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        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 74761039    10 KPKPTPDYLMQLMNDKKLMSSLPNfcgIFNHLERLLDEEISRVRKDMYNDTLNGS 64
Cdd:pfam16544   1 KPRSTPDYLAQLLKDKKQLAAFPN---VFPHLERLLDEEISRVRGDLFNKGFGDK 52

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74761039   211 SPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPlirqiqTAVMPNGTPHPTAAIVPPGPEAGLIYTPYEY 290
Cdd:PHA03247 2716 VSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPA------RPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          90       100
                  ....*....|....*....|....
gi 74761039   291 PytLAPATSILEYPIEPSGVLGAV 314
Cdd:PHA03247 2790 S--LSESRESLPSPWDPADPPAAV 2811

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74761039  83 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRD-KKKEEQNRGKPNWEhlnEDLHVLIT--VED 159
Cdd:COG5176 149 QNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEgKISSDTPESLKNAE---AVLHCLIEadSED 225

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
gi 74761039 160 AQNRAEIKLKRAVEEVKKllVPaaEGEDSLKKMQLMELAILNGTYRD 206
Cdd:COG5176 226 KICRLIKSQLNAIREARR--NP--EGQNDLKRFQLRWLAHLNGTLRA 268

Putative nuclear localization signal of quaking; Quaking_NLS is the very C-terminal region of quaking proteins that is purported to be the nuclear localization signal.

                          10        20        30
                  ....*....|....*....|....*....|
gi 74761039   312 GAVATKVRRHDMRVHPYQRIVTADRAATGN 341
Cdd:pfam16551   1 GAMATKVRRHDKRVHPYQRIVTPDRAATGN 30

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 74761039    84 EKLYVPVKeypdfnFVGRILGPRGLTAKQLEAETGCKIMVRGKGS 128
Cdd:pfam00013   2 VEILVPSS------LVGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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 74761039  81 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRGKPNWEHLNEDLHVLITVEDA 160
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANRGKPNWEHLNDDLHVLITVEDT 80

                        90       100
                ....*....|....*....|.
gi 74761039 161 QNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22383  81 ENRAHIKLAKAVEEVKKLLIP 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 74761039  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQ--NRGKPNWEHLNEDLHVLITV 157
Cdd:cd22384   3 IKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEElrKSGDPKYAHLNEDLHVLIEA 82

                        90       100
                ....*....|....*....|
gi 74761039 158 EDAQNRAEIKLKRAVEEVKK 177
Cdd:cd22384  83 FAPPAEAYARLAHALAELRK 102

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74761039  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITV 157
Cdd:cd22468   3 MKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRkgGDPKYAHLNMDLHVFIEV 82

                        90       100
                ....*....|....*....|....
gi 74761039 158 EDAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22468  83 FGPPCEAYARMAHAMEEVKKFLVP 106

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 74761039  80 VQLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITV 157
Cdd:cd22469   5 IKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRksGEAKYAHLSDELHVLIEV 84

                        90       100
                ....*....|....*....|....
gi 74761039 158 EDAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22469  85 FAPPGEAYSRMSHALEEIKKFLVP 108

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 74761039  81 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 158
Cdd:cd22470   8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVF 87

                        90       100
                ....*....|....*....|...
gi 74761039 159 DAQNRAEIKLKRAVEEVKKLLVP 181
Cdd:cd22470  88 APPAEAYARMGHALEEIKKFLIP 110

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 74761039  82 LQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKeeQNRGKPNWEHLNEDLHVLITVEDAQ 161
Cdd:cd22382   2 VSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSVKEGKV--GRKDGQPLPGEDEPLHALVTANTAE 79

                        90
                ....*....|....*...
gi 74761039 162 NraeikLKRAVEEVKKLL 179
Cdd:cd22382  80 S-----VKKAVDKIKEII 92

Putative nuclear localization signal of quaking; Quaking_NLS is the very C-terminal region of quaking proteins that is purported to be the nuclear localization signal.

                          10        20        30
                  ....*....|....*....|....*....|
gi 74761039   312 GAVATKVRRHDMRVHPYQRIVTADRAATGN 341
Cdd:pfam16551   1 GAMATKVRRHDKRVHPYQRIVTPDRAATGN 30

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
                ....*....|....*....|....*....|....*....|....*
gi 74761039  84 EKLYVPVKeypdfnFVGRILGPRGLTAKQLEAETGCKIMVRGKGS 128
Cdd:cd00105   1 EEIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39

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
                ....*....|....*....|....*....|
gi 74761039  94 PDfNFVGRILGPRGLTAKQLEAETGCKIMV 123
Cdd:cd22396   8 PD-KMVGLIIGRGGEQINRLQAESGAKIQI 36

sixth 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 sixth one.

                        10        20
                ....*....|....*....|....*..
gi 74761039 100 GRILGPRGLTAKQLEAETGCKIMVRGK 126
Cdd:cd22451  13 RAIIGKGGAVLRELEAETGCRIQVPKK 39

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74761039   211 SPALAFSLAATAQAAPRIITGPAPVLPPAALRTPTPAGPTIMPlirqiqTAVMPNGTPHPTAAIVPPGPEAGLIYTPYEY 290
Cdd:PHA03247 2716 VSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPA------RPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          90       100
                  ....*....|....*....|....
gi 74761039   291 PytLAPATSILEYPIEPSGVLGAV 314
Cdd:PHA03247 2790 S--LSESRESLPSPWDPADPPAAV 2811