first 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 first one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939620316 125 AKTFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLL 201
Cdd:cd22425    1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 939620316  63 EGMEVEVFTRTNDRETCGWWVGIIKMRKAEIYAVAYIGFETSYTEICELGRLRAKNSNPPITAKTF 128
Cdd:cd20475    1 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66

Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 939620316  359 HLSHLKEVEQLRQEKMEIDQQLRAIqesSMGSTqsfPVTRR---SERGYSSD 407
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQI---GGGFR---PGSGRrppKEKGYTTD 46

first 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 first one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939620316 125 AKTFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLL 201
Cdd:cd22425    1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 939620316 222 YVEEFRVRDDLMGLAIGSHGSNIQAARTVDGVTNIELEEKSCTFKISGETEESVQRARAMLE 283
Cdd:cd22426    2 FIEEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIDVDEEDGTFRIYGETPEAVEKARALLE 63

first Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1), and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), 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. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 939620316   3 DLLVEVRLDNGAYYKGQVTAVADDGIFVDVDG-VPESMKYPFVNVRLPPE 51
Cdd:cd20402    1 DLAVEVRGPNGAYYKAFVKDVHEDEVTVAFENdWQPERKVPFSDVRLPPP 50

Fragile X-related 1 protein core C terminal; This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 939620316  359 HLSHLKEVEQLRQEKMEIDQQLRAIqesSMGSTqsfPVTRR---SERGYSSD 407
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQI---GGGFR---PGSGRrppKEKGYTTD 46

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 939620316   289 FQVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEQDQNIprelahvpfVFIGTVESIANAKVLLE 357
Cdd:smart00322   7 VLIPADKVGLIIGKGGSTIKKIEEETGV-KIDIPGPGSEERVV---------EITGPPENVEKAAELIL 65

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 939620316   221 NYVEEFRVRDDLMGLAIGSHGSNIQAARTVDGVtNIELEEKSC---TFKISGEtEESVQRARAMLE 283
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGV-KIDIPGPGSeerVVEITGP-PENVEKAAELIL 65

first 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 first one.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939620316 125 AKTFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLL 201
Cdd:cd22425    1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77

third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939620316 284 YAEEFFQVPRELVGKVIGKNGRIIQEIVDKSGVFRIKIAGDDeqDQNIPRELAHVPFVFIGTVESIANAKVLLEYHLSHL 363
Cdd:cd22510    1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDN--ENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 78

FMRP KH0 domain; This entry corresponds to the KH0 domain from the FMRP protein. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein. KH0 does not have the canonical G-X-X-G motif between helices A and B. It has been suggested that this domain may be involved in RNA binding.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939620316  127 TFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLLKRTEE 206
Cdd:pfam17904   3 TFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRTEE 82

                  ...
gi 939620316  207 AAR 209
Cdd:pfam17904  83 AAK 85

second 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 second one.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 939620316 222 YVEEFRVRDDLMGLAIGSHGSNIQAARTVDGVTNIELEEKSCTFKISGETEESVQRARAMLE 283
Cdd:cd22508    2 FQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELDEETCTFRIYGETPEAVKQARSYLE 63

second 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 second one.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 939620316 224 EEFRVRDDLMGLAIGSHGSNIQAARTVDGVTNIELEEKSCTFKISGETEESVQRARAMLE 283
Cdd:cd22509    4 EQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63

first 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 first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 939620316 127 TFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLL 201
Cdd:cd22505    3 SFFKVTIAVPEDLKEACSNENVHKEFKKAIGANCIFFNTSNNELIILSTNESTVKRASLLSDMHFRSIRTKLMLM 77

second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1) and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), 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. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 939620316  63 EGMEVEVFTRTndreTCGWWVGIIKMRKAEIYAVAYIGFETSYTEICELGRLR 115
Cdd:cd20403    1 EGDEVEVYSRA----PDGWWEGVVKMVKGEFYVVEFPGFDETYTEIVELERLR 49

first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 939620316 127 TFYQFTLPVPEELREEAQKDGIHKEFQRTIDAGVCNYSRDLDALIVISKFEHTQKRASMLKDMHFRNLSQKVMLL 201
Cdd:cd22504    3 TFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), 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. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 939620316  63 EGMEVEVFTRTNDRETCGWWVGIIKMRKAEIYAVAYIGFETSYTEICELGRLRAKNSNPP 122
Cdd:cd20474    4 ESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 939620316 287 EFFQVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEQDQNiprelahVPFVFIGTVESIANAKVLLE 357
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGA-RIQIPKEGEGSGE-------RVVTITGTPEAVEKAKELIE 63

Fragile X mental retardation Tudor domain; This is the N-terminal Tudor domain (Tud1) found in Fragile X mental retardation syndrome-related protein 1 (Fxr1). The Tud1 domain forms a canonical Tudor barrel. It is usually found in tandem with Agenet domain pfam05641.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 939620316    4 LLVEVRLDNGAYYKGQVTAVADDGIFVDVDGVPES-MKYPFVNVRLPP 50
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPeRQVPFNDVRLPP 48

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 939620316   289 FQVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEQDQNIprelahvpfVFIGTVESIANAKVLLE 357
Cdd:smart00322   7 VLIPADKVGLIIGKGGSTIKKIEEETGV-KIDIPGPGSEERVV---------EITGPPENVEKAAELIL 65

first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins; FMR1, also called fragile X mental retardation protein 1 (FMRP), 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. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 939620316   1 MEDLLVEVRLDNGAYYKGQVTAVADDGIFVDVDG--VPESmKYPFVNVRLPP 50
Cdd:cd20471    1 MEELVVEVRGSNGAFYKAFVKDVHEDSITVAFENnwQPER-QIPFHDVRFPP 51

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAgdDEQDQNIPRElahvpfVFI-GTVESIANAKVLL 356
Cdd:cd22439    8 IPNDLIGCIIGKGGTKINEIRQLSGA-TIKIA--NSEDGSTERS------VTItGTPEAVSLAQYLI 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 939620316 289 FQVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIagddEQDQNIprelahvpFVFIGTVESIANAKVLLE 357
Cdd:cd02393    8 IKIPPDKIGDVIGPGGKTIRAIIEETGA-KIDI----EDDGTV--------TIFATDKESAEAAKAMIE 63

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 939620316 290 QVPRELVGKVIGKNGRIIQEIVDKSGVFrIKIAGDDEQDQNIprelahvpfVFIGTVESIANAKVLLE 357
Cdd:cd02394    7 EIDPKFHGHIIGKGGANIKRIREESGVS-IRIPDDEANSDEI---------RIEGSPEGVKKAKAEIL 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 939620316 287 EFFQVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDdeqDQNIPRElahvPFVFIGTVESIANAKVLL 356
Cdd:cd22480    3 EEYKVPDKMVGFIIGRGGEQISRIQLESGC-KIQIAPD---SGGMPER----PCVLTGTPESIEQAKRLL 64

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 939620316 289 FQVPRELVGKVIGKNGRIIQEIVDKSGVFrIKIAgddeQDQNiPRELAHVPFVFIGTVESIANAKVLLE 357
Cdd:cd22463    6 FQIPEAVVGLIIGKSGNTIKQISERSGAF-VAIV----QDRY-PLEETQKILRISGTEEQLKRAQSLVE 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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 939620316 223 VEEFRVRDDLMGLAIGSHGSNIQAARTVDGVTnIELEEkSCTFKISGETEESVQRARAMLE 283
Cdd:cd02393    5 ITTIKIPPDKIGDVIGPGGKTIRAIIEETGAK-IDIED-DGTVTIFATDKESAEAAKAMIE 63

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEQDqniPRELAHV 338
Cdd:cd22485    7 VPRHSVGVVIGRSGEMIKKIQNDAGV-RIQFKQDDGTG---PEKIAHI 50

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.

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gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEqdqNIPRELAHVpfvfIGTVESIANAK 353
Cdd:cd22398    6 VPRFAVGVVIGKGGEMIKKIQNETGA-RVQFKPDDG---NSPDRICVI----TGPPDQVQHAA 60

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.

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gi 939620316 290 QVPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDEQDQNIPRELahvpfVFIGTVESIANAK 353
Cdd:cd22428   10 KVPREAVGLIIGRQGATIKQIQKETGA-RIDFKDEGSGGELPERVL-----LIQGNPVQAQRAE 67

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.

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gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKiAGDDEQDQNIPRELahvpfVFIGTVESIANA 352
Cdd:cd22456    6 IPHSLIGSIIGKGGARIKEIQDGSGA-RLV-ASKEFLPLSTERIL-----EVQGTPDAIHNA 60

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.

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                 ....*....|....*....|....*....|....*
gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDD 325
Cdd:cd22486    9 VPRFAVGIVIGRNGEMIKKIQNDAGV-RIQFKPDD 42

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.

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gi 939620316 291 VPRELVGKVIGKNGRIIQEIVDKSGVfRIKIAGDDE 326
Cdd:cd22514    7 VPDEHIGAILGRGGRTINEIQQHSGA-RIKISDRGD 41

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.

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gi 939620316 285 AEEFFQVPRELVGKVIGKNGRIIQEIVDKSGVF 317
Cdd:cd22453    2 AEISFYVPEKYHKRIIGKGGQNIQRIMKKYNVF 34