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 61835172  38 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 114
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

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 61835172   269 HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG--------------------------------PNYTSGYGT 316
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRPPKekgyttdngesassgslhgsrsyggrgrgrrgGGYTSGYGT 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835172   317 NSELSNPSETESERKDELSDWSLAGED-DRDSRHQRDS 353
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 61835172   469 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDDISKLQRTPGEE--KINTLKEENTQEaAVLNGV 535
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 61835172  38 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 114
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

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 61835172    38 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLMSRN 117
Cdd:pfam17904   1 KDTFHKIELEVPEDLREMCAKESAHKDFKKAVGAASVTYDSENNQLVILSRNESTKKRASMLSDMHFRNLRQKLLLLSRT 80

                  ....*
gi 61835172   118 EEATK 122
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 61835172   377 KSSISSVLKDPDSNPYSLLDNTESDQTADTDASESHHSTNRRRRSRRRRTDEDAVLMDGMTESDTASVNENGLV 450
Cdd:pfam16096   3 SSSISSVLKDPDSNPYSLLDNNETDQTADTDASESQLPANRRRRSRRRRTDEDATMMDGMSESDNASVSENGLE 76

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
                ....*....|....*....|....*....|....*....|.
gi 61835172   1 MMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 41
Cdd:cd20475  26 MMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVTKNTF 66

K homology RNA-binding domain;

                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 61835172    201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNEN 239
Cdd:smart00322   7 VLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIPGPGSE 44

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835172  201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 259
Cdd:PRK11824 558 IKIPPDKIRDVIGPGGKTIREITEETG-AKIDIE---------DDGTV-KIAATDGEAA 605

transcription elongation factor NusA-like protein; Validated

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835172  138 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTF-------------RIYGESADAVKkargflefvedFIQ 202
Cdd:PRK08406  36 FVVKEGDMGLAIGKGGENVKRLEEKLGkdIELVEYSDDPEEFiknifapaavrsvTIKKKNGDKVA-----------YVE 104

                         90
                 ....*....|....*..
gi 61835172  203 VPRNLVGKVIGKNGKVI 219
Cdd:PRK08406 105 VAPEDKGIAIGKNGKNI 121

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 61835172  38 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETTQLMILSASEATVKRVNILSDMHLRSIRTKLMLM 114
Cdd:cd22504   1 KNTFFKCTVDVPEDLREACANENAHKDFKKAVGACRIFYHPETNQLVILSASEATVKRVSILSDMHLRSIRTKLMLM 77

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 61835172 196 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVVRVRIEGDNENKLPREDGMVPFVFVGTKESIGNVQVLLEYHIAYL 273
Cdd:cd22512   1 FAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENDKNIPQEEGMVPFVFVGTKDSITNATVLLDYHLNYL 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 61835172 133 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 195
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 61835172   269 HIAYLKEVEQLRMERLQIDEQLRQIGSRSYSGRGRGRRG--------------------------------PNYTSGYGT 316
Cdd:pfam12235   1 HLSYLKEVEQLRLERLQIDEQLRQIGGGFRPGSGRRPPKekgyttdngesassgslhgsrsyggrgrgrrgGGYTSGYGT 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 61835172   317 NSELSNPSETESERKDELSDWSLAGED-DRDSRHQRDS 353
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 61835172 133 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 195
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 61835172 134 FHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 195
Cdd:cd22509   2 FHEQFIVREDLMGLAIGTHGANIQQARKVPGVTAIDLDEDTCTFHIYGEDQEAVKKARSYLE 63

second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 61835172 133 AFHEEFVVREDLMGLAIGTHGSNIQQARKVPGVTAIELDEDTGTFRIYGESADAVKKARGFLE 195
Cdd:cd22426   1 GFIEEFKVDPDLIGLAIGSHGSNIQQARKIPGVESIDVDEEDGTFRIYGETPEAVEKARALLE 63

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 61835172   469 PRETLAKNKKEMAKDVIEEHGPSEKAINGPTSASGDDISKLQRTPGEE--KINTLKEENTQEaAVLNGV 535
Cdd:pfam16097   1 PRDNLAKNKKEMAQDVIEEHSPSEKAINGPTNASGDETSKPQRTPEERtqKVTYQGDGNKQE-AVLNGV 68

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
                ....*....|....*....|....*....|....*....|.
gi 61835172   1 MMKGEFYVIEYAACDATYNEIVTFERLRPVNQNKTVKKNTF 41
Cdd:cd20476  28 MMKGDFYVIEYAACDATYNEIVTLERLRPVNPNPLSTKNSF 68

second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family; The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1) and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                        10        20
                ....*....|....*....|....*....
gi 61835172   1 MMKGEFYVIEYAACDATYNEIVTFERLRP 29
Cdd:cd20403  22 MVKGEFYVVEFPGFDETYTEIVELERLRP 50

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENKLPREdgmvpFVFVGTKESI 259
Cdd:cd00105   3 IEVPSELVGLIIGKGGSTIKEIEEETG-ARIQIPKEGEGSGERV-----VTITGTPEAV 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 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGVVrVRIEGDNENKLPREdgmvpFVFVGTKESIGNVQVLL 266
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 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGVVrVRIEgdnENKLPREDGMVPFVFVGTKESIGNVQ 263
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 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNENKLPRedgmvPFVFVGTKESIGNVQVLLEYHI 270
Cdd:cd22396   5 YKVPDKMVGLIIGRGGEQINRLQAESG-AKIQIAPDSGGLPER-----PCTLTGTPDAIETAKRLIDQIV 68

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 61835172    136 EEFVVREDLMGLAIGTHGSNIQQARKVPGVTA--IELDEDTGTFRIYGEsADAVKKARGFLE 195
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIdiPGPGSEERVVEITGP-PENVEKAAELIL 65

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 61835172  201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEgdnenklprEDGMVpFVFVGTKESI 259
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 61835172   138 FVVREDLMGLAIGTHGSNIQQARKVPG--VTAIELDEDTGTFrIYGESADAVKKARGFLEFVED---FIQVPRNLVGKVI 212
Cdd:TIGR01952  37 FVVKEGEMGAAIGKGGENVKRLEELIGksIELIEYSENLEEF-VANKLAPAEVKNVTVSEFNGKkvaYVEVHPRDKGIAI 115

                          90
                  ....*....|..
gi 61835172   213 GKNGKVIQEIVD 224
Cdd:TIGR01952 116 GKGGKNIERAKE 127

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRI---EGDNENKLPREDGMVPFVFVG 254
Cdd:cd22447   8 VPIPASTRARIIGKKGANLKQIREKTG-VRIDIpprDADAAPADEDDDTMVEVTITG 63

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

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 61835172 196 FVEDFIQVPRNLVGKVIGKNGKVIQEIVDKSGVV-----------RVRIEGDNEN 239
Cdd:cd02394   1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSiripddeansdEIRIEGSPEG 55

polynucleotide phosphorylase/polyadenylase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 61835172  143 DLMGLAIGTHGSNIQQARKVPGVTaIELDEDtGTFRIYGESADAVKKARgflEFVEDFIQVPRnlVGKVIgkNGKVIqEI 222
Cdd:PRK11824 563 DKIRDVIGPGGKTIREITEETGAK-IDIEDD-GTVKIAATDGEAAEAAK---ERIEGITAEPE--VGEIY--EGKVV-RI 632

                 ..
gi 61835172  223 VD 224
Cdd:PRK11824 633 VD 634

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

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gi 61835172 201 IQVPRNLVGKVIGKNGKVIQEIVDKSGvVRVRIEGDNEN 239
Cdd:cd22398   4 VPVPRFAVGVVIGKGGEMIKKIQNETG-ARVQFKPDDGN 41

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.

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gi 61835172   140 VREDLMGLAIGTHGSNIQQARKVPGVTaIELDEDTGTFRIYGESADAVK--KA--------RGF-----LEFVED----- 199
Cdd:TIGR03665   4 IPKDRIGVLIGKGGETKKEIEERTGVK-LDIDSETGEVKIEPEDEDPLAvmKArevvkaigRGFspekaLKLLDDdymle 82

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gi 61835172   200 ------FIQVPRNLV---GKVIGKNGKVIQEIVDKSGV 228
Cdd:TIGR03665  83 vidlkeYGKSPNALRrikGRIIGEGGKTRRIIEELTGV 120

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.

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gi 61835172 203 VPRNLVGKVIGKNGKVIQEIVDKSGV-VRVRIEGDN 237
Cdd:cd22460   6 VASSQAGSLIGKGGAIIKQIREESGAsVRILPEEEL 41