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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61835148 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22510   1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 78

second 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 second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835148 218 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 280
Cdd:cd22507   1 AFHEEFTVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESAEAVKKARSYLE 63

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 61835148   354 HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG--------------------------------PNYTSGYGT 401
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRPPKekgyttdngesassgslhgsrsyggrgrgrrgGGYTSGYGT 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835148   402 NSELSNPSETESERKDELSDWSLAGED-DRDSRHQRDS 438
Cdd:pfam12235  81 NSELSNASETESERRDELSDWSLAGTErERGPRPQRDS 118

Fragile X-related 1 protein C-terminal region 3; FXR_C1 is a small highly conserved region at the very C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013, PF16096.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 61835148   554 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDDISKLQRTPGEE--KINTLKEENTQEaAVLNGV 620
Cdd:pfam16097   1 PRDNLAKNKKEMAQDVIEEHSPSEKAINGPTNASGDETSKPQRTPEERtqKVTYQGDGNKQE-AVLNGV 68

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61835148 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22510   1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 78

second 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 second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835148 218 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 280
Cdd:cd22507   1 AFHEEFTVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESAEAVKKARSYLE 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 61835148   123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRN 202
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80

                  ....*
gi 61835148   203 EEATK 207
Cdd:pfam17904  81 EEAAK 85

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 61835148   462 KSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLV 535
Cdd:pfam16096   3 SSSISSVLKDPDSNPYSLLDNNETDQTADTDASESQLPANRRRRSRRRRTDEDATMMDGMSESDNASVSENGLE 76

Fragile X-related 1 protein C-terminal region 3; FXR_C1 is a small highly conserved region at the very C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013, PF16096.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 61835148   554 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDDISKLQRTPGEE--KINTLKEENTQEaAVLNGV 620
Cdd:pfam16097   1 PRDNLAKNKKEMAQDVIEEHSPSEKAINGPTNASGDETSKPQRTPEERtqKVTYQGDGNKQE-AVLNGV 68

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 61835148    62 GDEVEVYSraNDQEPCG-WWLAKV-RMMKGEFYVIEYAACD-----ATYNEIVTFERLRPVNQ 117
Cdd:pfam05641   1 GDKVEVLS--DEEGFRGaWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 61835148    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 61835148   223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 297
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 61835148   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 61835148     58 EISEGDEVEVYSRandqepCGWWLAKVR-MMKGEFYVIEYAACDATYNEIVTFERLRPV 115
Cdd:smart00743   2 DFKEGDRVEVFSE------DSWWEAVVTkVLGDGKYLVEYKGESEPLELTVDWSDLRPH 54

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61835148 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22510   1 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 78

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 61835148 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 358
Cdd:cd22511   1 FSEDSVQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRVEGDNDKKNPREEGMVPFIFVGTKENISNAQALLEYHLSYL 78

second 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 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 61835148  59 ISEGDEVEVYSRANDQEPCGWWLAKVRMMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 126
Cdd:cd20476   1 ITEGDEVEVYSRANEQEPCGWWLARVRMMKGDFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68

second 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 second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835148 218 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 280
Cdd:cd22507   1 AFHEEFTVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESAEAVKKARSYLE 63

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 61835148   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 61835148   354 HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG--------------------------------PNYTSGYGT 401
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRPPKekgyttdngesassgslhgsrsyggrgrgrrgGGYTSGYGT 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835148   402 NSELSNPSETESERKDELSDWSLAGED-DRDSRHQRDS 438
Cdd:pfam12235  81 NSELSNASETESERRDELSDWSLAGTErERGPRPQRDS 118

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 61835148 218 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 280
Cdd:cd22508   1 AFQEEFTVREDLMGLAIGTHGANIQQARKVPGVTAIELDEETCTFRIYGETPEAVKQARSYLE 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 61835148 219 FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 280
Cdd:cd22509   2 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63

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 61835148   4 LTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 57
Cdd:cd20473   2 LAVEVRGSNGAFYKGFIKDVHEDSVTIFFENNWQPERQIPFGDVRLPPPADYHK 55

first 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 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 61835148 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 199
Cdd:cd22506   1 KDTFHKIKLDVPEDLRQMCAKESAHKDFKKAVGAFSVTYDSENYQLVILSINEVTSKRAHMLIDMHFRSLRTKLSLI 77

Fragile X-related 1 protein C-terminal region 3; FXR_C1 is a small highly conserved region at the very C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013, PF16096.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 61835148   554 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDDISKLQRTPGEE--KINTLKEENTQEaAVLNGV 620
Cdd:pfam16097   1 PRDNLAKNKKEMAQDVIEEHSPSEKAINGPTNASGDETSKPQRTPEERtqKVTYQGDGNKQE-AVLNGV 68

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 61835148   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 61835148   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 61835148 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 344
Cdd:cd02393   8 IKIPPDKIGDVIGPGGKTIRAIIEETG-AKIDIE---------DDGTV-TIFATDKESA 55

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 61835148 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGVVrVRIEGDNENKLPREdgmvpFVFVGTKESIGNVQVLL 351
Cdd:cd22439   6 ITIPNDLIGCIIGKGGTKINEIRQLSGAT-IKIANSEDGSTERS-----VTITGTPEAVSLAQYLI 65

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835148 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 61835148 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.

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                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835148 217 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDtGTFRIYGESADAVKKARgflEFVEDFIQVP 289
Cdd:cd02393   2 APRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAK-IDIEDD-GTVTIFATDKESAEAAK---AMIEDIVAEP 69

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835148  286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 344
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETG-AKIDIE---------DDGTV-KIAATDGEAA 605

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 61835148   223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 297
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 61835148   298 GKNGKVIQEIVD 309
Cdd:TIGR01952 116 GKGGKNIERAKE 127

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 61835148 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 61835148 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVV-----------RVRIEGDNEN 324
Cdd:cd02394   1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSiripddeansdEIRIEGSPEG 55

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

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835148     58 EISEGDEVEVYSRandqepCGWWLAKVR-MMKGEFYVIEYAACDATYNEIVTFERLRPV 115
Cdd:smart00743   2 DFKEGDRVEVFSE------DSWWEAVVTkVLGDGKYLVEYKGESEPLELTVDWSDLRPH 54

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 61835148 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDnenklpreDGMVP 334
Cdd:cd22486   7 VSVPRFAVGIVIGRNGEMIKKIQNDAG-VRIQFKPD--------DGISP 46

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 61835148 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNEN 324
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETG-ARVQFKPDDGN 41

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.

                        10        20        30
                ....*....|....*....|....*....|....*.
gi 61835148 288 VPRNLVGKVIGKNGKVIQEIVDKSGV-VRVRIEGDN 322
Cdd:cd22460   6 VASSQAGSLIGKGGAIIKQIREESGAsVRILPEEEL 41