first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 162 GDGVFMQDVEINNVRN--RYILVRASTLSEIENKSGVQLFSKGRYYPNKALAT--DKDPPLYLHIVSHNRKDLTVALQEI 237
Cdd:cd22385   1 GDDLYVAEIEINDLPNtcRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATfnPGERPLYLHVQAPTKEAVDRAVNKI 80

                ....
gi 19114115 238 ESWI 241
Cdd:cd22385  81 NEII 84

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115   390 RDQNQGNRAYNPPNRNQAFSARD--------SRQEKTQPTNASPAPLVTPSLPVPSIP-----AVPGMEAMAMPPGVTSS 456
Cdd:PHA03247 2668 RRLGRAAQASSPPQRPRRRAARPtvgsltslADPPPPPPTPEPAPHALVSATPLPPGPaaarqASPALPAAPAPPAVPAG 2747

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 19114115   457 IAVPTTSSMPlqGMPTMFGAPGVSAPGTEAPGTGTPGLTTPGVDPYAA 504
Cdd:PHA03247 2748 PATPGGPARP--ARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSE 2793

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 162 GDGVFMQDVEINNVRN--RYILVRASTLSEIENKSGVQLFSKGRYYPNKALAT--DKDPPLYLHIVSHNRKDLTVALQEI 237
Cdd:cd22385   1 GDDLYVAEIEINDLPNtcRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATfnPGERPLYLHVQAPTKEAVDRAVNKI 80

                ....
gi 19114115 238 ESWI 241
Cdd:cd22385  81 NEII 84

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114115    308 AIVGPQGAYVKHIQQETRTRVQIkgqgsafiepstnRESDEPIHLCIMSHDPNAIQRAKVLCEDLI 373
Cdd:smart00322  16 LIIGKGGSTIKKIEEETGVKIDI-------------PGPGSEERVVEITGPPENVEKAAELILEIL 68

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19114115   304 HLRQAIVGPQGAYVKHIQQETRTRVQIKGQGSafiePSTNREsdepihlCIMSHDPNAIQRAKVLCED 371
Cdd:pfam00013   9 SLVGLIIGKGGSNIKEIREETGAKIQIPPSES----EGNERI-------VTITGTPEAVEAAKALIEE 65

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 162 GDGVFMQDVEINNVRN--RYILVRASTLSEIENKSGVQLFSKGRYYPNKALAT--DKDPPLYLHIVSHNRKDLTVALQEI 237
Cdd:cd22385   1 GDDLYVAEIEINDLPNtcRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATfnPGERPLYLHVQAPTKEAVDRAVNKI 80

                ....
gi 19114115 238 ESWI 241
Cdd:cd22385  81 NEII 84

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114115 162 GDGVFMQDVEINNV--RNRYILVRASTLSEIENKSGVQLFSKGRYYPNKALATDKDPPLYLHI 222
Cdd:cd22471   1 AESSIAREIVINDAppSVRHHLTKRSTQDEIQSKTGVVVVTRGRYYPPGTPPPDNEKPLYLHI 63

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 162 GDGVFMQDVEINNVRN--RYILVRASTLSEIENKSGVQLFSKGRYYPNKALATDKDPPLYLHIVSHNRKDLTVALQEIES 239
Cdd:cd22387   1 NNGNFVEEFEINDYPQiaRLKVTSKEVLNSIMEETGATITIKGQYYPPGKKPKPGERKLYLLIEGATEESVQSARNEIKR 80

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
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19114115 308 AIVGPQGAYVKHIQQETRTRVQIKGqgsafiepstnRESDEPIHLCIMSHDPNAIQRAKVLCE 370
Cdd:cd00105  12 LIIGKGGSTIKEIEEETGARIQIPK-----------EGEGSGERVVTITGTPEAVEKAKELIE 63

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        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 290 EEKVYINLTPSrgfHLRQAIVgpQGAYVKHIQQETRTRVQIKGQgsaFIEPSTNRESDE-PIHLCIMSHDPNAIQRAKVL 368
Cdd:cd22387   6 VEEFEINDYPQ---IARLKVT--SKEVLNSIMEETGATITIKGQ---YYPPGKKPKPGErKLYLLIEGATEESVQSARNE 77

                ....*
gi 19114115 369 CEDLI 373
Cdd:cd22387  78 IKRVL 82

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115     4 SRQNSQREDNYSRDRRSRfteDSYSRRDSQ-----RSGNEAPRESRYYRKEEHLQERSRSRSPARDSRWKSSSSGFAPAH 78
Cdd:TIGR01642  41 SRERSYREDSRPRDRRRY---DSRSPRSLRyssvrRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKRSLWDIK 117

                  ..
gi 19114115    79 PP 80
Cdd:TIGR01642 118 PP 119

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 19114115 289 LEEKVYI--NLTPSRGFHLRqaIVGPQGAYVKHIQQETRTRVQIKGQGS--------AFIEPSTNRESDEPIHLCIMSHD 358
Cdd:cd22383   2 LSEKVYVpvDEYPDYNFVGR--ILGPRGMTAKQLEQDTGCKIMIRGKGSmrdkkkeeANRGKPNWEHLNDDLHVLITVED 79

                ....*....
gi 19114115 359 PNAIQRAKV 367
Cdd:cd22383  80 TENRAHIKL 88

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
                ....*....|....*....|....*....|....*....|....*..
gi 19114115 289 LEEKVYINLTPSRGFHLRQAIVGPQGAYVKHIQQETRTRVQIKGQGS 335
Cdd:cd22384   5 LSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGS 51

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19114115 309 IVGPQGAYVKHIQQETRTRVQIKgqgsafiepstnRESDE-PIHLCIMSHDPNAIQRAKVLCEDLI 373
Cdd:cd22396  15 IIGRGGEQINRLQAESGAKIQIA------------PDSGGlPERPCTLTGTPDAIETAKRLIDQIV 68

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
                ....*....|....*....|....*....|....*....|....*..
gi 19114115 289 LEEKVYINLTPSRGFHLRQAIVGPQGAYVKHIQQETRTRVQIKGQGS 335
Cdd:cd22468   5 LKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGS 51

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        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114115 308 AIVGPQGAYVKHIQQETRTRVQIKGQGSaFIEPSTNREsdepihlCIMSHDPNAIQRAKVL 368
Cdd:cd09031  14 AILGKGGKTLVEIQELTGARIQISKKGE-FVPGTRNRK-------VTITGTPAAVQAAQYL 66

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114115 295 INLTPSRGFHLRQAIVGPQGAYVKHIQQETRTRVQIKGQGSAfiEPSTNRESDEPIHLCImSHDPNAIQRAKVLCEDLIA 374
Cdd:cd22447   4 QNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDAD--AAPADEDDDTMVEVTI-TGDEFNVQHAKQRIEEIIS 80

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114115 306 RQA---IVGPQGAYVKHIQQETRTRVQikgqgsaFIEPSTNresdEPIHLCIMSHDPNAIQRAKVLCEDLI 373
Cdd:cd22398   8 RFAvgvVIGKGGEMIKKIQNETGARVQ-------FKPDDGN----SPDRICVITGPPDQVQHAARMIQELI 67