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 1002273012 139 KKVVRIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLRDKPGYEHLNDPLHVLVEAEFP 218
Cdd:cd22467     1 KKVLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDKPGYEHLNEPLHVLIEAELP 80

                          90       100
                  ....*....|....*....|.
gi 1002273012 219 SDIVDVRLNQAVAILEDLLKP 239
Cdd:cd22467    81 ANIIDARLQHAQEIIEDLLKP 101

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 1002273012 139 KKVVRIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLRDKPGYEHLNDPLHVLVEAEFP 218
Cdd:cd22467     1 KKVLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDKPGYEHLNEPLHVLIEAELP 80

                          90       100
                  ....*....|....*....|.
gi 1002273012 219 SDIVDVRLNQAVAILEDLLKP 239
Cdd:cd22467    81 ANIIDARLQHAQEIIEDLLKP 101

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1002273012  38 YLAELLAERQKLAPFMQVLPFCNRLLNQEILRASSLPPNPNFVE 81
Cdd:pfam16544   8 YLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1002273012 141 VVRIDVPVDKypnynfVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDS 190
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSESEGNE 44

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 1002273012 139 KKVVRIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLRDKPGYEHLNDPLHVLVEAEFP 218
Cdd:cd22467     1 KKVLRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLRDKPGYEHLNEPLHVLIEAELP 80

                          90       100
                  ....*....|....*....|.
gi 1002273012 219 SDIVDVRLNQAVAILEDLLKP 239
Cdd:cd22467    81 ANIIDARLQHAQEIIEDLLKP 101

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, 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 to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. 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. 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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002273012 138 VKKVVRIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLR--DKPGYEHLNDPLHVLVEA 215
Cdd:cd22384     3 IKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRksGDPKYAHLNEDLHVLIEA 82

                          90
                  ....*....|....*.
gi 1002273012 216 EFPSDIVDVRLNQAVA 231
Cdd:cd22384    83 FAPPAEAYARLAHALA 98

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 1002273012 146 VPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLRDKPGYEHLNDPLHVLVEAEFPSDIVDVR 225
Cdd:cd22465     8 VPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDAQNRAEIK 87

                          90
                  ....*....|....
gi 1002273012 226 LNQAVAILEDLLKP 239
Cdd:cd22465    88 LKRAVEEVKKLLVP 101

Splicing factor (branch point binding protein) [RNA processing and modification];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002273012  77 PNFVEPERVNHG--SPLRLTGHPMNGQPMDLEGWSGMQTEQMGVLQSP--SMGWNVAPGVAGSPVVKKVvRIDVPVDKYP 152
Cdd:COG5176    82 PDGVPSKRELRSpsPPPRYDEIGRRLNTREARYNKKLEDERLWLKERAqkILPRFVLPNDYIRPSKYQN-KIYIPVQEYP 160

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002273012 153 NYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLrdKPGYEHLNDPLHVLVEAEFPSDIVDVRLNQAVAI 232
Cdd:COG5176   161 ESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDT--PESLKNAEAVLHCLIEADSEDKICRLIKSQLNAI 238

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1002273012 233 LEDLLKPvdESMDYYKKQQLRELAILNGTLREE 265
Cdd:COG5176   239 REARRNP--EGQNDLKRFQLRWLAHLNGTLRAD 269

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002273012 143 RIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGsvkdSVKEDKLRDKPG--YEHLNDPLHVLVEA 215
Cdd:cd22382     5 KVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKG----SVKEGKVGRKDGqpLPGEDEPLHALVTA 75

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002273012 143 RIDVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSVKEDKLRD--KPGYEHLNDPLHVLVEAEFPSD 220
Cdd:cd22470    12 KVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKsgEAKYFHLNDDLHVLIEVFAPPA 91

                          90
                  ....*....|....*....
gi 1002273012 221 IVDVRLNQAVAILEDLLKP 239
Cdd:cd22470    92 EAYARMGHALEEIKKFLIP 110

Homodimerization region of STAR domain protein; This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1002273012  38 YLAELLAERQKLAPFMQVLPFCNRLLNQEILRASSLPPNPNFVE 81
Cdd:pfam16544   8 YLAQLLKDKKQLAAFPNVFPHLERLLDEEISRVRGDLFNKGFGD 51

K homology RNA-binding domain;

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1002273012  139 KKVVRIDVPVDKypnynfVGRLLGPRGNSLKRVEATTQCRVYIRGRGSVKDSV 191
Cdd:smart00322   2 PVTIEVLIPADK------VGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVV 48

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains 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 second one.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1002273012 145 DVPVDKYPNYNFVGRLLGPRGNSLKRVEATTQCRVYI 181
Cdd:cd22493     4 EVPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITI 40