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 1571902454 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 1571902454  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 1571902454   3 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 57
Cdd:cd20472     1 ELTVEVRGSNGAFYKGFIKDVHEDSLTVVFENNWQPERQVPFNEVRLPPPPDIKK 55

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 1571902454 583 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDEISKLQRTPGEE--KINTLKEENTQEaAVLNGV 649
Cdd:pfam16097   1 PRDNLAKNKKEMAQDVIEEHSPSEKAINGPTNASGDETSKPQRTPEERtqKVTYQGDGNKQE-AVLNGV 68

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 1571902454 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 1571902454  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 1571902454   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 1571902454 491 KSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLV 564
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 1571902454 583 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDEISKLQRTPGEE--KINTLKEENTQEaAVLNGV 649
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 1571902454  62 GDEVEVYSraNDQEPCG-WWLAKV-RMMKGEFYVIEYAACD-----ATYNEIVTFERLRPVNQ 117
Cdd:pfam05641   1 GDKVEVLS--DEEGFRGaWFRAKViKVLKGDKYLVEYDDLLdedggGPLEEWVPASDIRPCPP 61

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1571902454  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 1571902454 223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 297
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 1571902454 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 1571902454   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 1571902454 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 1571902454  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 1571902454 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 1571902454 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 1571902454  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 1571902454 123 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRN 202
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80

                  ....*
gi 1571902454 203 EEATK 207
Cdd:pfam17904  81 EEAAK 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 1571902454 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 1571902454 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 1571902454   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 1571902454 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 1571902454 583 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDEISKLQRTPGEE--KINTLKEENTQEaAVLNGV 649
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 1571902454   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 1571902454 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 1571902454 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 1571902454 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGVVrVRIEGDNENKLPREdgmvpFVFVGTKESIGNVQVLL 351
Cdd:cd22439     6 ITIPNDLIGCIIGKGGTKINEIRQLSGAT-IKIANSEDGSTERS-----VTITGTPEAVSLAQYLI 65

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

                          10        20
                  ....*....|....*....|....*...
gi 1571902454 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGV 313
Cdd:cd22395     4 FEVPSELVGRLIGKQGRNVKQLKQKSGA 31

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 1571902454 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 1571902454 217 AAFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDtGTFRIYGESADAVKKARgflEFVEDFIQVP 289
Cdd:cd02393     2 APRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAK-IDIEDD-GTVTIFATDKESAEAAK---AMIEDIVAEP 69

polynucleotide phosphorylase/polyadenylase; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1571902454 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 1571902454 223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 297
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 1571902454 298 GKNGKVIQEIVD 309
Cdd:TIGR01952 116 GKGGKNIERAKE 127

transcription elongation factor NusA-like protein; Validated

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571902454 223 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTF-------------RIYGESADAVKkargflefvedFIQ 287
Cdd:PRK08406   36 FVVKEGDMGLAIGKGGENVKRLEEKLGkdIELVEYSDDPEEFiknifapaavrsvTIKKKNGDKVA-----------YVE 104

                          90
                  ....*....|....*..
gi 1571902454 288 VPRNLVGKVIGKNGKVI 304
Cdd:PRK08406  105 VAPEDKGIAIGKNGKNI 121

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 1571902454 281 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVV-----------RVRIEGDNEN 324
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSiripddeansdEIRIEGSPEG 55

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1571902454 286 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENKLPRED 330
Cdd:cd22446    11 ISVPSSVRGAIIGSRGKNLKSIQDKTG-TKIQIPKRNEEGNYDED 54

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 1571902454 225 VREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDTGTFRIYGESADAVK--KA--------RGF-----LEFVED----- 284
Cdd:TIGR03665   4 IPKDRIGVLIGKGGETKKEIEERTGVK-LDIDSETGEVKIEPEDEDPLAvmKArevvkaigRGFspekaLKLLDDdymle 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1571902454 285 ------FIQVPRNLV---GKVIGKNGKVIQEIVDKSGV 313
Cdd:TIGR03665  83 vidlkeYGKSPNALRrikGRIIGEGGKTRRIIEELTGV 120

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1571902454 281 FVEDFiQVPRNLVGKVIGKNGKVIQEIVDKSGVVRV---------RIEGDNENKL 326
Cdd:cd22426     2 FIEEF-KVDPDLIGLAIGSHGSNIQQARKIPGVESIdvdeedgtfRIYGETPEAV 55