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 61835164 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 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 61835164  61 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 126
Cdd:cd20475   1 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66

first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 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 61835164   3 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 57
Cdd:cd20472   1 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 55

Fragile X-related 1 protein C-terminal region 2; FXR_C1 is a small highly conserved region of the C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013. This family is immediately C-terminal to the core C terminal region, PF12235, and contains at least one block of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 61835164   462 KSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLG 535
Cdd:pfam16096   3 SSSISSVLKDPDSNPYSLLDNNETDQTADTDASESQLPANRRRRSRRRRTDEDATMMDGMSESDNASVSENGLE 76

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 61835164 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 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 61835164  61 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 126
Cdd:cd20475   1 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66

first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 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 61835164   3 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 57
Cdd:cd20472   1 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 55

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835164   354 HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG--------------------------------PNYTSGYGT 401
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRPPKekgyttdngesassgslhgsrsyggrgrgrrgGGYTSGYGT 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835164   402 NSELSNPSETESERKDELSDWSLAGED-DRDSRHQRDS 438
Cdd:pfam12235  81 NSELSNASETESERRDELSDWSLAGTErERGPRPQRDS 118

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 61835164     4 LTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49

Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835164    62 GDEVEVYSraNDQEPCG-WWLAKV-RMMKGEFYVIEYAACD-----ATYNEIVTFERLRPVNQ 117
Cdd:pfam05641   1 GDKVEVLS--DEEGFRGaWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 61835164    221 EEFVVREDLMGLAIGTHGSNIQQARKVPGVTA--IELDEDTGTFRIYGEsADAVKKARGFLE 280
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIdiPGPGSEERVVEITGP-PENVEKAAELIL 65

NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835164   223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 297
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 61835164   298 GKNGKVIQEIVD 309
Cdd:TIGR01952 116 GKGGKNIERAKE 127

Tudor-like domain present in plant sequences; Domain in plant sequences with possible chromatin-associated functions.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835164     58 EISEGDEVEVYSRandqepCGWWLAKVR-MMKGEFYVIEYAACDATYNEIVTFERLRPV 115
Cdd:smart00743   2 DFKEGDRVEVFSE------DSWWEAVVTkVLGDGKYLVEYKGESEPLELTVDWSDLRPH 54

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 61835164 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins; FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 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 61835164  61 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 126
Cdd:cd20475   1 EGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61835164 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22512   1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEEGMVPFVFVGTKDSITNATVLLDYHLNYL 78

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 61835164 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENK-LPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22427   1 FAEEIFQVPRDLVGKVIGKNGRVIQEIVDKSGVVRVKIEGDNEDGpRPREEGLVPFIFVGTREAIANAKLLLEYHLAHL 79

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 61835164  58 EISEGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKT 120
Cdd:cd20474   1 DINESDEVEVYSRANEKEPCCWWLAKVRMIKGEFYVIEYAACDATYNEIVTIERLRSVNPNKP 63

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 61835164   123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRN 202
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80

                  ....*
gi 61835164   203 EEATK 207
Cdd:pfam17904  81 EEAAK 85

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 61835164 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22425   1 KSTFFKHTIDVPEDLREYCKDESAHRDFKKACGAISVRYDEDTNALVVISTSESAIKRASLLSDMHFRNLRQKLLLL 77

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 61835164 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22505   1 KNSFFKVTIAVPEDLKEACSNENVHKEFKKAIGANCIFFNTSNNELIILSTNESTVKRASLLSDMHFRSIRTKLMLM 77

Fragile X-related 1 protein C-terminal region 2; FXR_C1 is a small highly conserved region of the C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013. This family is immediately C-terminal to the core C terminal region, PF12235, and contains at least one block of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 61835164   462 KSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLG 535
Cdd:pfam16096   3 SSSISSVLKDPDSNPYSLLDNNETDQTADTDASESQLPANRRRRSRRRRTDEDATMMDGMSESDNASVSENGLE 76

first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins; FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 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 61835164   4 LTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 57
Cdd:cd20473   2 LAVEVRGSNGAFYKGFIKDVHEDSVTIFFENNWQPERQIPFGDVRLPPPADYHK 55

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 61835164     4 LTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPP 52
Cdd:pfam18336   1 LVVEVRGSNGAFYKAFVKDVHEDSLTVAFENNWQPERQVPFNDVRLPPP 49

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 61835164   3 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPP 52
Cdd:cd20402   1 DLAVEVRGPNGAYYKAFVKDVHEDEVTVAFENDWQPERKVPFSDVRLPPP 50

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 61835164   286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENKLPREdgmvpFVFVGTKESIGNVQVLLE 352
Cdd:pfam00013   4 ILVPSSLVGLIIGKGGSNIKEIREETG-AKIQIPPSESEGNERI-----VTITGTPEAVEAAKALIE 64

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
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 344
Cdd:cd02393   8 IKIPPDKIGDVIGPGGKTIRAIIEETG-AKIDIE---------DDGTV-TIFATDKESA 55

Agenet domain; This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835164    62 GDEVEVYSraNDQEPCG-WWLAKV-RMMKGEFYVIEYAACD-----ATYNEIVTFERLRPVNQ 117
Cdd:pfam05641   1 GDKVEVLS--DEEGFRGaWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGVVrVRIEgdnENKLPREDGMVPFVFVGTKESIGNVQ 348
Cdd:cd22403   4 IRVPSSMVGRIIGKGGQNVRELQRLTGAI-IKLP---RDQTPDEGDEVPVEIIGNFYATQSAQ 62

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENKLPRedgmvPFVFVGTKESIGNVQVLLEYHI 355
Cdd:cd22396   5 YKVPDKMVGLIIGRGGEQINRLQAESG-AKIQIAPDSGGLPER-----PCTLTGTPDAIETAKRLIDQIV 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        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835164 217 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDtGTFRIYGESADAVKKARgflEFVEDFIQVP 289
Cdd:cd02393   2 APRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAK-IDIEDD-GTVTIFATDKESAEAAK---AMIEDIVAEP 69

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835164  286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 344
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETG-AKIDIE---------DDGTV-KIAATDGEAA 605

ATPase; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 61835164  286 IQVPRNLVGKVIGKNGKVIQEIVDKSGV-VRVRIEGDNENKLPREDGMVPFV 336
Cdd:PRK13764 485 VYVPEKDIPKVIGKGGKRIKKIEKKLGIdIDVRPLDEEPGEEAEEGEEVTVE 536

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENklprEDGMVPFVFVGTKESIGNVQVLLE 352
Cdd:cd22457   3 ISIPPDMVGCIIGKGGSKIQEIRRLSG-CKISIAKAPHD----ETGERMFTITGTPEANDRALRLLY 64

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
                ....*....|....*....|....*....|....*....|....*....|....*
gi 61835164 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVV-----------RVRIEGDNEN 324
Cdd:cd02394   1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSiripddeansdEIRIEGSPEG 55

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835164  228 DLMGLAIGTHGSNIQQARKVPGVTaIELDEDtGTFRIYGESADAVKKARgflEFVEDFIQVPRnlVGKVIgkNGKVIqEI 307
Cdd:PRK11824 563 DKIRDVIGPGGKTIREITEETGAK-IDIEDD-GTVKIAATDGEAAEAAK---ERIEGITAEPE--VGEIY--EGKVV-RI 632

                 ..
gi 61835164  308 VD 309
Cdd:PRK11824 633 VD 634

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835164   225 VREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDTGTFRIYGESADAVK--KA--------RGF-----LEFVED----- 284
Cdd:TIGR03665   4 IPKDRIGVLIGKGGETKKEIEERTGVK-LDIDSETGEVKIEPEDEDPLAvmKArevvkaigRGFspekaLKLLDDdymle 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835164   285 ------FIQVPRNLV---GKVIGKNGKVIQEIVDKSGV 313
Cdd:TIGR03665  83 vidlkeYGKSPNALRrikGRIIGEGGKTRRIIEELTGV 120

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.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNEN 324
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETG-ARVQFKPDDGN 41

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 61835164 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGV-VRVRIEGDNENKLPR 328
Cdd:cd22428   9 MKVPREAVGLIIGRQGATIKQIQKETGArIDFKDEGSGGELPER 52

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 61835164   221 EEFVVREDLMGLAIGTHGSNIQQARKVPGVT----AIELDEDTGTFRIYGeSADAVKKARGFLE 280
Cdd:pfam00013   2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKiqipPSESEGNERIVTITG-TPEAVEAAKALIE 64