Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145  267 REDNRPCPICGLKDHKRYDCP-----------NRKIPNIQGIVCKICGQTGHFSRDCN-SSSQRMSRFDRNATVNNSAPI 334
Cdd:COG5082  57 REENPVCFNCGQNGHLRRDCPhsicyncswdgHRSNHCPKPKKCYNCGETGHLSRDCNpSKDQQKSCFDCNSTRHSSEDC 136

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6323145  335 QSNDVHYNSN---THPIQAPKRSRYDNNSTEPPLKFPASSRYaPSPSPPASHISR 386
Cdd:COG5082 137 PSIWKHYVLNngdGHPIKKFCYSCGSAGHFGDDCKEPRSSRV-PYVCGKKGYVSF 190

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145     33 SLWRKNTVESDVHRFNSLPSKISGALTREQIYSYQVMFRIQEITIKLRTNDF-VPPSRKNRSPSPPPVYDAQGKRTNTRE 111
Cdd:pfam16275   3 SRWGGEPEKTDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLgVPPSPEERSPSPPPIYDANGKRTNTRE 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 6323145    112 QRYRKKLEDERIKLVEIALKTIPYFVPPDDYK 143
Cdd:pfam16275  83 VRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145  267 REDNRPCPICGLKDHKRYDCP-----------NRKIPNIQGIVCKICGQTGHFSRDCN-SSSQRMSRFDRNATVNNSAPI 334
Cdd:COG5082  57 REENPVCFNCGQNGHLRRDCPhsicyncswdgHRSNHCPKPKKCYNCGETGHLSRDCNpSKDQQKSCFDCNSTRHSSEDC 136

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6323145  335 QSNDVHYNSN---THPIQAPKRSRYDNNSTEPPLKFPASSRYaPSPSPPASHISR 386
Cdd:COG5082 137 PSIWKHYVLNngdGHPIKKFCYSCGSAGHFGDDCKEPRSSRV-PYVCGKKGYVSF 190

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 6323145     146 TKFQDKYYIPVdqypdvNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGS 194
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145    363 PPLKFPAS-------SRYAPSPSPPASHiSRQAQNVTPTPPPGLTSSSFSSGVPGIAPPPLQSPPESEQPKfslPPPPGM 435
Cdd:PHA03247 2556 PPAAPPAApdrsvppPRPAPRPSEPAVT-SRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPD---PPPPSP 2631

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145     33 SLWRKNTVESDVHRFNSLPSKISGALTREQIYSYQVMFRIQEITIKLRTNDF-VPPSRKNRSPSPPPVYDAQGKRTNTRE 111
Cdd:pfam16275   3 SRWGGEPEKTDKPPIPGLPTAIPGGLTPEQLDAYLLQFRIEEITRKLRTGDLgVPPSPEERSPSPPPIYDANGKRTNTRE 82

                          90       100       110
                  ....*....|....*....|....*....|..
gi 6323145    112 QRYRKKLEDERIKLVEIALKTIPYFVPPDDYK 143
Cdd:pfam16275  83 VRYRKKLEKERHRLIEEAMKINPNFRPPADYK 114

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145  267 REDNRPCPICGLKDHKRYDCP-----------NRKIPNIQGIVCKICGQTGHFSRDCN-SSSQRMSRFDRNATVNNSAPI 334
Cdd:COG5082  57 REENPVCFNCGQNGHLRRDCPhsicyncswdgHRSNHCPKPKKCYNCGETGHLSRDCNpSKDQQKSCFDCNSTRHSSEDC 136

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 6323145  335 QSNDVHYNSN---THPIQAPKRSRYDNNSTEPPLKFPASSRYaPSPSPPASHISR 386
Cdd:COG5082 137 PSIWKHYVLNngdGHPIKKFCYSCGSAGHFGDDCKEPRSSRV-PYVCGKKGYVSF 190

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 6323145  147 KFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGK--NASDLPPGAMNFEDPLHCLIIA-DS 223
Cdd:cd22383   1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKkeEANRGKPNWEHLNDDLHVLITVeDT 80

                        90
                ....*....|....*..
gi 6323145  224 EDKIQKGIKVCQNIVIK 240
Cdd:cd22383  81 ENRAHIKLAKAVEEVKK 97

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; 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 6323145  145 PTKFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEgKNASDLPPGAMNFE---DPLHCLI-I 220
Cdd:cd22466   3 SVTLSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRD-KKKEDLNRGKPNWEhlnDELHVLItV 81

                        90       100
                ....*....|....*....|...
gi 6323145  221 ADSED----KIQKGIKVCQNIVI 239
Cdd:cd22466  82 EDTENrakvKLQRAVEEVRKLLV 104

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 6323145  154 IPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDL--PPGAMNFEDPLHCLIIAD-SEDKIQKG 230
Cdd:cd22467   8 VPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLrdKPGYEHLNEPLHVLIEAElPANIIDAR 87

                ....*...
gi 6323145  231 IKVCQNIV 238
Cdd:cd22467  88 LQHAQEII 95

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
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6323145  147 KFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDLPPGA 208
Cdd:cd22468   4 KLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGG 65

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6323145  147 KFQDKYYIPVDQYPDVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKNASDLPPGA----MNFEDPLHCLI 219
Cdd:cd22470   8 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGeakyFHLNDDLHVLI 84

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 6323145     146 TKFQDKYYIPVdqypdvNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGS 194
Cdd:smart00322   1 DPVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43

universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 6323145   269 DNRPCPICGLKDHKRYDCPNRKIPNIQGIVCKICGQTGHFSRDCNSS 315
Cdd:PTZ00368 102 ARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPDK 148

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
                ....*....|....*....|....*....|....*..
gi 6323145  161 DVNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKE 197
Cdd:cd00105   6 PSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG 42

universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 6323145   273 CPICGLKDHKRYDCPN-RKIPNIQGIVCKICGQTGHFSRDCNSS 315
Cdd:PTZ00368   3 CYRCGGVGHQSRECPNsAPAGAAKARPCYKCGEPGHLSRECPSA 46

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 6323145  160 PDvNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRGSVKEGKN 200
Cdd:cd22514   8 PD-EHIGAILGRGGRTINEIQQHSGARIKISDRGDFVSGTR 47

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30
                ....*....|....*....|....*....|....
gi 6323145  160 PDvNFVGLLLGPRGRTLRKLQEDSNCKIAIRGRG 193
Cdd:cd09031   8 PE-NLVGAILGKGGKTLVEIQELTGARIQISKKG 40

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 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
                ....*....|....*....|....*..
gi 6323145  163 NFVGLLLGPRGRTLRKLQEDSNCKIAI 189
Cdd:cd22495   9 NFVGRLIGKEGRNLKKIEQDTDTKITI 35

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 6323145  160 PDvNFVGLLLGPRGRTLRKLQEDSNCKIAI 189
Cdd:cd22396   8 PD-KMVGLIIGRGGEQINRLQAESGAKIQI 36

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323145    363 PPLKFPAS-------SRYAPSPSPPASHiSRQAQNVTPTPPPGLTSSSFSSGVPGIAPPPLQSPPESEQPKfslPPPPGM 435
Cdd:PHA03247 2556 PPAAPPAApdrsvppPRPAPRPSEPAVT-SRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPLPPDTHAPD---PPPPSP 2631

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 6323145  175 TLRKLQEDSNCKIAIRGRGSVKEGKNasdlPPGamnfEDPLHCLIIADSEDKIQKGIKVCQNIV 238
Cdd:cd22387  27 VLNSIMEETGATITIKGQYYPPGKKP----KPG----ERKLYLLIEGATEESVQSARNEIKRVL 82

second 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 second one.

                        10        20
                ....*....|....*....|....*..
gi 6323145  163 NFVGLLLGPRGRTLRKLQEDSNCKIAI 189
Cdd:cd22401   9 NLCGRLIGKDGRNIKKIMEDTNTKITI 35