type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 168
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1338686480 169 VKKAVEQIRNILK 181
Cdd:cd22382    81 VKKAVDKIKEIIK 93

zinc finger;

                           10
                   ....*....|....*.
gi 1338686480  232 VCTKCGGAGHIASDCK 247
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 168
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1338686480 169 VKKAVEQIRNILK 181
Cdd:cd22382    81 VKKAVDKIKEIIK 93

Splicing factor 1 helix-hairpin domain; This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1338686480  29 KSLHRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHTLITEMVALNPDFKPPADYK 84
Cdd:pfam16275  59 SPEERSPSPPPIYDANGKRTNTREVRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  91 SDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKImirgkgsvkegkvgrkdgQMLPGEDEPLHALVT-ANTMENV 169
Cdd:pfam00013   1 TVEILVPSS------LVGLIIGKGGSNIKEIREETGAKI------------------QIPPSESEGNERIVTiTGTPEAV 56

                  ....*....
gi 1338686480 170 KKAVEQIRN 178
Cdd:pfam00013  57 EAAKALIEE 65

zinc finger;

                           10
                   ....*....|....*.
gi 1338686480  232 VCTKCGGAGHIASDCK 247
Cdd:smart00343   1 KCYNCGKEGHIARDCP 16

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 1338686480  94 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVKegkvgrkdgqMLPGEDEPLHALvtantmenvkKA 172
Cdd:TIGR03665   2 VKIPKDR------IGVLIGKGGETKKEIEERTGVKLDIDSEtGEVK----------IEPEDEDPLAVM----------KA 55

                  ....*..
gi 1338686480 173 VEQIRNI 179
Cdd:TIGR03665  56 REVVKAI 62

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMEN 168
Cdd:cd22382     1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGQPLPGEDEPLHALVTANTAES 80

                          90
                  ....*....|...
gi 1338686480 169 VKKAVEQIRNILK 181
Cdd:cd22382    81 VKKAVDKIKEIIK 93

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKvGRKDGQMLPGEDEPLHALVTANTMEN 168
Cdd:cd02395     1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGK-GRSDPQPDPDEEEDLHVLITADTEEK 79

                          90
                  ....*....|..
gi 1338686480 169 VKKAVEQIRNIL 180
Cdd:cd02395    80 VDKAAKLIEKLL 91

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  90 VSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEG-KVGRKDGQmlPGE---DEPLHALVTANT 165
Cdd:cd22383     2 LSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKkKEEANRGK--PNWehlNDDLHVLITVED 79

                          90       100
                  ....*....|....*....|.
gi 1338686480 166 MEN-----VKKAVEQIRNILK 181
Cdd:cd22383    80 TENrahikLAKAVEEVKKLLI 100

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKV-----GRKDGQMLpgeDEPLHALVTA 163
Cdd:cd22465     1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeqnrGKPNWEHL---NEDLHVLITV 77

                          90       100
                  ....*....|....*....|..
gi 1338686480 164 NTMEN-----VKKAVEQIRNIL 180
Cdd:cd22465    78 EDAQNraeikLKRAVEEVKKLL 99

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  96 IPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE-GKVGRKDGQmlPGED---EPLHALVTANTMENV-- 169
Cdd:cd22467     8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDtAKEEKLRDK--PGYEhlnEPLHVLIEAELPANIid 85

                          90
                  ....*....|....*
gi 1338686480 170 ---KKAVEQIRNILK 181
Cdd:cd22467    86 arlQHAQEIIEDLLK 100

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGS----VKEGKVGRKDGQMLPGEDEPLHALVT-- 162
Cdd:cd22469     6 KLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSmrdkAKEEELRKSGEAKYAHLSDELHVLIEvf 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1338686480 163 ---ANTMENVKKAVEQIRNILkqgieTPEDQNDLRKMQ 197
Cdd:cd22469    86 appGEAYSRMSHALEEIKKFL-----VPDYNDEIRQEQ 118

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1338686480  89 RVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKE 139
Cdd:cd22470     8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRD 58

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  92 DKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSvkegkvgrkdgqmlpgEDEPLHALVTAnTMENVKK 171
Cdd:cd00105     1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE----------------GSGERVVTITG-TPEAVEK 57

                  ....*.
gi 1338686480 172 AVEQIR 177
Cdd:cd00105    58 AKELIE 63

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  93 KVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedeplhalVTANTMENVKKA 172
Cdd:cd02393     7 TIKIPPD------KIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVT----------------------IFATDKESAEAA 58

                  ....*....
gi 1338686480 173 VEQIRNILK 181
Cdd:cd02393    59 KAMIEDIVA 67

first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins; The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1338686480  94 VMIPQDEypeinfVGLLIGPRGNTLKNIEKECNAKIMIRGK-GSVK 138
Cdd:cd22389     3 VKIPKER------IGVLIGKKGETKREIEERTGVKITVDSEtGEVI 42

polynucleotide phosphorylase/polyadenylase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1338686480  78 KPPADYKPPATRVsDKVMIPQDeypeinFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKegkvgrkdgqmlpgedepl 157
Cdd:PRK11824  543 EPRAELSPYAPRI-ETIKIPPD------KIRDVIGPGGKTIREITEETGAKIDIEDDGTVK------------------- 596

                          90       100
                  ....*....|....*....|..
gi 1338686480 158 halVTANTMENVKKAVEQIRNI 179
Cdd:PRK11824  597 ---IAATDGEAAEAAKERIEGI 615

type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); The DDX46 family includes DEAD box protein 46 (DDX46), fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5, Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this family contain a divergent KH domain that lacks the RNA-binding GXXG motif.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1338686480 117 TLKNIEKECNAKIMIRGKGSVKEGKVgrkdgqmLPGEdEPLHALVTANTMENVKKAVEQIRNIL 180
Cdd:cd22387    27 VLNSIMEETGATITIKGQYYPPGKKP-------KPGE-RKLYLLIEGATEESVQSARNEIKRVL 82

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1338686480 107 VGLLIGPRGNTLKNIEKECNAKIMIRGKGsvkegkvgrkdgqmlPGEDEPLHALVTANTMENVKKAVEQIRNIL 180
Cdd:cd22428    16 VGLIIGRQGATIKQIQKETGARIDFKDEG---------------SGGELPERVLLIQGNPVQAQRAEEAIHQII 74

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.

                          10
                  ....*....|....*.
gi 1338686480 232 VCTKCGGAGHIASDCK 247
Cdd:pfam00098   2 KCYNCGEPGHIARDCP 17