Citrus Sinensis ID: 002340

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------920-------930----

MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

cccccccHHcccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHcccHHHHHccccccccHHHcccHHHHcccccccccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEEEEEEcccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEEcccccccccccccccHHHHcccccEEEEEEcccccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccccccccHHHcccHHHHHHHHHHHccccccccHHHHHccccHHHHHHHcccccccccccccEEEccEEEEEccccEEcccHHHHHHHccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEEEccccHHHHHHHHcccEEcccccEEEcccEEEEEEcEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcc

cccccccccccccccccHHccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEcccccccccccccccccccccccHHccccccccHHcccccccccccHccccccccccHccccccccccEEEEEEcccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcEEEccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccEEEEEEccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccEEEEEEEcccHHccccEEEEcccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHccEEccccccccEEcccEEcccccEEEEccHHHHHHHHcEEccccccEEEEccccccccccHccHHccccccccccccEEEEcccccccccccccccccccccccEEEEcccccccccEEEccHHHHHHHHHHccccccEEEEEEcccccccEEEcEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccHHcccccccccccHHHcccccccccccccccccEEEccccccEEEEEEcc

mrtrqdsktqkdqasgkestvrgalrdsesshnetgtlaetSREGVGKFLRHVnarsssrskkqdcAVGLTTSVLkvsgkqevdkrvtwsdvdahgcsrdamgntlreldegrlqdnvldggeemydsdwedgsipvacskenhpesdikgvtiefdaadsvtkkpvrrasAEDKELAELVHKVHLLCLLARgrlidsvcddplIQASLLSLLPSYLLKISEVSKLTANALSPivswfhdnfhvrssvstrrSFHSDLAHAlesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgggifnaptlmvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskkspvscelssgnldpsssmacsdiseachpkeksqALKRKGDLEFEMQLEMALSATnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkvgaplYWAEVYcsgenltgkwvhvdaanaiIDGEQKVEAAAAACKTSLRYIVAFAgcgakdvtRRYCMKWYRIASKRVNSAWWDAVLAPlrelesgatgdlnvessakdsfvadrnsleDMELEtralteplptnqqaykNHQLYVIERWLNKYQilypkgpilgfcsghavyprscvQTLKTKERWLREALQVKAnevpvkviknsskskkgqdfepedydevdargnielygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprvYSVAKRleidsapamvgfefrngrstpvfdgIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRlnncygnnstsqsssnfqnvkktnsnvgvdssqndwqspnqvdrgdtklhapspfqseehehvyliedqsfdeensvttkrchcgftiqveel

mrtrqdsktqkdqasgkestvrgalrdsesshnetgtlaetsregvGKFLRHVnarsssrskkqdcavglttsvlkvsgkqevdkrvtwsdvdahgcsrdamgntlreldegrlQDNVLDGGEEMYDSDWEDGSIPVACSKenhpesdikgvtiefdaadsvtkkpVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHalesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgGGIFNAPTLMVAKPEEVLASpvksfscdkkenvcetsskgspeckysspksnntqskksPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSAtnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFagcgakdvTRRYCMKWYRIASKRVNSAWWDAVLAPLRELEsgatgdlnvessakdsfvadrNSLEDMELETralteplptnqqayKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREAlqvkanevpvkviknsskskkgqdfepedydevdARGNIELygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKrreaqatsrwYQLLSSIVTRQRLNNCYGNnstsqsssnfqnVKKTNsnvgvdssqndwQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQAsllsllpsyllKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEvpvkviknsskskkGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYaeeeekreaeekkrreaQATSRWYQLLSSIVTRQRLNNCYGnnstsqsssnfqnVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

*****************************************************************CAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGC*******************************************************************************LAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSV**********************EIAALSVALFRALKLTTRFVSILDVAS*********************IFNAPTLMV**********************************************************************************************************************************************CLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLREL********************************************AYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV*********************DARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAY*********************RWYQLLSSIVTRQRLNNCY*********************************************************VYLIE*********VTTKRCHCGFTIQ****

*********************************************************************************************************************************WE**********************************************AELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVR***********DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVA*******************************************************************************************************************************************************************************************APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV************************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEK**********AQATSRWYQLLSSIVTRQRLN**************************************************************LIEDQSFDEE*SVTTKRCHCGFTIQVEEL

******************************************REGVGKFLRHV**************VGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAA**************DKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVR***********DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK**************RVGGGIFNAPTLMVAKPEEVLASPVKSFSCD**************************************************SDISEA**********KRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKN**************YDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAE*****************TSRWYQLLSSIVTRQRLNNCYGN***********NVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

****************************************************************************************W****A*****************************EMYDSDWEDGSIPVACS**NHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK*************************************************************************************************************************************************************************************KVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELE*****D**V*****DSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNS********************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYG************************************************************EDQSFDEENSVTTKRCHCGFTIQVEEL

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		934	2.2.26 [Sep-21-2011]
P51612		930	DNA repair protein comple	yes	no	0.673	0.676	0.320	1e-73
Q01831		940	DNA repair protein comple	yes	no	0.358	0.356	0.376	1e-59
Q24595		1293	DNA repair protein comple	yes	no	0.359	0.259	0.344	4e-54
Q10445		638	DNA repair protein rhp41	yes	no	0.346	0.507	0.295	9e-33
P87235		686	DNA repair protein rhp42	no	no	0.361	0.492	0.280	5e-25
P14736		754	DNA repair protein RAD4 O	yes	no	0.380	0.470	0.258	2e-24
Q7F0R1		447	Peptide-N(4)-(N-acetyl-be	no	no	0.070	0.147	0.319	6e-05

>sp\|P51612\|XPC_MOUSE DNA repair protein complementing XP-C cells homolog OS=Mus musculus GN=Xpc PE=1 SV=2	Back alignment and function desciption

 Score =  278 bits (711), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 230/717 (32%), Positives = 336/717 (46%), Gaps = 88/717 (12%)

Query: 174 DKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSP 233
           +KE+ E +HKVHLLCLLA G   +S+C  P + A  LS++P    K+  +    A  LS 
Sbjct: 194 NKEVQENMHKVHLLCLLASGFYRNSICRQPDLLAIGLSIIPIRFTKVP-LQDRDAYYLSN 252

Query: 234 IVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGT-----PEEIAALSVALFRALKLTTR 288
           +V WF   F V + +S   S   DL   LE R         EE+  + + + RAL+L TR
Sbjct: 253 LVKWFIGTFTVNADLSA--SEQDDLQTTLERRIAIYSARDNEELVHIFLLILRALQLLTR 310

Query: 289 FVSILDVASLKPEADKNVSSNQDSSRVGGG-----------IFNAPTL-MVAKPEEVLAS 336
            V  L    LK    K   S++++S  G G             N PT     K EE L+ 
Sbjct: 311 LVLSLQPIPLKSAVTKGRKSSKETSVEGPGGSSELSSNSPESHNKPTTSRRIKEEETLSE 370

Query: 337 -------------------PVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPV 377
                                +  SC + E   E   +G P  +     +  +  ++S  
Sbjct: 371 GRGKATARGKRGTGTAGSRQRRKPSCSEGEEA-EQKVQGRPHARKRRVAAKVSYKEESES 429

Query: 378 SCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSN 437
               S  + +PSS        E C P  + Q  KR        Q   A S +   T + +
Sbjct: 430 DGAGSGSDFEPSSGEGQHSSDEDCEPGPRKQ--KRAS----APQRTKAGSKSASKTQRGS 483

Query: 438 ICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGEN 497
            C +       SS+    KR KK+ SG         +  +  RK      W EVYC  + 
Sbjct: 484 QC-EPSSFPEASSSSSGCKRGKKVSSG---------AEEMADRKPAGVDQWLEVYCEPQ- 532

Query: 498 LTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIAS 556
              KWV VD  + ++   Q V     A K  + Y+V     G  +DVT+RY   W     
Sbjct: 533 --AKWVCVDCVHGVVG--QPVACYKYATK-PMTYVVGIDSDGWVRDVTQRYDPAWMTATR 587

Query: 557 K-RVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPT 615
           K RV++ WW   L P R                  S + +R   ED E + + L +PLPT
Sbjct: 588 KCRVDAEWWAETLRPYR------------------SLLTEREKKEDQEFQAKHLDQPLPT 629

Query: 616 NQQAYKNHQLYVIERWLNKYQILYPK-GPILGFCSGHAVYPRSCVQTLKTKERWLREALQ 674
           +   YKNH LY ++R L K+Q +YP+   +LG+C G AVY R CV TL +++ WL++A  
Sbjct: 630 SISTYKNHPLYALKRHLLKFQAIYPETAAVLGYCRGEAVYSRDCVHTLHSRDTWLKQARV 689

Query: 675 VKANEVPVKVIKN-SSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVP 733
           V+  EVP K++K  S++++K +  EP+ +D  D    + LYG WQ E  + P AV+G VP
Sbjct: 690 VRLGEVPYKMVKGFSNRARKARLSEPQLHDHND----LGLYGHWQTEEYQPPIAVDGKVP 745

Query: 734 RNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIV 793
           RNE G V ++    +P G V + LP +  VA++L ID   A+ GF+F  G   PV DG +
Sbjct: 746 RNEFGNVYLFLPSMMPVGCVQMTLPNLNRVARKLGIDCVQAITGFDFHGGYCHPVTDGYI 805

Query: 794 VCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNS 850
           VC EF+D +L A+  E+   E +EK+++E +A   W  L+  ++ R+RL   YG  S
Sbjct: 806 VCEEFRDVLLAAWENEQAIIEKKEKEKKEKRALGNWKLLVRGLLIRERLKLRYGAKS 862

The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the Xpc:Rad23b dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad23b induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1.
Mus musculus (taxid: 10090)

>sp\|Q01831\|XPC_HUMAN DNA repair protein complementing XP-C cells OS=Homo sapiens GN=XPC PE=1 SV=4	Back alignment and function description

>sp\|Q24595\|XPC_DROME DNA repair protein complementing XP-C cells homolog OS=Drosophila melanogaster GN=mus210 PE=1 SV=2	Back alignment and function description

>sp\|Q10445\|RHP41_SCHPO DNA repair protein rhp41 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rhp41 PE=3 SV=1	Back alignment and function description

>sp\|P87235\|RHP42_SCHPO DNA repair protein rhp42 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rhp42 PE=3 SV=1	Back alignment and function description

>sp\|P14736\|RAD4_YEAST DNA repair protein RAD4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD4 PE=1 SV=3	Back alignment and function description

>sp\|Q7F0R1\|PNG1_ORYSJ Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase OS=Oryza sativa subsp. japonica GN=PNG1 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		934
225453199		1103	PREDICTED: DNA repair protein complement	0.960	0.813	0.638	0.0
224079463		868	predicted protein [Populus trichocarpa]	0.905	0.974	0.632	0.0
356552017		926	PREDICTED: uncharacterized protein LOC10	0.961	0.969	0.572	0.0
255582247		683	DNA repair protein xp-C / rad4, putative	0.699	0.956	0.679	0.0
449445198		923	PREDICTED: DNA repair protein complement	0.935	0.946	0.563	0.0
449479948		923	PREDICTED: DNA repair protein complement	0.935	0.946	0.562	0.0
297807689		868	DNA repair protein Rad4 family [Arabidop	0.901	0.970	0.524	0.0
22326854		865	xeroderma pigmentosum group C-complement	0.891	0.963	0.529	0.0
357492015		1052	DNA repair protein complementing XP-C ce	0.701	0.622	0.623	0.0
357141401		889	PREDICTED: DNA repair protein complement	0.855	0.898	0.505	0.0

>gi\|225453199\|ref\|XP_002275277.1\| PREDICTED: DNA repair protein complementing XP-C cells-like [Vitis vinifera]	Back alignment and taxonomy information

 Score = 1082 bits (2799), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 591/926 (63%), Positives = 696/926 (75%), Gaps = 29/926 (3%)

Query: 32   HNETGTLAETSREGVGKFLRHVNARSSSRSKKQD-CAVGLTTSVLKVSGKQEV---DKRV 87
            ++E+GTLAE SRE VGK LR  N R SS  +K D C+    ++ L  S + E+     RV
Sbjct: 184  NDESGTLAEISREAVGKLLRRANPRRSSGIRKLDSCSQQCESTGLIGSKRSEILDTGGRV 243

Query: 88   TWSDVDAHGCSRDAMGNTL--RELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHP 145
            TW+ +D+ GC R A+G +   +E+DE   QD  L+ GE++ +SDWE+GSIP   S +NH 
Sbjct: 244  TWNALDSEGCGRSAIGRSTLEKEVDEKSSQDTYLNSGEDINESDWEEGSIPTLDSVDNHQ 303

Query: 146  ESDIKGVTIEFDAA-DSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPL 204
             + IK VTIE     DS  +KP+RRASAEDKELAELVHKVHLLCLLARGRLIDS C+DPL
Sbjct: 304  NAGIKEVTIELSGLLDSSQQKPIRRASAEDKELAELVHKVHLLCLLARGRLIDSACNDPL 363

Query: 205  IQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALES 264
            +QASLLSLLP+ LLKISE+ +LTANA + +V WFHDNF VRS  S  R  HS LA ALE+
Sbjct: 364  VQASLLSLLPADLLKISEIPRLTANAFTLLVRWFHDNFRVRSPSSVERPLHSSLAFALEA 423

Query: 265  REGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPT 324
             EGTPEE+AALSVALFRAL LTTRFVSILDVA LKP ADK+ S+ Q+++R  GGIF+  T
Sbjct: 424  HEGTPEEVAALSVALFRALNLTTRFVSILDVAPLKPGADKSESAIQNANRASGGIFDNST 483

Query: 325  LMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSG 384
            LMVA+  +V +SPVKS SC  K NVCE S   +   K         QS  SP+S +L+  
Sbjct: 484  LMVARKNQVSSSPVKSSSCHVKGNVCEPSQNNACTNKDLKSTRKTAQSTDSPISDQLNDR 543

Query: 385  NLDPSSSMACSD---ISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSD 441
             LD   S+AC +   ISE C   +K +  KRKGDLEF+MQLEMALSAT V  ++SN  S+
Sbjct: 544  MLD---SLACKEQFAISEDCI-TDKPEGSKRKGDLEFKMQLEMALSATAVGINESNGGSN 599

Query: 442  VKDLNSNSSTVL-PVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTG 500
            VK+L S SS+   P+KR+K+I+  E  T   GISTAVGSRK+GAPLYWAEV+C+GENLTG
Sbjct: 600  VKELFSESSSFSSPLKRVKRIKIEEYPTPSQGISTAVGSRKIGAPLYWAEVFCTGENLTG 659

Query: 501  KWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVN 560
            KWVH+DA NAIIDGE+KVEAAAAACKTSLRY+VAF+G GAKDVTRRYCMKWYRIAS+R+N
Sbjct: 660  KWVHIDAINAIIDGEEKVEAAAAACKTSLRYVVAFSGNGAKDVTRRYCMKWYRIASQRIN 719

Query: 561  SAWWDAVLAPLRELESGATGDLNV----------ESSAKDSFVADRNSLEDMELETRALT 610
            SAWWDAVLAPL+ELE+GA G + V          ESS +++FVA R+SLEDMELETRALT
Sbjct: 720  SAWWDAVLAPLKELEAGAVGGVEVLKENVKKVRAESSDRNAFVATRDSLEDMELETRALT 779

Query: 611  EPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLR 670
            EPLPTNQQAYKNHQLY +ERWL KYQIL+PKGP+LGFCSGH VYPR+CVQTLKTK+RWLR
Sbjct: 780  EPLPTNQQAYKNHQLYAMERWLTKYQILHPKGPVLGFCSGHPVYPRTCVQTLKTKQRWLR 839

Query: 671  EALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNG 730
            E LQVKA+E P KV+K SSK  K Q  E  DY + D  G I LYG+WQ+EPL LP AVNG
Sbjct: 840  EGLQVKADEHPTKVLKCSSKLSKVQALEAVDYGDADPGGTIALYGRWQMEPLCLPCAVNG 899

Query: 731  IVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFD 790
            IVP+NE GQVDVWSEKCLPPGTVHLR+PRV  +AK+LEID APAMVGFEFRNGRS PVFD
Sbjct: 900  IVPKNEWGQVDVWSEKCLPPGTVHLRVPRVVPIAKKLEIDFAPAMVGFEFRNGRSIPVFD 959

Query: 791  GIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNS 850
            GIVVCAEFKDTILE YA+EEE+R+AEEK+  EA A SRWYQLLSSIV RQRLNN YGN  
Sbjct: 960  GIVVCAEFKDTILEVYADEEERRQAEEKRGIEAHAVSRWYQLLSSIVIRQRLNNSYGNGL 1019

Query: 851  TSQSSSNFQNVKKTNSNVGVDSSQNDWQ--SPNQVDRGDTKLHAPSPFQSEEHEHVYLIE 908
             S +S+  + V    S+  V+   ND Q     Q    DT L  PS    E+HEHV++ E
Sbjct: 1020 LSDTSNGIKKV-NNRSSWQVEGRDNDRQFLECQQGYVEDTNLDPPSMVFREDHEHVFIAE 1078

Query: 909  DQSFDEENSVTTKRCHCGFTIQVEEL 934
             + FDEEN V TKRC CGF+IQVEEL
Sbjct: 1079 -EGFDEENLVRTKRCGCGFSIQVEEL 1103

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224079463\|ref\|XP_002305874.1\| predicted protein [Populus trichocarpa] gi\|222848838\|gb\|EEE86385.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356552017\|ref\|XP_003544368.1\| PREDICTED: uncharacterized protein LOC100818100 [Glycine max]	Back alignment and taxonomy information

>gi\|255582247\|ref\|XP_002531915.1\| DNA repair protein xp-C / rad4, putative [Ricinus communis] gi\|223528425\|gb\|EEF30459.1\| DNA repair protein xp-C / rad4, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449445198\|ref\|XP_004140360.1\| PREDICTED: DNA repair protein complementing XP-C cells-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449479948\|ref\|XP_004155756.1\| PREDICTED: DNA repair protein complementing XP-C cells-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297807689\|ref\|XP_002871728.1\| DNA repair protein Rad4 family [Arabidopsis lyrata subsp. lyrata] gi\|297317565\|gb\|EFH47987.1\| DNA repair protein Rad4 family [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi|22326854|ref|NP_197166.2| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|79327993|ref|NP_001031894.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|17065358|gb|AAL32833.1| Unknown protein [Arabidopsis thaliana] gi|34098839|gb|AAQ56802.1| At5g16630 [Arabidopsis thaliana] gi|332004936|gb|AED92319.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|332004937|gb|AED92320.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|357492015\|ref\|XP_003616296.1\| DNA repair protein complementing XP-C cells-like protein [Medicago truncatula] gi\|355517631\|gb\|AES99254.1\| DNA repair protein complementing XP-C cells-like protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|357141401\|ref\|XP_003572211.1\| PREDICTED: DNA repair protein complementing XP-C cells homolog [Brachypodium distachyon]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		934
TAIR\|locus:2174160		865	RAD4 [Arabidopsis thaliana (ta	0.610	0.658	0.527	9.2e-213
MGI\|MGI:103557		930	Xpc "xeroderma pigmentosum, co	0.866	0.869	0.264	4.5e-66
UNIPROTKB\|F1N806		826	Gga.54220 "Uncharacterized pro	0.673	0.761	0.303	4.8e-64
UNIPROTKB\|E1BUG1		936	Gga.54220 "Uncharacterized pro	0.673	0.672	0.303	2.1e-60
UNIPROTKB\|E1BDJ1		932	XPC "Uncharacterized protein"	0.268	0.269	0.365	1.2e-59
RGD\|1305760		933	Xpc "xeroderma pigmentosum, co	0.854	0.855	0.274	3.1e-55
UNIPROTKB\|Q01831		940	XPC "DNA repair protein comple	0.849	0.843	0.272	1.7e-54
UNIPROTKB\|E9PH69		903	XPC "DNA repair protein-comple	0.711	0.736	0.284	6.3e-54
UNIPROTKB\|F1SPI2		944	XPC "Uncharacterized protein"	0.308	0.305	0.327	2.5e-50
UNIPROTKB\|E2RCR3		949	XPC "Uncharacterized protein"	0.270	0.266	0.370	1.2e-49

TAIR\|locus:2174160 RAD4 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1484 (527.5 bits), Expect = 9.2e-213, Sum P(2) = 9.2e-213
 Identities = 322/610 (52%), Positives = 395/610 (64%)

Query:   346 KENVCETSSKGSPECKYSS--PKSNNTQSK-KSPVSCELSSGNLDPSSSMACSDISEACH 402
             K  +  TS+   P+ +  S  PK +++  K KSP   +   GN   S  +  + ++ +C 
Sbjct:   275 KHGIFRTSTLMVPKQQAISSYPKKSSSHVKNKSPFE-KPQLGNPLGSDQVQDNAVNSSCE 333

Query:   403 P--KEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKK 460
                  KS   +RKGD+EFE Q+ MALSAT          +D    N  SS V   K++++
Sbjct:   334 AGMSIKSDGTRRKGDVEFERQIAMALSAT----------AD----NQQSSQVNNTKKVRE 379

Query:   461 IE--SGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKV 518
             I   S  SS S   ISTA GS+KV +PL W EVYC+GEN+ GKWVHVDA N +ID EQ +
Sbjct:   380 ITKISNSSSVSDQVISTAFGSKKVDSPLCWLEVYCNGENMDGKWVHVDAVNGMIDAEQNI 439

Query:   519 EAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGA 578
             EAAAAACKT LRY+VAFA  GAKDVTRRYC KW+ I+SKRV+S WWD VLAPL  LESGA
Sbjct:   440 EAAAAACKTVLRYVVAFAAGGAKDVTRRYCTKWHTISSKRVSSVWWDMVLAPLVHLESGA 499

Query:   579 TGD----------LN-VES--SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQL 625
             T D          LN V S  S+  S    R++LEDMEL TRALTE LPTNQQAYK+H++
Sbjct:   500 THDEDIALRNFNGLNPVSSRASSSSSSFGIRSALEDMELATRALTESLPTNQQAYKSHEI 559

Query:   626 YVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEXXXXXX 685
             Y IE+WL+K QIL+PKGP+LGFCSGH VYPR+CVQTLKTKERWLR+ LQ+KANE      
Sbjct:   560 YAIEKWLHKNQILHPKGPVLGFCSGHPVYPRTCVQTLKTKERWLRDGLQLKANEVPSKIL 619

Query:   686 XXXXXXXXGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSE 745
                      +DFE  D +       +ELYGKWQ+EPL LP AVNGIVP+NERGQVDVWSE
Sbjct:   620 KRNSKFKKVKDFEDGDNNIKGGSSCMELYGKWQMEPLCLPPAVNGIVPKNERGQVDVWSE 679

Query:   746 KCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEA 805
             KCLPPGTVHLR PR+++VAKR  ID APAMVGFE+R+G +TP+F+GIVVC EFKDTILEA
Sbjct:   680 KCLPPGTVHLRFPRIFAVAKRFGIDYAPAMVGFEYRSGGATPIFEGIVVCTEFKDTILEA 739

Query:   806 YXXXXXXXXXXXXXXXXXQATSRWYQLLSSIVTRQRLNNCYGXXXXXXXXXXXXXVKKTN 865
             Y                 QA SRWYQLLSSI+TR+RL N Y                + N
Sbjct:   740 YAEEQEKKEEEERRRNEAQAASRWYQLLSSILTRERLKNRYANNSNDVEAKSL----EVN 795

Query:   866 SNVGVDSSQNDWQSPNQV-DRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCH 924
             S   V +         +V  RG+      S  + E HEHV+L E+++FDEE SV TKRC 
Sbjct:   796 SETVVKAKNVKAPEKQRVAKRGEKSRVRKSRNEDESHEHVFLDEEETFDEETSVKTKRCK 855

Query:   925 CGFTIQVEEL 934
             CGF+++VE++
Sbjct:   856 CGFSVEVEQM 865

GO:0003677 "DNA binding" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA;ISS

GO:0006289 "nucleotide-excision repair" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=IDA

MGI\|MGI:103557 Xpc "xeroderma pigmentosum, complementation group C" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|F1N806 Gga.54220 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BUG1 Gga.54220 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E1BDJ1 XPC "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

RGD\|1305760 Xpc "xeroderma pigmentosum, complementation group C" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q01831 XPC "DNA repair protein complementing XP-C cells" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E9PH69 XPC "DNA repair protein-complementing XP-C cells" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SPI2 XPC "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E2RCR3 XPC "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.IV.3592.1	hypothetical protein (871 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.00020503	hypothetical protein (758 aa)		•	•	0.508
	eugene3.00290111	hypothetical protein (982 aa)		•	•	0.481
	estExt_fgenesh4_pm.C_LG_I0627	hypothetical protein (558 aa)		•	•	0.450
	gw1.V.5266.1	hypothetical protein (289 aa)	•	•		0.414
	gw1.70.559.1	hypothetical protein (329 aa)		•	•	0.409

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		934
TIGR00605		713	TIGR00605, rad4, DNA repair protein rad4	4e-76
COG5535		650	COG5535, RAD4, DNA repair protein RAD4 [DNA replic	4e-43
pfam10405		75	pfam10405, BHD_3, Rad4 beta-hairpin domain 3	9e-35
smart01032		75	smart01032, BHD_3, Rad4 beta-hairpin domain 3	2e-33
pfam03835		142	pfam03835, Rad4, Rad4 transglutaminase-like domain	2e-21
smart01030		54	smart01030, BHD_1, Rad4 beta-hairpin domain 1	6e-18
pfam10403		57	pfam10403, BHD_1, Rad4 beta-hairpin domain 1	6e-17
pfam10404		56	pfam10404, BHD_2, Rad4 beta-hairpin domain 2	1e-10
smart01031		56	smart01031, BHD_2, Rad4 beta-hairpin domain 2	7e-09
pfam01841		108	pfam01841, Transglut_core, Transglutaminase-like s	2e-04

>gnl\|CDD\|233048 TIGR00605, rad4, DNA repair protein rad4	Back alignment and domain information

 Score =  263 bits (674), Expect = 4e-76
 Identities = 189/722 (26%), Positives = 275/722 (38%), Gaps = 85/722 (11%)

Query: 164 KKPVRRASAED-KELAELVHKVHLLCLLARGRLIDSVCDDP--LIQASLLSLLPSYLLKI 220
           +  +RR        L EL H+V L+C L      D V   P  L  +  +          
Sbjct: 38  EPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSVPDSLSVSEEIPSREEDYD-S 96

Query: 221 SEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEE-----IAAL 275
            E   +    LS +V+ F          S   S   D A  L     + E         +
Sbjct: 97  REFEDVY---LSNLVAEFETISVEIKPSSKAES--DDDAETLSRNVCSNEARKDRKYIHI 151

Query: 276 SVALFRALKLTTRFVSILDVASLKPEADKNVSSNQD------SSRVGGGIFNAPTLMVAK 329
              L   + L TR    L  A LK     N+   +       S R    + +     + K
Sbjct: 152 LYLLCLMVHLFTRNEWSLS-APLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRK 210

Query: 330 P-EEVLASPVKSFSC-------DKKENVCETS---SKGSPECKYSSPKSNN----TQSKK 374
           P  E L   ++++            + +       SK     K S+ K       T  + 
Sbjct: 211 PLVEKLKKCMETWQKGLRKTTKGLLKLLNGGRYSRSKWEEIEKSSNRKLGGRKYRTLKRG 270

Query: 375 SPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATS 434
           S +        L  S  +           +  S+    K       Q  +    +   TS
Sbjct: 271 SILENLNVPTRLVFSDFLLSVSKGHNDP-EISSEGFVPKLSACNANQRLIMSCESADRTS 329

Query: 435 KSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCS 494
           +  +  D   L   S+     K                       R +    +W EV+  
Sbjct: 330 RFRMKKDPS-LPGFSAYSDMDKSPIFTCEEGDKFI---------DRWITYVDFWVEVFIE 379

Query: 495 GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTS---LRYIVAF-AGCGAKDVTRRYCMK 550
            E    KWV VDA          V       + +   + Y+ A+      KDVTRRYC +
Sbjct: 380 QEE---KWVCVDAV-----HSGVVPKGVTCFEPATLMMTYVFAYDRDGYVKDVTRRYCDQ 431

Query: 551 WYRIASK-RVNSAWWD-AVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRA 608
           W     K RV  A +      P+     GA                     ED E   R 
Sbjct: 432 WSTKVRKRRVEKADFGETWFRPIF----GALHKRKRTIDDI----------EDQEFLRRH 477

Query: 609 LTEPLPTNQQAYKNHQLYVIERWLNKYQILYP--KGPILGFCSGHA-VYPRSCVQTLKTK 665
            +E +P + Q  KNH LYV+ER L K Q L P  K   LGF +G A VY R  V  LK+ 
Sbjct: 478 ESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSA 537

Query: 666 ERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 725
           E+W ++   +K  E P KV+K  ++++  +  + E  +E      + LY   Q E    P
Sbjct: 538 EQWYKKGRVIKLGEQPYKVVK--ARARTVRLPKGEAEEED-----LGLYSYEQTELYIPP 590

Query: 726 SAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRS 785
            AV+GIVP+N  G +D++    +P G VHLRLP     AK+L ID APA+ GF+F  G S
Sbjct: 591 PAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYS 650

Query: 786 TPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNC 845
            PV DGI+VC EF++ I  A+ E E+ +E +E+++   +A   W  LL  +  R+RL   
Sbjct: 651 KPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKET 710

Query: 846 YG 847
           YG
Sbjct: 711 YG 712

All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 713

>gnl\|CDD\|227822 COG5535, RAD4, DNA repair protein RAD4 [DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|192572 pfam10405, BHD_3, Rad4 beta-hairpin domain 3	Back alignment and domain information

>gnl\|CDD\|198100 smart01032, BHD_3, Rad4 beta-hairpin domain 3	Back alignment and domain information

>gnl\|CDD\|217753 pfam03835, Rad4, Rad4 transglutaminase-like domain	Back alignment and domain information

>gnl\|CDD\|214984 smart01030, BHD_1, Rad4 beta-hairpin domain 1	Back alignment and domain information

>gnl\|CDD\|220733 pfam10403, BHD_1, Rad4 beta-hairpin domain 1	Back alignment and domain information

>gnl\|CDD\|220734 pfam10404, BHD_2, Rad4 beta-hairpin domain 2	Back alignment and domain information

>gnl\|CDD\|214985 smart01031, BHD_2, Rad4 beta-hairpin domain 2	Back alignment and domain information

>gnl\|CDD\|216735 pfam01841, Transglut_core, Transglutaminase-like superfamily	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		934
TIGR00605		713	rad4 DNA repair protein rad4. This family is based	100.0
KOG2179		669	consensus Nucleotide excision repair complex XPC-H	100.0
COG5535		650	RAD4 DNA repair protein RAD4 [DNA replication, rec	100.0
PF10405		76	BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR01	99.97
PF03835		145	Rad4: Rad4 transglutaminase-like domain; InterPro:	99.87
PF10403		57	BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR01	99.76
KOG0909		500	consensus Peptide:N-glycanase [Posttranslational m	99.76
PF10404		64	BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR01	99.63
TIGR00605		713	rad4 DNA repair protein rad4. This family is based	99.15
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	96.81
KOG2179		669	consensus Nucleotide excision repair complex XPC-H	95.66
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	95.22
TIGR00598		172	rad14 DNA repair protein. This family is based on	95.02
COG1305		319	Transglutaminase-like enzymes, putative cysteine p	92.04
COG5145		292	RAD14 DNA excision repair protein [DNA replication	87.13
KOG4017		274	consensus DNA excision repair protein XPA/XPAC/RAD	86.73
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	85.76
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	85.0

>TIGR00605 rad4 DNA repair protein rad4	Back alignment and domain information

Probab=100.00  E-value=9.6e-122  Score=1078.37  Aligned_cols=542  Identities=28%  Similarity=0.435  Sum_probs=424.9

Q ss_pred             cChHHHHHHHHHHHHHHHHHhhhhhHHHhhcCc-HHHHHHhhcccccccccccCcc---------ccccccchhhHHhhh
Q 002340          170 ASAEDKELAELVHKVHLLCLLARGRLIDSVCDD-PLIQASLLSLLPSYLLKISEVS---------KLTANALSPIVSWFH  239 (934)
Q Consensus       170 ~t~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd-~~lQa~llSlLP~~~~~~~~~~---------~~~~~~L~~lv~WF~  239 (934)
                      ++.++|+.|++||++||||||.|+.+||.|||| +++|+.|..+||.++....++.         ....++|++|+.-|+
T Consensus       138 ~~~~eR~~R~~iH~~~ll~ll~h~~~RN~w~n~~~~~~~~L~~~~p~k~~~~l~p~~~~~~~~~s~s~~~~~~~l~~~~k  217 (713)
T TIGR00605       138 CSNEARKDRKYIHILYLLCLMVHLFTRNEWSLSAPLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRKPLVEKLK  217 (713)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhhhhHhhhhhhCChHHHhHHHhhhCCHHHHHhcCccccccccccchhhhhhhHHHHHhhh
Confidence            789999999999999999999999999999999 7999999999999987665433         234688889999999


Q ss_pred             cceeecccCccc---c------------chhhHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCccccc
Q 002340          240 DNFHVRSSVSTR---R------------SFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADK  304 (934)
Q Consensus       240 ~~F~v~~~~~~~---~------------~~~~~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp~sLKp~~~k  304 (934)
                      ..|+++.+-..+   .            ..+.++..+..+++||++.++||||||||++|+.+||||||||+|+..... 
T Consensus       218 k~~~it~~g~~~~~~~~~~~~~~~~~~~~~~~ef~~~a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~-  296 (713)
T TIGR00605       218 KCMETWQKGLRKTTKGLLKLLNGGRYSRSKWEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHN-  296 (713)
T ss_pred             hcchhcccccccCcccccccchhhHHhhhhHHHHHHhhhccccccchhhhHHHHHHhhhcccccccccccccCcccCCC-
Confidence            999998653100   0            003346677788999999999999999999999999999999988755310 


Q ss_pred             ccCCCCCCCCcCCCccCCCcccccCccccccCCCcccccCccccccccCCCCCCCCCCCCCCCCCccCCCCCccccccCC
Q 002340          305 NVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSG  384 (934)
Q Consensus       305 ~~~~~~~~s~~~~g~~~~~~p~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~e~~~~  384 (934)
                                          +.-+..+..  .+..                             ++..            
T Consensus       297 --------------------~~~~~~~~~--~~~~-----------------------------~~~~------------  313 (713)
T TIGR00605       297 --------------------DPEISSEGF--VPKL-----------------------------SACN------------  313 (713)
T ss_pred             --------------------Ccccccccc--cccc-----------------------------cccc------------
Confidence                                000000000  0000                             0000            


Q ss_pred             CCCCCCccccCCccccC-CCccchhhhccCCChhHHHHHHHHhhccccccccccccccccccCCCCCccccccccccccc
Q 002340          385 NLDPSSSMACSDISEAC-HPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIES  463 (934)
Q Consensus       385 ~~~~~~~~~~~~~~e~~-~~~~~~~~~rr~g~~~~~~q~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~  463 (934)
                          +...+..+ ..++ .+ ......++.+.|.|..                            +  ..+.++.+.. .
T Consensus       314 ----~~q~~~~s-~~S~~~t-sR~~l~~~l~~P~fs~----------------------------~--~~~~k~~~~~-~  356 (713)
T TIGR00605       314 ----ANQRLIMS-CESADRT-SRFRMKKDPSLPGFSA----------------------------Y--SDMDKSPIFT-C  356 (713)
T ss_pred             ----cccccccc-cCCCCcc-ccccccccCCCCCccc----------------------------c--ccCCCCCccc-h
Confidence                00000000 0000 00 0000123333332210                            0  0000100000 0


Q ss_pred             CCCCCccCCcccccCCccCCCCceeEEEEeccCCCCCceEEecccc-cccccchh-hhHhHHhccCCeeEEEEEcCCC-c
Q 002340          464 GESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQK-VEAAAAACKTSLRYIVAFAGCG-A  540 (934)
Q Consensus       464 ~~s~~~~~~~s~~~~~~~l~~P~fWvEV~~~~e~~~~kWI~VDPv~-~~vd~p~~-~Ep~~~~~~~~msYVVAfd~DG-a  540 (934)
                      .        ......+.+++||+||+|||++.   +++||||||++ ++++++.. +|+    +.++|+|||||++|| |
T Consensus       357 ~--------~~~~~~~~~~~~p~~W~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~  421 (713)
T TIGR00605       357 E--------EGDKFIDRWITYVDFWVEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYV  421 (713)
T ss_pred             h--------cccccccccCCCCeeEEEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCce
Confidence            0        01112456788999999999986   49999999999 88988764 443    569999999999997 9


Q ss_pred             ccchhhhhhhHHH-hhcccCCHHHHHHH-HhhhhhcccCcCCCccccccccCcccccCCchHHHHHHHHHccCCCCcChh
Q 002340          541 KDVTRRYCMKWYR-IASKRVNSAWWDAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQ  618 (934)
Q Consensus       541 kDVTrRYa~~w~k-~~rkRv~~~Ww~~~-L~~~~~~~s~~~~~~~i~~~~~~~~~~~rd~~Ed~EL~~~~~~epmPtsi~  618 (934)
                      +|||+||+++|++ +++.||+..||..+ |++|.+..             .++... +|..||.||.+++++||||+|++
T Consensus       422 kDVT~RY~~~~~~k~r~~Rv~~~w~~~~w~~~~~~~~-------------~~r~~~-~d~~Ed~el~~~~~~e~~P~si~  487 (713)
T TIGR00605       422 KDVTRRYCDQWSTKVRKRRVEKADFGETWFRPIFGAL-------------HKRKRT-IDDIEDQEFLRRHESEGIPKSIQ  487 (713)
T ss_pred             eechhhHhhhhhhhhheeeecccchHHHHHHHHhhhh-------------ccCccc-hhhhhhhHhhhhhcccCCChhHH
Confidence            9999999999996 67789998888887 77765321             011222 78899999999999999999999


Q ss_pred             hhccCCceeeccccccccccCCC--CCcceeeccee-eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCC
Q 002340          619 AYKNHQLYVIERWLNKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQ  695 (934)
Q Consensus       619 ~fKnHP~YvLerhL~k~EvI~P~--a~v~G~~~GEp-VY~RsdV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~  695 (934)
                      +|||||+|||||||++||+|||+  ++++|+++|++ ||+|+||++|||+++||++||+||+||+|+|+|+.+++..+. 
T Consensus       488 ~fKnHP~YvLer~L~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~r~r~~~~-  566 (713)
T TIGR00605       488 DLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKARARTVRL-  566 (713)
T ss_pred             HhhcCceEEehhhcccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEeccccccccc-
Confidence            99999999999999999999994  46789999998 999999999999999999999999999999999987432211 


Q ss_pred             CCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeece
Q 002340          696 DFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAM  775 (934)
Q Consensus       696 ~~~~~~~~~~~~~~~~~LY~~wQTe~y~PPpvvdG~VPkN~yGNVdlf~psMlP~G~VHL~l~~i~rvAkkLgIDyApAV  775 (934)
                        ..++.    ...+++|||+||||+|+|||++||+||||+|||||||+|+|||+|||||++++|.+||++||||||+||
T Consensus       567 --~~~~~----~~~~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP~G~vhi~~~~~~rvak~LgIDyA~AV  640 (713)
T TIGR00605       567 --PKGEA----EEEDLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAV  640 (713)
T ss_pred             --ccccc----cccccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCCCCcEEecCccHHHHHHHhCCCeeeee
Confidence              11111    114789999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eceeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 002340          776 VGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN  848 (934)
Q Consensus       776 tGFeFk~G~a~PvidGIVV~eE~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~Wk~Llk~LrIreRL~~~Yg~  848 (934)
                      |||+|++|+++|||+|||||+||+++|++||.++++.++++++++++++||++|++||++|||++||+.+||.
T Consensus       641 tGFeF~~g~~~Pv~~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~Wk~ll~~LrIr~Rl~~~Yg~  713 (713)
T TIGR00605       641 TGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKETYGK  713 (713)
T ss_pred             eceeecCCceeEeeceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999995

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]	Back alignment and domain information

>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]	Back alignment and domain information

>PF10405 BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR018328 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome	Back alignment and domain information

>PF03835 Rad4: Rad4 transglutaminase-like domain; InterPro: IPR018325 RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation	Back alignment and domain information

>PF10403 BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR018326 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome	Back alignment and domain information

>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF10404 BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR018327 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome	Back alignment and domain information

>TIGR00605 rad4 DNA repair protein rad4	Back alignment and domain information

>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i	Back alignment and domain information

>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]	Back alignment and domain information

>smart00460 TGc Transglutaminase/protease-like homologues	Back alignment and domain information

>TIGR00598 rad14 DNA repair protein	Back alignment and domain information

>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]	Back alignment and domain information

>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG4017 consensus DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair]	Back alignment and domain information

>smart00460 TGc Transglutaminase/protease-like homologues	Back alignment and domain information

>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		934
2qsh_A		538	Crystal Structure Of Rad4-Rad23 Bound To A Mismatch		6e-18
2qsf_A		533	Crystal Structure Of The Rad4-Rad23 Complex Length		7e-18

>pdb|2QSH|A Chain A, Crystal Structure Of Rad4-Rad23 Bound To A Mismatch Dna Length = 538

Back alignment and structure

Iteration: 1

Score = 89.7 bits (221), Expect = 6e-18, Method: Compositional matrix adjust. Identities = 85/344 (24%), Positives = 140/344 (40%), Gaps = 54/344 (15%) Query: 482 VGAPLYWAEVYCSGENLTGKWVHVDAANAI----IDGEQKVEAAAAAC--KTSLRYIVAF 535 V P++W EV+ + + KW+ VD N + K+ AC + LRY++A+ Sbjct: 216 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 272 Query: 536 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 587 G +DVTRRY +W RI W+ V+ L + D Sbjct: 273 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 326 Query: 588 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 647 ED R +E +P + Q KNH YV+E+ + + QI+ P G+ Sbjct: 327 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 374 Query: 648 CSGHA-------VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPE 700 H VY + + LK+ +W +K G E E Sbjct: 375 LKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAE 431 Query: 701 DYDE-VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPR 759 + DE + + + ELY + PL ++ +G + +N G ++V++ +P + P Sbjct: 432 EEDERLYSFEDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPV 484 Query: 760 VYSVAKRLEIDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 802 A+ L ++ APA+ F+F G + PV GIVV ++ I Sbjct: 485 AIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 528

PyMOL of 2qsh

>pdb|2QSF|A Chain A, Crystal Structure Of The Rad4-Rad23 Complex Length = 533

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		934
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	6e-78
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	6e-16
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	1e-21
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	5e-16
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>2qsf_A RAD4, DNA repair protein RAD4; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_A* 2qsh_A* Length = 533	Back alignment and structure

 Score =  262 bits (671), Expect = 6e-78
 Identities = 84/353 (23%), Positives = 134/353 (37%), Gaps = 52/353 (14%)

Query: 480 RKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEA------AAAACKTSLRYIV 533
             V  P++W EV+        KW+ VD  N     + ++ +       A   +  LRY++
Sbjct: 209 DMVKYPIFWCEVWDKFSK---KWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVI 265

Query: 534 AFAGCG-AKDVTRRYCMKW------YRIASKRVNSAWWDAVLAPLRELESGATGDLNVES 586
           A+      +DVTRRY           RI        W+  V+  L               
Sbjct: 266 AYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHH------------- 312

Query: 587 SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILG 646
                     +  ED     R  +E +P + Q  KNH  YV+E+ + + QI+ P     G
Sbjct: 313 ----RKRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECG 368

Query: 647 FCSGHA-------VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEP 699
           +   H        VY +  +  LK+  +W      +K      KVIK +    KG+  E 
Sbjct: 369 YLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEE 428

Query: 700 EDYDEVDARGNIELYGKWQLEPLRLPSA-VNGIVPRNERGQVDVWSEKCLPPGTVHLRLP 758
           +            LY     E    P A  +G + +N  G ++V++   +P     +  P
Sbjct: 429 D----------ERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENP 478

Query: 759 RVYSVAKRLEIDSAPAMVGFEFRNGRS-TPVFDGIVVCAEFKDTILEAYAEEE 810
                A+ L ++ APA+  F+F  G +  PV  GIVV    ++ I  A    E
Sbjct: 479 VAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIE 531

PyMOL of 2qsf

>2qsf_A RAD4, DNA repair protein RAD4; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_A* 2qsh_A* Length = 533	Back alignment and structure

>2f4m_A Peptide N-glycanase; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: d.3.1.4 PDB: 2f4o_A* Length = 295	Back alignment and structure

>1x3z_A Peptide: N-glycanase; hydrolase-hydrolase inhibitor complex; HET: SUC; 2.80A {Saccharomyces cerevisiae} SCOP: d.3.1.4 PDB: 1x3w_A* 3esw_A* Length = 335	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		934
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	100.0
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	99.93
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	99.85
3isr_A		293	Transglutaminase-like enzymes, putative cysteine;	95.93
3kd4_A		506	Putative protease; structural genomics, joint cent	93.85
1ex0_A		731	Coagulation factor XIII A chain; transglutaminase,	82.76
1g0d_A		695	Protein-glutamine gamma-glutamyltransferase; tissu	82.12
1vjj_A		692	Protein-glutamine glutamyltransferase E; transglut	80.78
2q3z_A		687	Transglutaminase 2; transglutaminase 2, tissue tra	80.68

>2qsf_A RAD4, DNA repair protein RAD4; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_A* 2qsh_A*	Back alignment and structure

Probab=100.00  E-value=4.1e-121  Score=1054.36  Aligned_cols=467  Identities=22%  Similarity=0.372  Sum_probs=372.0

Q ss_pred             CCCceEEEEecCCc--ccc--ccccccChHHHHHHHHHHHHHHHHHhhhhhHHHhhcCcHHHHHHhhcccccccccccCc
Q 002340          148 DIKGVTIEFDAADS--VTK--KPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEV  223 (934)
Q Consensus       148 ~~~~veIeie~~~~--~kk--k~~RR~t~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd~~lQa~llSlLP~~~~~~~~~  223 (934)
                      +.++|+|||+....  .++  ++.+.+|+.||++|+++||+||||||+|+++||.||||++||++|+|+||.++....++
T Consensus         7 ~~~~l~itl~~~~~~~~~~~~~~kk~~S~~ER~~R~~~Hk~hvl~LL~H~~~RN~W~nD~~lq~~L~sllP~~i~~~l~p   86 (533)
T 2qsf_A            7 GVEDISVEIKPSSKRNSDARRTSRNVCSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLHP   86 (533)
T ss_dssp             --------------------CCCTTBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHGGGSCHHHHHHTSC
T ss_pred             CCCCeEEEecCCccccchhhhccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhhCc
Confidence            56779999987632  221  12234899999999999999999999999999999999999999999999998654432


Q ss_pred             cc----------cccccchhhHHhhhcceeecccC---ccccc----------------h--hhHHHHHHHHhcCCHHHH
Q 002340          224 SK----------LTANALSPIVSWFHDNFHVRSSV---STRRS----------------F--HSDLAHALESREGTPEEI  272 (934)
Q Consensus       224 ~~----------~~~~~L~~lv~WF~~~F~v~~~~---~~~~~----------------~--~~~L~~~l~~~~Gs~de~  272 (934)
                      ..          ...++|+.|+.||+.+|.|+++.   +....                +  ..+|..++++++|++|++
T Consensus        87 ~~~~~~~~~~~~~~~~~Lk~L~~ww~~~F~it~p~~~~g~~~~~w~e~~~~~~~~~~f~~~~~~~f~~~~~~~~Gs~d~~  166 (533)
T 2qsf_A           87 QKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDIS  166 (533)
T ss_dssp             CCCSSCTHHHHHHHHHHHHHHHHHHHHHCCEECCCSSCTTSCCCHHHHHHTTTTCCCEECCCHHHHHHHHHHTEECHHHH
T ss_pred             CCCccccccchHHHHHHHHHHHHHHHhhEEEcCCccCCCccccCccccchhhccccccccccHHHHHHHHHhcCCChhHH
Confidence            11          12478999999999999998752   11100                1  246889999999999999


Q ss_pred             HHHHHHHHHhcCCceEEEEeeccccCCcccccccCCCCCCCCcCCCccCCCcccccCccccccCCCcccccCcccccccc
Q 002340          273 AALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCET  352 (934)
Q Consensus       273 aqLF~aLLRaLgl~aRLV~sLqp~sLKp~~~k~~~~~~~~s~~~~g~~~~~~p~~~k~~~~~~~~~~~~~~~~~~~~~~~  352 (934)
                      ||||||||||||+.||||+||||+++....                      +        ..++               
T Consensus       167 AqlF~aLlRalG~~aRlV~SLqP~~f~~~k----------------------~--------~~~~---------------  201 (533)
T 2qsf_A          167 VQGFVAMLRACNVNARLIMSCQPPDFTNMK----------------------I--------DTSL---------------  201 (533)
T ss_dssp             HHHHHHHHHHTTCCEEEEEEECCCCTTCCB----------------------S--------CCCC---------------
T ss_pred             HHHHHHHHHHCCCceEEEeccccccccccc----------------------c--------ccCc---------------
Confidence            999999999999999999999988654310                      0        0000               


Q ss_pred             CCCCCCCCCCCCCCCCCccCCCCCccccccCCCCCCCCccccCCccccCCCccchhhhccCCChhHHHHHHHHhhccccc
Q 002340          353 SSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVA  432 (934)
Q Consensus       353 ~~~~~~~~~~~~~~~~~~~s~~~~~s~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~rr~g~~~~~~q~~~a~~a~~~~  432 (934)
                                                                        +       +  ....               
T Consensus       202 --------------------------------------------------~-------k--~~~~---------------  207 (533)
T 2qsf_A          202 --------------------------------------------------N-------G--NNAY---------------  207 (533)
T ss_dssp             --------------------------------------------------C------------CH---------------
T ss_pred             --------------------------------------------------c-------c--CCcc---------------
Confidence                                                              0       0  0000               


Q ss_pred             cccccccccccccCCCCCcccccccccccccCCCCCccCCcccccCCccCCCCceeEEEEeccCCCCCceEEeccccc-c
Q 002340          433 TSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANA-I  511 (934)
Q Consensus       433 ~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~s~~~~~~~s~~~~~~~l~~P~fWvEV~~~~e~~~~kWI~VDPv~~-~  511 (934)
                                                                    ..++.+|+||+|||++.   +++||||||+++ +
T Consensus       208 ----------------------------------------------~~~~~~P~~W~EV~s~~---~~rWi~VDp~~~~~  238 (533)
T 2qsf_A          208 ----------------------------------------------KDMVKYPIFWCEVWDKF---SKKWITVDPVNLKT  238 (533)
T ss_dssp             ----------------------------------------------HHHTTSCSEEEEEEETT---TTEEEEEESSSSCE
T ss_pred             ----------------------------------------------ccccCCCeEEEEEEEcC---CCeEEEEecccccc
Confidence                                                          01224899999999975   599999999975 4


Q ss_pred             c---ccchhhhHhH--HhccCCeeEEEEEcCCC-cccchhhhhhhHHH-hhcccCC-----HHHHHHHHhhhhhcccCcC
Q 002340          512 I---DGEQKVEAAA--AACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-IASKRVN-----SAWWDAVLAPLRELESGAT  579 (934)
Q Consensus       512 v---d~p~~~Ep~~--~~~~~~msYVVAfd~DG-akDVTrRYa~~w~k-~~rkRv~-----~~Ww~~~L~~~~~~~s~~~  579 (934)
                      +   +.+..|||..  .++.++|+|||||++|| |+|||+||+.+|.. +++.|+.     ++||..+|+.|++      
T Consensus       239 id~~~~~~~~Ep~~~~~~~~~~m~YViAf~~d~~~kDVT~RY~~~~~~k~rr~Ri~~~~~~~~W~~~~L~~~~~------  312 (533)
T 2qsf_A          239 IEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHH------  312 (533)
T ss_dssp             EECCSSCCTTSCCSTTTTSSCCCCEEEEECTTCCEEECHHHHCTTCCCCCGGGSGGGSHHHHHHHHHHHHHHCC------
T ss_pred             ccccccccccccccccccccCceeEEEEEcCCCceEecchhhhhchhhhhheeeecCCcchHHHHHHHHHHHhc------
Confidence            4   4577899843  25789999999999987 99999999998874 4556764     7899999999974      


Q ss_pred             CCccccccccCcccccCCchHHHHHHHHHccCCCCcChhhhccCCceeeccccccccccCCCCCcceeecc-------ee
Q 002340          580 GDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG-------HA  652 (934)
Q Consensus       580 ~~~~i~~~~~~~~~~~rd~~Ed~EL~~~~~~epmPtsi~~fKnHP~YvLerhL~k~EvI~P~a~v~G~~~G-------Ep  652 (934)
                                 +....+|..||+||+.+.++||||+|+++|||||+|||||||++||+|||+++++|+|+|       ||
T Consensus       313 -----------~~~~~~d~~Ed~el~~~~~~e~~P~s~~~fK~HP~yvLer~L~k~E~i~P~a~~~g~~~~~~k~~~~E~  381 (533)
T 2qsf_A          313 -----------RKRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLK  381 (533)
T ss_dssp             -----------SCCCHHHHHHHHHHHHHHHHSCCCSSTGGGTTCSSEEEGGGSCTTEEECTTCCCSEEEECCSTTCCEEE
T ss_pred             -----------CCccccchhHHHHHHHHHhcCCCCccHHHHcCCcHhhhhhhhccceeeCCCCceeeEEecCcCCCcccc
Confidence                       234567889999999999999999999999999999999999999999999999999987       99


Q ss_pred             eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCC-CCCC
Q 002340          653 VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSA-VNGI  731 (934)
Q Consensus       653 VY~RsdV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~~~~~~~~~~~~~~~~~~LY~~wQTe~y~PPpv-vdG~  731 (934)
                      ||+|+||++|||+++|+++||+||+||+|+|+|+.++.+..    .+++      ..+++|||+||||+|+|||+ +||+
T Consensus       382 VY~R~~V~~l~S~e~W~~~gR~vk~ge~P~K~v~~r~~~~~----~~~~------~~~~~Ly~~~QTe~y~Pp~~~~dG~  451 (533)
T 2qsf_A          382 VYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPK----GEAE------EEDERLYSFEDTELYIPPLASASGE  451 (533)
T ss_dssp             EEEGGGEEECBCHHHHHTTTEEECSSCCCSEEECC----------------------CEEEBCGGGEEECCCCCCCTTCC
T ss_pred             eeehhhhheeecHHHHHHcCCccCCCCeeeeEEecccCCcc----cccc------cccccccCHHhCccccCCCCccCCc
Confidence            99999999999999999999999999999999998754321    1111      25689999999999999999 9999


Q ss_pred             ccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeeceeceeecCC-eeeeeEceEEEccccHHHHHHHHHHH
Q 002340          732 VPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNG-RSTPVFDGIVVCAEFKDTILEAYAEE  809 (934)
Q Consensus       732 VPkN~yGNVdlf~psMlP~G~VHL~l~~i~rvAkkLgIDyApAVtGFeFk~G-~a~PvidGIVV~eE~~e~l~~a~~e~  809 (934)
                      ||||+|||||||+|+|||+|||||++++++++|++||||||+|||||+|++| +++|||+|||||+||+++|++||++.
T Consensus       452 VPkN~yGNvd~~~p~m~P~G~vhi~~~~~~~~ar~L~Idya~Av~GFef~~g~~~~Pv~~GiVV~~e~~~~l~~a~~~~  530 (533)
T 2qsf_A          452 ITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGI  530 (533)
T ss_dssp             CCCCTTSCEECSSGGGSCTTEEEEECTTHHHHHHHTTCCCEEEEEEECC------CEEEEEEEEETTSHHHHHHHHHTG
T ss_pred             ccccCCCCEEeccCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeeCCCCcceEEeCeEEEehHHHHHHHHHHHhh
Confidence            9999999999999999999999999999999999999999999999999975 57999999999999999999999754

PyMOL of 2qsf

>1x3z_A Peptide: N-glycanase; hydrolase-hydrolase inhibitor complex; HET: SUC; 2.80A {Saccharomyces cerevisiae} SCOP: d.3.1.4 PDB: 1x3w_A* 3esw_A*	Back alignment and structure

>2f4m_A Peptide N-glycanase; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: d.3.1.4 PDB: 2f4o_A*	Back alignment and structure

>3isr_A Transglutaminase-like enzymes, putative cysteine; protease, hutchinsoni MCSG, structural genomics; 1.90A {Cytophaga hutchinsonii}	Back alignment and structure

>3kd4_A Putative protease; structural genomics, joint center for STR genomics, JCSG, protein structure initiative, PSI-2, hydrol; HET: MSE; 2.00A {Parabacteroides distasonis atcc 8503}	Back alignment and structure

>1ex0_A Coagulation factor XIII A chain; transglutaminase, blood coagulation, mutant, W279F, oxyanion, transferase; 2.00A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1evu_A 1fie_A 1f13_A 1ggt_A 1ggu_A 1ggy_A 1qrk_A	Back alignment and structure

>1g0d_A Protein-glutamine gamma-glutamyltransferase; tissue transglutaminase,acyltransferase; 2.50A {Pagrus major} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4	Back alignment and structure

>1vjj_A Protein-glutamine glutamyltransferase E; transglutaminase 3, X-RAY crystallography, metalloenzyme, calcium ION; HET: GDP; 1.90A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1sgx_A* 1l9m_A 1l9n_A* 1nud_A 1nuf_A 1nug_A 1rle_A*	Back alignment and structure

>2q3z_A Transglutaminase 2; transglutaminase 2, tissue transglutaminase, TG2, transferas; 2.00A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1kv3_A 3ly6_A*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		934
d1x3za1		320	d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Bak	6e-17
d2f4ma1		287	d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {M	4e-15

>d1x3za1 d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]} Length = 320	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Transglutaminase core
domain: Peptide:N-glycanase 1, PNG1
species: Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 80.7 bits (199), Expect = 6e-17
 Identities = 23/123 (18%), Positives = 43/123 (34%), Gaps = 15/123 (12%)

Query: 484 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDV 543
               W E + +      +WVHVD+     D               + Y +AF   G  DV
Sbjct: 209 EDHVWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSIN---WNKKMSYCIAFGKDGVVDV 262

Query: 544 TRRYCMKWYRIASKRVNSAWWDAVLAPL-RELESGATGDLNVESSAKDSFVADRNSLEDM 602
           ++RY ++   +   ++       +   + + L      D       +   +A R+  E +
Sbjct: 263 SKRYILQN-ELPRDQIKEEDLKFLCQFITKRLRYSLNDD-------EIYQLACRDEQEQI 314

Query: 603 ELE 605
           EL 
Sbjct: 315 ELI 317

PyMOL of d1x3za1

>d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 287	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		934
d1x3za1		320	Peptide:N-glycanase 1, PNG1 {Baker's yeast(Sacchar	99.87
d2f4ma1		287	Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus)	99.85

>d1x3za1 d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Transglutaminase core
domain: Peptide:N-glycanase 1, PNG1
species: Baker's yeast(Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.87  E-value=9.8e-23  Score=218.14  Aligned_cols=81  Identities=20%  Similarity=0.393  Sum_probs=73.9

Q ss_pred             ceeEEEEeccCCCCCceEEecccccccccchhhhHhHHhccCCeeEEEEEcCCCcccchhhhhhhHHHhhcccCCHHHHH
Q 002340          486 LYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWD  565 (934)
Q Consensus       486 ~fWvEV~~~~e~~~~kWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~DGakDVTrRYa~~w~k~~rkRv~~~Ww~  565 (934)
                      |+|+|||++.+   ++|||||||.+++|+|..||..   |.++|+|||||+.||++|||+||+.+| .+++.|++++||.
T Consensus       211 hvW~EVys~~~---kRWIhvDpce~~id~P~lye~g---w~k~msYVIAf~~dgv~DVT~RY~~k~-~~rR~rv~E~wl~  283 (320)
T d1x3za1         211 HVWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSIN---WNKKMSYCIAFGKDGVVDVSKRYILQN-ELPRDQIKEEDLK  283 (320)
T ss_dssp             EEEEEEEETTT---TEEEEEETTTTEESCTHHHHTT---SCCCBCCEEEEETTEEEECHHHHCSSS-BCCCCSSCHHHHH
T ss_pred             ceEEEEeeccc---CeEEEEcCCCCccCCcceeccC---CCCceEEEEEecCCcceechhhhcccc-cCccccCCHHHHH
Confidence            58999999864   8999999999999999999865   889999999999999999999999885 4678899999999


Q ss_pred             HHHhhhhh
Q 002340          566 AVLAPLRE  573 (934)
Q Consensus       566 ~~L~~~~~  573 (934)
                      .+|..++.
T Consensus       284 ~~L~~l~~  291 (320)
T d1x3za1         284 FLCQFITK  291 (320)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998875

PyMOL of d1x3za1

>d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure