 E-value: 2.50e-14

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948   427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqlpPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:smart00322   4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDI-----PGPGSEERVVEITGPPENVEKAAELILEIL 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: 68.52 E-value: 2.99e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22429    5 ELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRE-SDDTLDLVRLITITGTKKEVDAAKSLILEKVS 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: 66.55 E-value: 7.04e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIN 388
Cdd:cd00105    3 IEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

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: 65.78 E-value: 1.33e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIE 493
Cdd:cd00105    2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGE---RVVTITGTPEAVEKAKELIE 63

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: 65.70 E-value: 2.06e-13

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA 205
Cdd:cd22437    5 VPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPgssERIVTITGSFDQVVKA 61

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 64.58 E-value: 4.39e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22462    5 IPAHAVGSVIGRGGSNINQIREISGAKVEV---LKPDSATGERIVLISGTPDQARHAQNLIEAFI 66

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 64.24 E-value: 6.14e-13

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948   235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVdkplRIIGDPYKVQQACEMVMDIL 304
Cdd:smart00322   3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVV----EITGPPENVEKAAELILEIL 68

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

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 63.81 E-value: 9.24e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIIND 389
Cdd:cd22396    7 VPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLIDQ 66

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: 63.12 E-value: 1.81e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22428    7 IEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGsgGELPERVLLIQGNPVQAQRAEEAIHQII 74

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: 62.70 E-value: 1.89e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVQQACEMVM 301
Cdd:cd00105    2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG--ERVVTITGTPEAVEKAKELIE 63

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: 63.04 E-value: 1.98e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 149 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22486    6 EVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGISPERVAQVMGPPDRCQHAAHIINELI 70

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: 62.64 E-value: 2.17e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD--DGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22397    2 IEIMIPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDgpQPTGQDKPLRITGDPQKVQRAKELVMELI 69

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 62.31 E-value: 2.53e-12

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948   326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDgtGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--SEERVVEITGPPENVEKAAELILEIL 68

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: 62.05 E-value: 3.64e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISpDSG----GLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22514    7 VPDEHIGAILGRGGRTINEIQQHSGARIKIS-DRGdfvsGTRNRKVTITGPQDAVQMAQYLL 67

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: 61.68 E-value: 4.75e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNgDPNFKLFVIRGSPQQIDHAKQLIE 493
Cdd:cd22463    6 FQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPL-EETQKILRISGTEEQLKRAQSLVE 68

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

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 61.10 E-value: 7.39e-12

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQIS--PDSGGLPERSVSLTGAPESVQKA 205
Cdd:cd22436    7 VPNSTAGMIIGKGGATIKAIMEQSGARVQISqkPESINLQERVVTVTGEPEANRKA 62

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: 61.08 E-value: 7.94e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22484    7 IPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRCQHAAEIITDLL 68

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: 60.55 E-value: 1.29e-11

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISP---DSGGlpERSVSLTGAPESVQKAKMML 209
Cdd:cd22457    5 IPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKaphDETG--ERMFTITGTPEANDRALRLL 63

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: 59.74 E-value: 2.61e-11

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 142 PRTSmTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLD 210
Cdd:cd22522    6 PPAS-THELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGSPANISLAQYLIN 73

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: 60.04 E-value: 2.71e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE--RSVSLTGAPESVQKAKMMLDDIVS 214
Cdd:cd22429    3 TEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDlvRLITITGTKKEVDAAKSLILEKVS 72

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: 59.22 E-value: 3.80e-11

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 156 MVGLIIGRGGEQINKIQQDSGCKVQIspDSGGlPERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22430   10 LVGAVIGRGGSKIRELEESTGSKIKI--IKGG-QEAEVKIFGSDEAQQKAKELIDELVGR 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: 59.25 E-value: 4.37e-11

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDL 390
Cdd:cd22454    6 IEVVIPNADVGKVIGKGGETIKRIEALTDTVITFERVNGGSPNREVQITGSPDNVAAAKRLIEDT 70

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: 57.99 E-value: 9.98e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAhIMGPPDRCEHAARIINDLLQSLRS 396
Cdd:cd22417    3 LTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDDEIT-ITGYEKNAEAAKDAILKIVQELES 72

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: 58.04 E-value: 1.02e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 157 VGLIIGRGGEQINKIQQDSGCKVQISpdSGGLPERSVSLTGAPESVQKA-KMM 208
Cdd:cd22438   10 VGSIIGKKGETIKKFREESGARINIS--DGSCPERIVTVTGTTDAVFKAfELI 60

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: 57.93 E-value: 1.07e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKA-KMMLDDI 212
Cdd:cd22435    8 VPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFYPgttERVCLIQGEVEAVNAVlDFILEKI 72

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: 57.67 E-value: 1.28e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQIS-PDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22400    6 VPSEFVGAIIGKGGATIRQITQQTGARIDIHrKENAGAAEKAITIYGTPEGCSSACKQILEIM 68

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: 56.43 E-value: 3.43e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGAPESVQKAKMML 209
Cdd:cd09031    7 VPENLVGAILGKGGKTLVEIQELTGARIQISKKGEFVPgtrNRKVTITGTPAAVQAAQYLI 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: 56.56 E-value: 3.86e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22434    8 IPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNAQYLLQNSVKQ 71

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: 56.10 E-value: 4.14e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 151 RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISP-DSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22402    6 YIPNKAVGAIIGTKGSHIRYIKRFSGASIKIAPaDSPDAPERKVTITGPPEAQWKAQLCI 65

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: 56.17 E-value: 4.56e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22454    8 VVIPNADVGKVIGKGGETIKRIEALTDTVITFE---RVNGGSPNREVQITGSPDNVAAAKRLIEDTI 71

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: 55.41 E-value: 9.83e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 395
Cdd:cd22478   10 VPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSCMLTGTPESVQSAKRLLDQIVEKGR 75

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: 54.90 E-value: 1.20e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 145 SMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22523    1 TSSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLI 65

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: 54.50 E-value: 1.43e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 156 MVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPErsVSLTGAPESVQKAKMMLDDIVS 214
Cdd:cd02394   12 FHGHIIGKGGANIKRIREESGVSIRIPDDEANSDE--IRIEGSPEGVKKAKAEILELVD 68

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

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 54.26 E-value: 2.67e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22428    5 IEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELPERVLLIQGNPVQAQRAEEAIHQII 74

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: 54.29 E-value: 2.92e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLD 210
Cdd:cd22521    6 SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLIN 69

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: 53.41 E-value: 4.42e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVQQACEMVMDI 303
Cdd:cd22396    4 EYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLP--ERPCTLTGTPDAIETAKRLIDQI 67

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: 53.00 E-value: 4.62e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP-ERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22399    1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPnEKLFIIRGNPQQIEHAKQLIRE 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: 53.02 E-value: 4.92e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 149 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIS-PDSGGlPERSVSLTGAPESVQKAK 206
Cdd:cd22462    2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVLkPDSAT-GERIVLISGTPDQARHAQ 59

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

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 52.60 E-value: 7.74e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNfklFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22404    5 VTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRR---ITIKGSADATRQAAQLINALIK 69

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: 52.65 E-value: 7.94e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22485    7 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 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: 52.61 E-value: 9.28e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 153 PDGMVGLIIGRGGEQINKIQQDSGCKVQIS---PDSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22401    7 HNNLCGRLIGKDGRNIKKIMEDTNTKITISslqDLTSYNPERTITIKGSLEAMSEAESLI 66

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: 51.84 E-value: 1.45e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNvDKPLRIIGDPYKVQQACEMV 300
Cdd:cd22399    3 TFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPPPNPN-EKLFIIRGNPQQIEHAKQLI 64

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: 51.89 E-value: 1.72e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGAPESVQKA 205
Cdd:cd02396    8 VPASQCGSLIGKGGSKIKEIRESTGASVQVASEM--LPnstERAVTISGSPEAITKC 62

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: 51.42 E-value: 1.74e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVdkplRIIGDPYKVQQACEMVMDI 303
Cdd:cd02394    2 AFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEI----RIEGSPEGVKKAKAEILEL 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: 51.47 E-value: 2.11e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMV 300
Cdd:cd22436    5 ILVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLQERVVTVTGEPEANRKAVSLI 66

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: 51.12 E-value: 2.56e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPnfKLFVIRGSPQQIDHAKQLI 492
Cdd:cd02396    8 VPASQCGSLIGKGGSKIKEIRESTGASVQVASEMLPNSTE--RAVTISGSPEAITKCVEQI 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: 51.06 E-value: 2.71e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22404    2 SKKVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLI 64

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: 51.05 E-value: 3.36e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 327 DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22480    4 EYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMPERPCVLTGTPESIEQAKRLLGQIV 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: 50.76 E-value: 3.99e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGAPESVQKA 205
Cdd:cd22456    6 IPHSLIGSIIGKGGARIKEIQDGSGARLVASKEF--LPlstERILEVQGTPDAIHNA 60

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: 50.71 E-value: 4.08e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22479    7 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGSPEAVQKAKMMLDDIV 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: 50.61 E-value: 4.48e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAG--VKMILIQD---GSQntnvDKPLRIIGDPYKVQQACEMVMDILR 305
Cdd:cd22435    6 LLVPNYAAGSIIGKGGQTIAQLQKETGarIKLSKNNDfypGTT----ERVCLIQGEVEAVNAVLDFILEKIR 73

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: 50.25 E-value: 4.72e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqlPPNGDPNfKLFVIRGSPQQIDHAKQLIE 493
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEV----PPNDSDS-ETITLRGPADKLGAALTLVY 62

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

Pssm-ID: 411826 [Multi-domain] Cd Length: 67 Bit Score: 50.34 E-value: 5.06e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22398    1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFK---PDDGNSPDRICVITGPPDQVQHAARMIQELI 67

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: 50.42 E-value: 6.34e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ 309
Cdd:cd22499    6 IKVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGHFYASQMAQRKIRDILAQVKQ 76

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: 49.94 E-value: 6.40e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22462    1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLIEAFI 66

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: 49.49 E-value: 8.24e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 438 GLVIGRGGENVKAINQQTGAFVEIsrqlpPNGDPNFKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd02394   14 GHIIGKGGANIKRIREESGVSIRI-----PDDEANSDEIRIEGSPEGVKKAKAEILELVD 68

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: 49.78 E-value: 8.83e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 151 RVPDGMVGLIIGRGGEQINKIQQDSGCKVQISpDSGglperSVSLTGA-PESVQKAKMMLDDIV 213
Cdd:cd02393    9 KIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE-DDG-----TVTIFATdKESAEAAKAMIEDIV 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: 49.35 E-value: 1.34e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22463    5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEETQKILRISGTEEQLKRAQSLVEGLI 71

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: 1.44e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNfKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22397    6 IPGNKVGLIIGKGGETIKQLQERAGVKMVMIQDGPQPTGQD-KPLRITGDPQKVQRAKELVMELI 69

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: 48.86 E-value: 1.58e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 157 VGLIIGRGGEQINKIQQDSGCKVQISpdSGGLPERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22515   13 VGSIIGKKGESVKKMREESGARINIS--EGNCPERIITLAGPTNAIFKAFAMIID 65

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

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 48.87 E-value: 1.63e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 431 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPnFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22428   10 KVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELP-ERVLLIQGNPVQAQRAEEAIHQII 74

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

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 48.42 E-value: 2.09e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd22400    6 VPSEFVGAIIGKGGATIRQITQQTGARIDIHR--KENAGAAEKAITIYGTPEGCSSACKQILE 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: 48.42 E-value: 2.28e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-EKIAHIMGPPDRCEHAARII 387
Cdd:cd22400    6 VPSEFVGAIIGKGGATIRQITQQTGARIDIHRKENAGAaEKAITIYGTPEGCSSACKQI 64

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: 48.95 E-value: 2.29e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 142 PRTSMTeeYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPER--------SVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22447    2 PKQNLT--VPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPAdedddtmvEVTITGDEFNVQHAKQRIEEII 79


                 .
gi 163954948 214 S 214
Cdd:cd22447   80 S 80

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: 48.20 E-value: 3.36e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 149 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPE--RSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22463    5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEEtqKILRISGTEEQLKRAQSLVEGLI 71

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: 48.21 E-value: 3.66e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ 309
Cdd:cd22500    6 IKVPSSAAGRVIGKGGKTVNELQNLTSAEVIVPRDQTPDENEEVIVKIIGHFFASQTAQRKIREIVQQVKQ 76

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: 48.10 E-value: 3.78e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 157 VGLIIGRGGEQINKIQQDSGCKVQISpdSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22517   13 VGSIIGKKGETVKRIREESSARITIS--EGSCPERITTITGSTDAVFRAFSMI 63

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: 47.70 E-value: 4.21e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 431 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd22434    7 TIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSED---RIITITGTQDQIQNAQYLLQN 67

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: 47.61 E-value: 4.35e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISrQLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22436    7 VPNSTAGMIIGKGGATIKAIMEQSGARVQIS-QKPESINLQERVVTVTGEPEANRKAVSLILQKI 70

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: 47.56 E-value: 4.43e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQIsPDSGGlPERSVSLTGapeSVQKAKMMLDDIV 213
Cdd:cd22432    8 IPSKAAGAIIGKGGENIKRLRTEYNASVSV-PDSSG-PERILTISA---DRETVLGILTEIL 64

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

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 47.60 E-value: 4.77e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22437    5 VPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPGSSERIVTITGSFDQVVKAVALILEKL 69

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: 47.31 E-value: 5.66e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 327 DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQD--DGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22481    5 EIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDgpQNTGADKPLRITGDPYKVQQAKEMVLELI 71

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

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 47.23 E-value: 6.89e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPdSGGLP------ERSVSLTGAPESVQKA 205
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVRILP-EEELPpcaspdDRVVQISGEAQAVKKA 64

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

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 46.49 E-value: 1.02e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGglpERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22449    5 TVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFEDKTG---EGNVEIKGSKKNVEEAKKRILSQIDE 70

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

Pssm-ID: 411944 Cd Length: 77 Bit Score: 47.02 E-value: 1.12e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 157 VGLIIGRGGEQINKIQQDSGCKVQISpdSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22516   20 VGSIIGKKGETVKKMREESGARINIS--EGNCPERIVTITGPTDAIFKAFAMI 70

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

Pssm-ID: 411831 [Multi-domain] Cd Length: 66 Bit Score: 46.46 E-value: 1.17e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQA 296
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEGDEVPVEIIGNFYATQSA 61

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: 46.46 E-value: 1.29e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQ--DDGTGPEKIAHIMGPPDRCEHAARII 387
Cdd:cd22436    7 VPNSTAGMIIGKGGATIKAIMEQSGARVQISQkpESINLQERVVTVTGEPEANRKAVSLI 66

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: 46.29 E-value: 1.33e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 431 SIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22502    6 SVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTGD---RIITIRGGTESTRQATQLINALIK 69

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: 46.32 E-value: 1.40e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 236 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSqntnvdkpLRIIG-DPYKVQQACEMVMDILRE 306
Cdd:cd02393    5 ITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDDGT--------VTIFAtDKESAEAAKAMIEDIVAE 68

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

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 46.11 E-value: 1.54e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22400    3 RILVPSEFVGAIIGKGGATIRQITQQTGAR-IDIHRKENAGAAEKAITIYGTPEGCSSACKQILEIM 68

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: 1.73e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 245 KAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVdkplRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22430   10 LVGAVIGRGGSKIRELEESTGSK-IKIIKGGQEAEV----KIFGSDEAQQKAKELIDELVGR 66

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

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 45.68 E-value: 2.11e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPER--SVSLTGAPES 201
Cdd:cd22459    8 CPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERviTISSSEAPEA 59

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 50.82 E-value: 2.72e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSqntnvdkpLRIIG-DPYKVQQACEMVMDILRE 306
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDDGT--------VKIAAtDGEAAEAAKERIEGITAE 618

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: 45.86 E-value: 2.87e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 141 PPRTSMTEeyrVPDGMVGLIIGRGGEQINKIQQDSGCKVQISP-DSGGLPER-------SVSLTGAPESVQKAKMMLDDI 212
Cdd:cd22446    5 PKVTITIS---VPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKrNEEGNYDEddddetvEISIEGDAEGVELAKKEIEAI 81


                 ..
gi 163954948 213 VS 214
Cdd:cd22446   82 VK 83

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: 45.14 E-value: 2.95e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQlpPNGDPNFKLFVIRGSPQQIDHAKQLIE 493
Cdd:cd22457    2 NISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKA--PHDETGERMFTITGTPEANDRALRLLY 64

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: 45.30 E-value: 3.30e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISR--QLPPNGDPNFKLFVIRGSPQQIDHAKQLI 492
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVRILPeeELPPCASPDDRVVQISGEAQAVKKALELV 68

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 50.43 E-value: 3.39e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 142 PRTSM------TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISpDSGglperSVSLTGA-PESVQKAKMMLDDIVS 214
Cdd:PRK11824 544 PRAELspyaprIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-DDG-----TVKIAATdGEAAEAAKERIEGITA 617

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 163954948 215 rgrggppgqfhdNANGGQ--NGTVQEIM-------IPAGKAGLV 249
Cdd:PRK11824 618 ------------EPEVGEiyEGKVVRIVdfgafveILPGKDGLV 649

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: 45.40 E-value: 3.54e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22478    8 YKVPDGMVGFIIGRGGEQISRIQQESGCKIQIA---PDSGGLPERSCMLTGTPESVQSAKRLLDQIVE 72

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: 44.92 E-value: 3.68e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 150 YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIS---PDSGGLPERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22489    4 YTIPADKCGLVIGKGGENIKSINQQSGAHVELQrnpPPNTDPNVRIFTIRGVPQQIEHARQLIDE 68

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: 45.03 E-value: 4.16e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 163954948 160 IIGRGGEQINKIQQDSGCKVQIsPDS--GGLPERS--VSLTGAPESVQKAKM 207
Cdd:cd22421   17 VIGKGGNNIKKVMEDTGCHIHF-PDSnrTSQAEKSnqVSIAGQPAGVESARA 67

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: 45.12 E-value: 4.61e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22503    5 LSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNGE---RMITIRGGTESTRYAVQLINALIQ 69

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins; The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance.

Pssm-ID: 411892 [Multi-domain] Cd Length: 66 Bit Score: 44.39 E-value: 5.12e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQlppNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22464    3 ISVDASLAGAIIGKGGVNSKQICRETGVKLSIRDH---ERDPNLKNVELEGSFEQIKEASGMVRELI 66

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: 44.59 E-value: 5.18e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 163954948 158 GLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKA 205
Cdd:cd22455   13 AVIIGKGGENIARLRATTGVKAGVSKVVPGVHDRVLTVSGPLEGVAKA 60

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: 45.10 E-value: 5.51e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 232 QNGTVQeimIPAGKAGLVIGKGGETIKQLQERAGVKM-ILIQDGSQNTNVDK-----PLRIIGDPYKVQQACEMVMDI 303
Cdd:cd22447    4 QNLTVP---IPASTRARIIGKKGANLKQIREKTGVRIdIPPRDADAAPADEDddtmvEVTITGDEFNVQHAKQRIEEI 78

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: 44.52 E-value: 6.12e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 323 GGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP--EKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22482    1 GTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVQQACEMVMDILR 72

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: 44.63 E-value: 6.59e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPnfKLFVIRGSPQQI 485
Cdd:cd22520    8 IPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNSTE--RAVTVSGVPDAI 59

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: 44.23 E-value: 7.31e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMIL--IQDGSQNTNVdkplRIIGDPYKVQQACEMVMDI 303
Cdd:cd22454    7 EVVIPNADVGKVIGKGGETIKRIEALTDTVITFerVNGGSPNREV----QITGSPDNVAAAKRLIEDT 70

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: 44.05 E-value: 8.37e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKA 205
Cdd:cd22395    1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKA 59

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: 44.25 E-value: 8.55e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 154 DGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGL---PERSVSLTGAPESVQKAKM 207
Cdd:cd22494    8 NSLVGRLIGKEGRNLKKIEQDTGTKITISSLQDLTiynPERTITVKGSIEACSSAEV 64

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: 43.76 E-value: 9.08e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 427 EMTfsIPTHKCGLVIGRGGENVKAINQQTGAFVEISRqlPPNGDPNfKLFVIRGSPQQIDHAKQLI 492
Cdd:cd22439    5 EIT--IPNDLIGCIIGKGGTKINEIRQLSGATIKIAN--SEDGSTE-RSVTITGTPEAVSLAQYLI 65

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: 44.33 E-value: 9.17e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 424 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQ---LPPNGDPNFKL--FVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22447    2 PKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRdadAAPADEDDDTMveVTITGDEFNVQHAKQRIEEII 79

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

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 43.75 E-value: 9.40e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAARII 387
Cdd:cd22437    5 VPNSSCGLIIGKGGSTIKELREDSNANIKISPKDQLLPgssERIVTITGSFDQVVKAVALI 65

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: 43.75 E-value: 9.54e-06

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVdkplRII 287
Cdd:cd22459    6 LLCPVSKAGSVIGKGGEIIKQLRQETGAR-IKVEDGVPGTEE----RVI 49

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

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 43.43 E-value: 1.09e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRqlppnGDPN--FKLFvirGSPQQIDHAKQLIEEKIE 497
Cdd:cd22430    3 CFKIDSSLVGAVIGRGGSKIRELEESTGSKIKIIK-----GGQEaeVKIF---GSDEAQQKAKELIDELVG 65

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: 43.76 E-value: 1.09e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 241 IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVD-KPLRIIGDPYKVQQACEMVMD 302
Cdd:cd22489    6 IPADKCGLVIGKGGENIKSINQQSGAHVELQRNPPPNTDPNvRIFTIRGVPQQIEHARQLIDE 68

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

Pssm-ID: 411948 [Multi-domain] Cd Length: 72 Bit Score: 43.86 E-value: 1.14e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGAPESV 202
Cdd:cd22520    8 IPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDL--LPnstERAVTVSGVPDAI 59

putative RNA-processing protein; Provisional

Pssm-ID: 237494 [Multi-domain] Cd Length: 180 Bit Score: 46.40 E-value: 1.34e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVK--------MILIQDGSQNT------------------NVDKPLRIIG 288
Cdd:PRK13763   3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKleidsetgEVIIEPTDGEDplavlkardivkaigrgfSPEKALRLLD 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 289 DpykvqqacEMVMDILRERDqggFGDRNEYGSRVGGGIdvpvprhsvgvvIGRSGEMIKKIQNDAGVRIQFKqddgtgpE 368
Cdd:PRK13763  83 D--------DYVLEVIDLSD---YGDSPNALRRIKGRI------------IGEGGKTRRIIEELTGVDISVY-------G 132

                        170       180
                 ....*....|....*....|....
gi 163954948 369 KIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:PRK13763 133 KTVAIIGDPEQVEIAREAIEMLIE 156

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

Pssm-ID: 411943 Cd Length: 70 Bit Score: 43.46 E-value: 1.42e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 335 VGVVIGRSGEMIKKIQNDAGVRIQFKQddGTGPEKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22515   13 VGSIIGKKGESVKKMREESGARINISE--GNCPERIITLAGPTNAIFKAFAMIIDKLE 68

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: 43.46 E-value: 1.63e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNfKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22481    8 IPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGAD-KPLRITGDPYKVQQAKEMVLELI 71

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: 1.66e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 163954948 335 VGVVIGRSGEMIKKIQNDAGVRIQFKQddGTGPEKIAHIMGPPD 378
Cdd:cd22516   20 VGSIIGKKGETVKKMREESGARINISE--GNCPERIVTITGPTD 61

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: 42.98 E-value: 1.87e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 437 CGLVIGRGGENVKAINQQTGAFVEISR-QLPPNGDPNfKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22401   11 CGRLIGKDGRNIKKIMEDTNTKITISSlQDLTSYNPE-RTITIKGSLEAMSEAESLISEKL 70

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

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 43.23 E-value: 1.88e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFkQDDGTgpekiAHIMGP-PDRCEHAARIINDLLQ 392
Cdd:cd02393   10 IPPDKIGDVIGPGGKTIRAIIEETGAKIDI-EDDGT-----VTIFATdKESAEAAKAMIEDIVA 67

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: 1.91e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQ------------DGSQNtNVDKPLRIIGD 289
Cdd:cd22395    3 EFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPhpytqnfqicsiEGTQQ-QIDKALKLIRK 65

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

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 42.85 E-value: 2.07e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 428 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqlppngDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd02393    6 TTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDI--------EDDGTVTIFATDKESAEAAKAMIED 64

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: 42.58 E-value: 2.20e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIsPDSGGlPERSVSLTGAPESVQKAKMML 209
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDL-PEENS-DSDVITITGKKEDVEKARERI 61

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

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 42.83 E-value: 2.30e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 326 IDVPVPRHsvGVVIGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEKIAhimGPPDRCEHAARII 387
Cdd:cd22451    5 IDIPKEYH--RAIIGKGGAVLRELEAETGCRIQVpKKDDPSGKIRIT---GARDGVEAATAKI 62

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

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 42.63 E-value: 2.35e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 145 SMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVqISPDSGGLPERSVSLTGAPESVQKAKMML 209
Cdd:cd22413    2 SFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARI-IFPTARDEDQELITIIGTKEAVEKAKEEL 65

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: 42.74 E-value: 2.63e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 330 VPRHSVGVVIGRSGEMIKKI--QNDAGVRIQFKQDDGTGpEKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22491    6 VPTQFVGAIIGKEGLTIKNItkQTQSKVDIHRKENAGAA-EKPITIHATPEGCSAACRMILEIMQ 69

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

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 42.91 E-value: 2.66e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP---EKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22435    8 VPNYAAGSIIGKGGQTIAQLQKETGARIKLSKNNDFYPgttERVCLIQGEVEAVNAVLDFILEKI 72

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: 2.69e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 335 VGVVIGRSGEMIKKIQNDAGVRIQFKqdDGTGPEKIAHIMGPPDRCEHAARII 387
Cdd:cd22438   10 VGSIIGKKGETIKKFREESGARINIS--DGSCPERIVTVTGTTDAVFKAFELI 60

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: 42.44 E-value: 3.25e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGlPERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22458    2 TWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNS-SQQTIHLSGTDKQIALAISSIEE 65

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

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 42.47 E-value: 3.61e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 141 PPrtsMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGAPESV 202
Cdd:cd22519    4 PP---VTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDM--LPnstERAVTISGTPDAI 63

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.

Pssm-ID: 411852 [Multi-domain] Cd Length: 72 Bit Score: 42.32 E-value: 3.69e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAF-VEISRQLPPngdpnfkLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22424   10 VPYRVVGLVVGPKGATIKRIQQQTHTYiVTPSRDKEP-------VFEVTGMPENVERAREEIEAHIA 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: 42.28 E-value: 3.79e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 246 AGLVIGKGGETIKQLQERAGVKmILIQDGSQNtNVDKPLRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22455   12 AAVIIGKGGENIARLRATTGVK-AGVSKVVPG-VHDRVLTVSGPLEGVAKAFGLIARTLNE 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: 41.85 E-value: 4.34e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEKIAHIMGPPD 378
Cdd:cd22402    7 IPNKAVGAIIGTKGSHIRYIKRFSGASIKIaPADSPDAPERKVTITGPPE 56

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: 4.34e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22491    4 ILVPTQFVGAIIGKEGLTIKNITKQTQSK-VDIHRKENAGAAEKPITIHATPEGCSAACRMILEIMQK 70

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: 41.86 E-value: 4.52e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 245 KAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22433   12 QAGCIIGRAGFKIKELREKTGAT-IKVYSECCPRSTDRVVQIGGKPDKVVECIREILELL 70

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: 4.69e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22502    2 SKKVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTGDRIITIRGGTESTRQATQLINALI 68

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

Pssm-ID: 411831 [Multi-domain] Cd Length: 66 Bit Score: 41.46 E-value: 5.87e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 149 EYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIsPDSGGLP---ERSVSLTGAPESVQKA 205
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKL-PRDQTPDegdEVPVEIIGNFYATQSA 61

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: 41.67 E-value: 6.14e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIsPDSGGlPERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22451    2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQV-PKKDD-PSGKIRITGARDGVEAATAKILNISDE 68

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: 41.95 E-value: 6.83e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 154 DGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGL---PERSVSLTGAPESVQKAK 206
Cdd:cd22495    8 NNFVGRLIGKEGRNLKKIEQDTDTKITISPLQDLTlynPERTITVKGSIETCAKAE 63

second 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 second one.

Pssm-ID: 411854 [Multi-domain] Cd Length: 63 Bit Score: 41.36 E-value: 6.99e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCK-VQISPDSGglperSVSLTG-APESVQKAKMMLD 210
Cdd:cd22426    3 IEEFKVDPDLIGLAIGSHGSNIQQARKIPGVEsIDVDEEDG-----TFRIYGeTPEAVEKARALLE 63

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: 41.43 E-value: 7.21e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQS 393
Cdd:cd22404    5 VTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLINALIKD 70

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: 41.42 E-value: 7.72e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGckVQIS-PDSGGLPERSVSLTGAPESVQKAKMMLDDIVS 214
Cdd:cd22417    7 VDPKYHPKIIGRKGAVITKLRDDHD--VNIQfPDKGDENDDEITITGYEKNAEAAKDAILKIVQ 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: 41.82 E-value: 7.81e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 327 DVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD--GTGPEKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22483    8 EILIPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGplPTGADKPLRITGDPFKVQQAREMVLEIIR 75

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

Pssm-ID: 411946 [Multi-domain] Cd Length: 78 Bit Score: 41.65 E-value: 7.82e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 143 RTSMTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSggLP---ERSVSLTGAPESV 202
Cdd:cd22518    4 RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDM--LPnstERAITIAGIPQSI 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: 41.48 E-value: 8.16e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 241 IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRII-GDPYKVQQACEMV 300
Cdd:cd22487    8 VPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIrGSPQQIDYARQLI 68

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: 41.42 E-value: 8.63e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22480    5 YKVPDKMVGFIIGRGGEQISRIQLESGCKIQIA---PDSGGMPERPCVLTGTPESIEQAKRLLGQIVD 69

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

Pssm-ID: 411945 Cd Length: 70 Bit Score: 41.17 E-value: 8.90e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 335 VGVVIGRSGEMIKKIQNDAGVRIQFKQddGTGPEKIAHIMGPPDRCEHAARII 387
Cdd:cd22517   13 VGSIIGKKGETVKRIREESSARITISE--GSCPERITTITGSTDAVFRAFSMI 63

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

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 41.31 E-value: 1.03e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 424 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPnfKLFVIRGSPQQI 485
Cdd:cd22519    4 PPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTE--RAVTISGTPDAI 63

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: 41.08 E-value: 1.04e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd22479    5 YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIS---PDSGGLPERSVSLTGSPEAVQKAKMMLDD 66

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: 40.90 E-value: 1.04e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 428 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlpPNGDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd22458    3 WEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLI----PISNSSQQTIHLSGTDKQIALAISSIEE 65

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

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 40.98 E-value: 1.16e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVeisrQLPPNGD--PNF--KLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22435    8 VPNYAAGSIIGKGGQTIAQLQKETGARI----KLSKNNDfyPGTteRVCLIQGEVEAVNAVLDFILEKI 72

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: 41.17 E-value: 1.24e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE--KIAHIMGPPDRCEHAARIIND 389
Cdd:cd22429    8 VPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDlvRLITITGTKKEVDAAKSLILE 69

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

Pssm-ID: 411946 [Multi-domain] Cd Length: 78 Bit Score: 40.88 E-value: 1.30e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 424 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPnfKLFVIRGSPQQI 485
Cdd:cd22518    5 PPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE--RAITIAGIPQSI 64

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

Pssm-ID: 411942 [Multi-domain] Cd Length: 71 Bit Score: 40.48 E-value: 1.51e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQlppnGD----PNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22514    4 TIGVPDEHIGAILGRGGRTINEIQQHSGARIKISDR----GDfvsgTRNRKVTITGPQDAVQMAQYLLEQKL 71

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

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 40.32 E-value: 1.64e-04

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 163954948 240 MIPAGK-AGLVIGKGGETIKQLQERAGVKmILIQDGS 275
Cdd:cd22438    3 MLMQGKeVGSIIGKKGETIKKFREESGAR-INISDGS 38

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: 40.23 E-value: 1.67e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 241 IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVdkplRIIGDPYKVQQACEMVM 301
Cdd:cd22408    6 VPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETI----TLRGPADKLGAALTLVY 62

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: 40.78 E-value: 1.89e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 236 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERD 308
Cdd:cd22429    3 TEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVRLITITGTKKEVDAAKSLILEKVSEEE 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: 39.96 E-value: 2.06e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 333 HSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDgtgPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22430    9 SLVGAVIGRGGSKIRELEESTGSKIKIIKGG---QEAEVKIFGSDEAQQKAKELIDELV 64

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

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 40.30 E-value: 2.24e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP-----EKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVRILPEEELPPcaspdDRVVQISGEAQAVKKALELVSSRLR 73

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.

Pssm-ID: 411852 [Multi-domain] Cd Length: 72 Bit Score: 40.01 E-value: 2.29e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDgtgPEKIAHIMGPPDRCEHAARII 387
Cdd:cd22424    6 IQVRVPYRVVGLVVGPKGATIKRIQQQTHTYIVTPSRD---KEPVFEVTGMPENVERAREEI 64

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

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 39.93 E-value: 2.35e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 438 GLVIGRGGENVKAINQQTGAFVEISRqlppNGDPNfKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22438   11 GSIIGKKGETIKKFREESGARINISD----GSCPE-RIVTVTGTTDAVFKAFELICRKLE 65

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: 40.00 E-value: 2.39e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 151 RVPDGMVGLIIGRGGEQINKIQQDSGCKVQIspdsgglPERS-----VSLTGAPESVQKAKMML 209
Cdd:cd22452    7 KVSPRYFGRIIGPGGSNINQIREKSGCFINV-------PKKNkesdvITLRGTKEGVEKAEEMI 63

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

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 39.81 E-value: 2.62e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22395    6 VPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKF 67

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

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 40.09 E-value: 2.69e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEKI-------AHIMGPPDRCEHA----ARIIN 388
Cdd:cd22447    6 LTVPIPASTRARIIGKKGANLKQIREKTGVRIDIpPRDADAAPADEdddtmveVTITGDEFNVQHAkqriEEIIS 80

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.

Pssm-ID: 411852 [Multi-domain] Cd Length: 72 Bit Score: 40.01 E-value: 2.73e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 151 RVPDGMVGLIIGRGGEQINKIQQDSGCKVqISPDSGGLPERSVslTGAPESVQKAKMMLDD 211
Cdd:cd22424    9 RVPYRVVGLVVGPKGATIKRIQQQTHTYI-VTPSRDKEPVFEV--TGMPENVERAREEIEA 66

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins; The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance.

Pssm-ID: 411892 [Multi-domain] Cd Length: 66 Bit Score: 39.77 E-value: 3.01e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMIlIQDGSQNTNVdKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22464    3 ISVDASLAGAIIGKGGVNSKQICRETGVKLS-IRDHERDPNL-KNVELEGSFEQIKEASGMVRELI 66

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: 39.51 E-value: 3.08e-04

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP 466
Cdd:cd22459    8 CPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVP 42

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: 39.55 E-value: 3.18e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 425 GGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22486    2 GGSIEVSVPRFAVGIVIGRNGEMIKKIQNDAGVRIQFK---PDDGISPERVAQVMGPPDRCQHAAHIINELI 70

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

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 39.61 E-value: 3.21e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVkMILIQDGSQNTNvDKPLRIIGDPYKVQQA 296
Cdd:cd22434    2 TTTQVTIPKDLAGSIIGKGGQRIRQIRHESGA-SIKIDEPLPGSE-DRIITITGTQDQIQNA 61

third 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 third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 39.50 E-value: 3.21e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPErsVSLTGAPESVQKAK 206
Cdd:cd22407    1 TERLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDE--IVVSGEKEGVAQAV 58

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: 39.71 E-value: 3.91e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 423 PPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIEEK 495
Cdd:cd22522    6 PPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSE---RQITITGSPANISLAQYLINAR 75

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: 39.11 E-value: 4.00e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGpEKIAhIMGPPDRCEHAARIIN 388
Cdd:cd22411    2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDS-DVIT-ITGKKEDVEKARERIL 62

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

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 39.17 E-value: 4.09e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 163954948 441 IGRGGENVKAINQQTGAFVeisrQLPPNGDPNFKLFVIRGSPQQIDHAKQLIE 493
Cdd:cd22413   18 IGRGGANIRKIRDNTGARI----IFPTARDEDQELITIIGTKEAVEKAKEELE 66

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

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 39.52 E-value: 4.12e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 247 GLVIGKGGETIKQLQERAGVKMIL--IQDGSQNtNVDKPLRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22401   12 GRLIGKDGRNIKKIMEDTNTKITIssLQDLTSY-NPERTITIKGSLEAMSEAESLISEKLRE 72

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: 39.69 E-value: 4.20e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 330 VPRHSVGVVIGRSGEMIKKI--QNDAGVRIQFKQDDGTGpEKIAHIMGPPDRCEHAARIINDLLQ 392
Cdd:cd22490    6 VPTQYVGAIIGKEGATIRNItkQTQSKIDVHRKENAGAA-EKAISIHSTPEGCSAACKMILEIMQ 69

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: 39.17 E-value: 4.46e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 150 YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQI--SPDSGGLPE-RSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22487    6 FIVPTGKTGLIIGKGGETIKSISQQSGARIELqrNPPPNADPNmKLFTIRGSPQQIDYARQLIEE 70

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

Pssm-ID: 411911 [Multi-domain] Cd Length: 83 Bit Score: 39.51 E-value: 4.64e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 432 IPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLP-PNGDPnfKLFVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd22483   11 IPASKVGLVIGKGGETIKQLQERTGVKMIMIQDGPlPTGAD--KPLRITGDPFKVQQAREMVLEII 74

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: 39.11 E-value: 4.65e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLI 492
Cdd:cd22523    6 FLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSE---RHVTITGSPVSITLAQYLI 65

KH domain;

Pssm-ID: 429574 [Multi-domain] Cd Length: 78 Bit Score: 39.46 E-value: 4.74e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 163954948  238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDK 282
Cdd:pfam07650  28 IVVIRASQPGIVIGKGGSRIKKIGKELRKDIEKLLGKKVYLNIVK 72

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: 4.92e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSG-GLPERSVSLTGAPESVQKAK 206
Cdd:cd22497    9 IPTQAVGAIIGKKGQHIKQLARFAGASIKIAPAEGpDVSERMVIITGPPEAQFKAQ 64

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 38.77 E-value: 4.97e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIqdGSQNTNVDKPLRIIGDPYKVQQA 296
Cdd:cd22462    2 EILIPAHAVGSVIGRGGSNINQIREISGAKVEVL--KPDSATGERIVLISGTPDQARHA 58

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

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 38.78 E-value: 5.23e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 163954948 339 IGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIaHIMGPPDRCEHA 383
Cdd:cd22413   18 IGRGGANIRKIRDNTGARIIFPTARDEDQELI-TIIGTKEAVEKA 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: 39.10 E-value: 5.47e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAhIMGPPDRCEHAARII 387
Cdd:cd09031    3 IELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGefvpGTRNRKVT-ITGTPAAVQAAQYLI 67

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: 39.30 E-value: 5.80e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQ 309
Cdd:cd22490    4 LLVPTQYVGAIIGKEGATIRNITKQTQSK-IDVHRKENAGAAEKAISIHSTPEGCSAACKMILEIMQKEAK 73

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 38.95 E-value: 6.28e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPE--KIAHIMGPPDRCEHAARIINDLL 391
Cdd:cd22463    4 IEFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPLEEtqKILRISGTEEQLKRAQSLVEGLI 71

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: 38.77 E-value: 6.39e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 237 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22479    3 EEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLP--ERSVSLTGSPEAVQKAKMMLDDIV 68

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: 38.76 E-value: 6.53e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 241 IPAGKAGLVIGKGGETIKQLQERAGVKM-ILIQDGSQ---NTNvDKPLRIIGDPYKVQQACEMVMDILR 305
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVrILPEEELPpcaSPD-DRVVQISGEAQAVKKALELVSSRLR 73

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

Pssm-ID: 411817 [Multi-domain] Cd Length: 70 Bit Score: 38.72 E-value: 6.99e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 237 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKmiLIQDGSQNTNVDKPLRIIgDPYKVQQACEMVMDILR 305
Cdd:cd22389    1 LYVKIPKERIGVLIGKKGETKREIEERTGVK--ITVDSETGEVIIEPEDEE-DPLNVMKAREVVRAIGR 66

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 43.11 E-value: 7.08e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlpPNGdpnfKLFVIRGSPQQIDHAKQLIEE 494
Cdd:PRK11824 557 TIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE----DDG----TVKIAATDGEAAEAAKERIEG 614

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: 39.66 E-value: 7.18e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 154 DGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGL---PERSVSLTGAPESVQKAKmmlDDIVSRGR 217
Cdd:cd22493   13 NNFVGRLIGKEGRNLKKVEQDTETKITISPLQDLTlynPERTITVKGSIEACCRAE---QEIMKKVR 76

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: 38.52 E-value: 7.33e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQA 296
Cdd:cd22501    4 IKVPSYAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVVVKITGHFYASQLA 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: 38.33 E-value: 8.18e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQ---LPpnGDPNFKLfVIRGSPQQIDHAKQLIEEKI 496
Cdd:cd09031    2 VIELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKgefVP--GTRNRKV-TITGTPAAVQAAQYLIEQRI 71

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: 38.93 E-value: 8.19e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 424 PGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRqLPPNGDPNFKL------FVIRGSPQQIDHAKQLIE 493
Cdd:cd22446    5 PKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPK-RNEEGNYDEDDddetveISIEGDAEGVELAKKEIE 79

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

Pssm-ID: 411886 [Multi-domain] Cd Length: 65 Bit Score: 38.20 E-value: 8.31e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 238 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIqdgSQNTNVDKPLRIIGDPYKVQQACEMV 300
Cdd:cd22458    4 EIKLPQALCGRLIGAKGKNIKALSEKSGASIRLI---PISNSSQQTIHLSGTDKQIALAISSI 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: 38.47 E-value: 9.12e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 237 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnvDKPLRIIGDPYKVqQACEMVMDILRER 307
Cdd:cd22478    6 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLP--ERSCMLTGTPESV-QSAKRLLDQIVEK 73

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: 37.93 E-value: 9.57e-04

                         10        20
                 ....*....|....*....|....
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQE 262
Cdd:cd22432    6 LLIPSKAAGAIIGKGGENIKRLRT 29

Domain of unknown function (DUF1897); This domain is found in Psi proteins produced by Drosophila, and in various eukaryotic hypothetical proteins. It has no known function.

Pssm-ID: 462653 Cd Length: 36 Bit Score: 37.39 E-value: 9.98e-04

                          10
                  ....*....|....*
gi 163954948  672 QPDYSAAWAEYYRQQ 686
Cdd:pfam09005   7 QPDYSAQWAEYYRSI 21

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: 38.16 E-value: 1.09e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 150 YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQIS---PDSGGLPERSVSLTGAPESVQKAKMMLDD 211
Cdd:cd22488    4 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqpPPNGDPNFKLFIIRGSPQQIDHAKQLIEE 68

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: 38.08 E-value: 1.14e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnVDKPLRIIGDPYK----VQQACEMVMD 302
Cdd:cd22520    6 LVIPASQCGSLIGKAGSKIKEIRESTGAQVQVAGDLLPNS-TERAVTVSGVPDAiiqcVRQICAVILE 72

type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) and similar proteins; PNPT1, also called 3'-5' RNA exonuclease OLD35, or PNPase old-35, or polynucleotide phosphorylase 1, or PNPase 1, or polynucleotide phosphorylase-like protein, is an RNA-binding protein implicated in numerous RNA metabolic processes. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'-to-5' direction. It acts as a mitochondrial intermembrane factor with RNA-processing exoribonulease activity. PNPT1 is a component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. It is involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules and required for correct processing and polyadenylation of mitochondrial mRNAs. PNPT1 also plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix.

Pssm-ID: 411809 [Multi-domain] Cd Length: 67 Bit Score: 37.94 E-value: 1.26e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 429 TFSIPTHKCGLVIGRGGENVKAINQQTGafVEISRQlppnGDPNFKLFvirgSPQQ--IDHAKQLIEE 494
Cdd:cd09033    9 TLEVPPSKRAKFVGPGGYNIKKLQAETG--VTITQV----DEETFSVF----APNQsaMDEAKEMIEE 66

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

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSG-GLPERSVSLTGAPESVQKAK 206
Cdd:cd22498   11 IPALAVGAIIGKQGQHIKQLSRFAGASIKIAPAEGpDAKLRMVIITGPPEAQFKAQ 66

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

Pssm-ID: 411941 [Multi-domain] Cd Length: 73 Bit Score: 37.80 E-value: 1.33e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 158 GLIIGRGGEQINKIQQDSGCKVQISPDSGGLP---ERSVSLTGA-PESVQKAKMMLDDIV 213
Cdd:cd22513   14 GSVIGKGGATINDFQAQSGARIQLSRAQEFFPgttDRVLLVSGSlNEVLTALNLILEKLL 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: 37.66 E-value: 1.50e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRI-----QFKQDDgtgpEKIAHIMGPPD 378
Cdd:cd22456    6 IPHSLIGSIIGKGGARIKEIQDGSGARLvaskeFLPLST----ERILEVQGTPD 55

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

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 37.63 E-value: 1.55e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 232 QNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDkplrIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22449    1 ENGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVK-IDFEDKTGEGNVE----IKGSKKNVEEAKKRILSQIDE 70

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: 1.60e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 426 GEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISrqlPPNGDPNFKLFVIRGSPQQIDHAKQLIEE 494
Cdd:cd22485    1 GGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFK---QDDGTGPEKIAHIMGPPDRCEHAARIIND 66

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: 37.73 E-value: 1.64e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 152 VPDGMVGLIIGRGGEQINKIQQDSGCKVQI-SPDSGGLPERSVSLTGAPESVQKAKMMLDDIVSR 215
Cdd:cd22491    6 VPTQFVGAIIGKEGLTIKNITKQTQSKVDIhRKENAGAAEKPITIHATPEGCSAACRMILEIMQK 70

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: 37.32 E-value: 1.83e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 321 RVGGGIDVPVPRHSVgvVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAH---IMGPPDRCEHAARII 387
Cdd:cd22421    2 RVTLKMDVSHTDHSH--VIGKGGNNIKKVMEDTGCHIHFPDSNRTSQAEKSNqvsIAGQPAGVESARAQI 69

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

Pssm-ID: 411817 [Multi-domain] Cd Length: 70 Bit Score: 37.56 E-value: 1.90e-03

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT 365
Cdd:cd22389    3 VKIPKERIGVLIGKKGETKREIEERTGVKITVDSETGE 40

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: 1.92e-03

                         10        20        30
                 ....*....|....*....|....*....|....
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQF 359
Cdd:cd22446    9 ITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQI 42

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411939 [Multi-domain] Cd Length: 78 Bit Score: 37.66 E-value: 2.00e-03

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAG-VRIQFKQDD 363
Cdd:cd22511    6 VQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRVEGDN 42

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: 37.18 E-value: 2.01e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 238 EIMIPAGKA--GLVIGKGGETIKQLQERAGVKMILIQDGSQntnvDKPLRIIGDPYKVQQACEMV 300
Cdd:cd22411    1 SIKVPIFKQfhKNIIGKGGATIKKIREETNTRIDLPEENSD----SDVITITGKKEDVEKARERI 61

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411814 [Multi-domain] Cd Length: 102 Bit Score: 38.31 E-value: 2.05e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 438 GLVIGRGGENVKAINQQTGAFVEI----SRQLPPNG----DPNFKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22386   22 GKLIGPGGSNVKHIQQETGAKVQLrgkgSGFIEPASgreaDEPLHLLISHPDPEGLQQAKKLCEDLLQ 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: 37.63 E-value: 2.27e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAG---VRIQFKQDDGTGPEK 369
Cdd:cd22512    6 IQVPRNLVGKVIGKNGKLIQEIVDKSGvvrVRIEAENDKNIPQEE 50

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: 37.63 E-value: 2.30e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 151 RVPDGMVGLIIGRGGEQINKIQQDSG-CKVQISPDSGGLPERSVSL-----TGAPESVQKAKMMLD 210
Cdd:cd22512    7 QVPRNLVGKVIGKNGKLIQEIVDKSGvVRVRIEAENDKNIPQEEGMvpfvfVGTKDSITNATVLLD 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: 37.28 E-value: 2.38e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNvDKPLRIIGDPYKVQQA 296
Cdd:cd22456    4 LLIPHSLIGSIIGKGGARIKEIQDGSGARLVASKEFLPLST-ERILEVQGTPDAIHNA 60

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: 37.34 E-value: 2.72e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 430 FSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDpnfKLFVIRGSPQQIDHAKQLIEEKIE 497
Cdd:cd22521    9 LTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTD---RQVTITGSAASISLAQYLINARLS 73

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: 36.82 E-value: 2.73e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 330 VPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDL 390
Cdd:cd22439    8 IPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLAQYLINAR 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: 36.96 E-value: 2.86e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFVIRGS---PQQIDHAKQLI 492
Cdd:cd22453    3 EISFYVPEKYHKRIIGKGGQNIQRIMKKYNVFIKFSNANDRADNYYPDNVVIRTPaknAANLISVKSDI 71

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: 37.05 E-value: 2.86e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 236 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMiliqdgsQNTNVDKP---LRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22451    2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRI-------QVPKKDDPsgkIRITGARDGVEAATAKILNISDE 68

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: 36.41 E-value: 3.16e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 427 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEIsrqlPPNGDPNFKLfVIRGSPQQIDHAKQLIE 493
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDL----PEENSDSDVI-TITGKKEDVEKARERIL 62

transcription elongation factor NusA-like protein; Validated

Pssm-ID: 181413 [Multi-domain] Cd Length: 140 Bit Score: 38.66 E-value: 3.20e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163954948 241 IPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGsqntnvDKPLRIIGD---PYKVQqacemVMDILRERDqggfgDRNE 317
Cdd:PRK08406  38 VKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS------DDPEEFIKNifaPAAVR-----SVTIKKKNG-----DKVA 101

                         90       100       110
                 ....*....|....*....|....*....|.
gi 163954948 318 YgsrvgggidVPVPRHSVGVVIGRSGEMIKK 348
Cdd:PRK08406 102 Y---------VEVAPEDKGIAIGKNGKNIER 123

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: 3.56e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV----DKPLRII--GDPYKVQQACEMVMDILRER 307
Cdd:cd22446   11 ISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYDedddDETVEISieGDAEGVELAKKEIEAIVKER 85

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: 37.20 E-value: 3.68e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 163954948 247 GLVIGKGGETIKQLQERAGVKmILI------------QDGSQNTNVDKPLR--IIGD-PYKVQQACEMVMDIL 304
Cdd:cd02395   20 GLIIGPRGNTQKRMEKESGAK-IAIrgkgsvkegkgrSDPQPDPDEEEDLHvlITADtEEKVDKAAKLIEKLL 91

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: 36.82 E-value: 3.80e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGC---KVQISPDSGGLPER----SVSLTGAPESVQKAKMMLD 210
Cdd:cd22427    3 EEIFQVPRDLVGKVIGKNGRVIQEIVDKSGVvrvKIEGDNEDGPRPREeglvPFIFVGTREAIANAKLLLE 73

fifth 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 fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 36.40 E-value: 3.88e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 146 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGcKVQISPDSGglpERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22409    2 VVAEVSAPSWLHRFIIGKKGANIKKITQDLP-KVHIEFTEG---EDKIELEGPPEEVEVVREQLEAIV 65

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

Pssm-ID: 411908 [Multi-domain] Cd Length: 71 Bit Score: 36.41 E-value: 3.98e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 237 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDgsQNTNVDKPLRIIGDPYKVQQACEMVMDIL 304
Cdd:cd22480    3 EEYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPD--SGGMPERPCVLTGTPESIEQAKRLLGQIV 68

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

Pssm-ID: 411947 [Multi-domain] Cd Length: 79 Bit Score: 36.69 E-value: 4.23e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163954948 239 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTnVDKPLRIIGDPYKVQQACEMVMDILRE 306
Cdd:cd22519   10 LVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNS-TERAVTISGTPDAIIQCVKQICVVMLE 76

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: 37.04 E-value: 4.42e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 147 TEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERSVSLTGAPESVQKAKMMLDDIV 213
Cdd:cd22503    2 SKKLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNGERMITIRGGTESTRYAVQLINALI 68

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: 36.53 E-value: 4.46e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 163954948 328 VPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPDRCEHA 383
Cdd:cd22434    6 VTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGSEDRIITITGTQDQIQNA 61

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: 36.43 E-value: 4.69e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 163954948 328 VPVPRhsVGVVIGRSGEMIKKIQNDAGVRIqfKQDDGT--GPEKIAHIMGPPDR 379
Cdd:cd22459    8 CPVSK--AGSVIGKGGEIIKQLRQETGARI--KVEDGVpgTEERVITISSSEAP 57

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

Pssm-ID: 411861 [Multi-domain] Cd Length: 70 Bit Score: 35.69 E-value: 6.65e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 163954948 157 VGLIIGRGGEQINKIQQDSGCKVQIS----PDSgglPERSVSLTGAPESV 202
Cdd:cd22433   13 AGCIIGRAGFKIKELREKTGATIKVYseccPRS---TDRVVQIGGKPDKV 59

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

Pssm-ID: 411885 [Multi-domain] Cd Length: 64 Bit Score: 35.51 E-value: 7.09e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 163954948 237 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKmILIQDGSQNTNVDKPLRIIGDPYKVQQACEMV 300
Cdd:cd22457    1 QNISIPPDMVGCIIGKGGSKIQEIRRLSGCK-ISIAKAPHDETGERMFTITGTPEANDRALRLL 63

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: 35.67 E-value: 7.53e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 235 TVQEIMIPAGKAGLVIGKGGETIKQLQERAGVkMILIQDgSQNTNVDKPLRIIGDPYKVQQA 296
Cdd:cd22439    2 TTQEITIPNDLIGCIIGKGGTKINEIRQLSGA-TIKIAN-SEDGSTERSVTITGTPEAVSLA 61

third 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 third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 35.78 E-value: 7.68e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 163954948 428 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVeisrQLP-PNGDPNFKLFV-IRGSPQQIDHAKQLI 492
Cdd:cd22422    4 MQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQI----HFPdPNNPPQRKSTVfISGSIDSVYLARQQL 66

third 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 third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 35.39 E-value: 8.39e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 163954948 160 IIGRGGEQINKIQQDSGCKVqISPDSGGLPER--SVSLTGAPESVQKAKMML 209
Cdd:cd22422   16 MLGRNGSNIKHIMQRTGAQI-HFPDPNNPPQRksTVFISGSIDSVYLARQQL 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: 35.22 E-value: 9.09e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163954948 326 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDgtGPEKIAHIMGPPDRCEHAARII 387
Cdd:cd22408    2 VSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPND--SDSETITLRGPADKLGAALTLV 61