Citrus Sinensis ID: 003292

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---

MGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

ccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHccccHHHcccccccccHHHHHcHHHHHHcccccccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEEEEEEcccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEEEcccccccccccccHHHHHcccccEEEEEEcccccccHHHHHHHHHHHHcccccHHHHHHHHHcHHHHHcccccccccccccccccHHHcccHHHHHHHHHHHccccccccHHHHHccccHHHHHHHcccccccccccccEEEccEEEEEccccEEEccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEEEccccHHHHHHHccccEEcccccEEEcccEEEEEEcEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcc

cccccccccccccHcHccccccccccccHHcccccccccHccccccccccEEEEEEcccHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcEEEccccccccccHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccEEEEEEccccccccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccEEEEEEEcccHHccccEEEEcccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHccEEccccccccEEcccEEcccccEEEEccHHHHHHHHcEEccccccEEEEccccccccccHccHHccccccccccccEEEEcccccccccccccccccccccccEEEEcccccccccEEEccHHHHHHHHHHccccccEEEEEEcccccccEEEcEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccEEEEcccccEEEEEEcc

mgntlreldegrlqdnvldggeemydsdwedgsipvacskenhpesdikgvtiefdaadsvtkkpvrrasAEDKELAELVHKVHLLCLLARgrlidsvcddplIQASLLSLLPSYLLKISEVSKLTANALSPivswfhdnfhvrssvstrrSFHSDLAHAlesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgggifnaptlmvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskkspvscelssgnldpsssmacsdiseachpkeksqALKRKGDLEFEMQLEMALSATnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkvgaplYWAEVYcsgenltgkwvhvdaanaiIDGEQKVEAAAAACKTSLRYIVAFAgcgakdvtRRYCMKWYRIASKRVNSAWWDAVLAPlrelesgatgdlnvessakdsfvadrnsleDMELEtralteplptnqqaykNHQLYVIERWLNKYQilypkgpilgfcsghavyprscvQTLKTKERWLREALQVKAnevpvkviknsskskkgqdfepedydevdargnielygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprvYSVAKRleidsapamvgfefrngrstpvfdgIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRlnncygnnstsqsssnfqnvkktnsnvgvdssqndwqspnqvdrgdtklhapspfqseehehvyliedqsfdeensvttkrchcgftiqveel

mgntlreldegrlqdnVLDGGEEMYDSDWEDGSIPVACSKenhpesdikgvtiefdaadsvtkkpVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHalesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgGGIFNAPTLMVAKPEEVLASpvksfscdkkenvcetsskgspeckysspksnntqskksPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSAtnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFagcgakdvTRRYCMKWYRIASKRVNSAWWDAVLAPLRELEsgatgdlnvessakdsfvadrNSLEDMELETralteplptnqqayKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREAlqvkanevpvkviknsskskkgqdfepedydevdARGNIELygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKrreaqatsrwYQLLSSIVTRQRLNNCYGNnstsqsssnfqnVKKTNsnvgvdssqndwQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

MGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQAsllsllpsyllKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEvpvkviknsskskkGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYaeeeekreaeekkrreaQATSRWYQLLSSIVTRQRLNNCYGnnstsqsssnfqnVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

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

****************************W*D*********************************************AELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFH*************DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDV****************************************************************************************************************************************************************************************RKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATG***VESSAKDSFVADRNSLEDMELETRAL*EPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPV**************************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKR*********AQATSRWYQLLSSIVTRQRLN*****************************************************************DQSFDEENSVTTKRCHCGFTIQVEEL

MGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAA**************DKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVR***********DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK**************RVGGGIFNAPTLMVAKPEEVLASPVKSFSCD**************************************************SDISEA**********KRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKN**************YDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAE*****************TSRWYQLLSSIVTRQRLNNCYGN***********NVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

***********************MYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK*************************************************************************************************************************************************************************************KVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELE****GD*NVE*S*KDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNS********************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYG***********************************************************IEDQSFDEENSVTTKRCHCGFTIQVEEL

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MGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

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		833	2.2.26 [Sep-21-2011]
P51612		930	DNA repair protein comple	yes	no	0.756	0.677	0.321	2e-73
Q01831		940	DNA repair protein comple	yes	no	0.751	0.665	0.311	1e-66
Q24595		1293	DNA repair protein comple	yes	no	0.403	0.259	0.344	8e-54
Q10445		638	DNA repair protein rhp41	yes	no	0.388	0.507	0.295	7e-33
P87235		686	DNA repair protein rhp42	no	no	0.408	0.495	0.279	6e-25
P14736		754	DNA repair protein RAD4 O	yes	no	0.426	0.470	0.258	2e-24
Q7F0R1		447	Peptide-N(4)-(N-acetyl-be	no	no	0.079	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 =  277 bits (709), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 230/716 (32%), Positives = 335/716 (46%), Gaps = 86/716 (12%)

Query: 73  DKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSP 132
           +KE+ E +HKVHLLCLLA G   +S+C  P + A  LS++P    K+  +    A  LS 
Sbjct: 194 NKEVQENMHKVHLLCLLASGFYRNSICRQPDLLAIGLSIIPIRFTKVP-LQDRDAYYLSN 252

Query: 133 IVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGT-----PEEIAALSVALFRALKLTTR 187
           +V WF   F V + +S   S   DL   LE R         EE+  + + + RAL+L TR
Sbjct: 253 LVKWFIGTFTVNADLSA--SEQDDLQTTLERRIAIYSARDNEELVHIFLLILRALQLLTR 310

Query: 188 FVSILDVASLKPEADKNVSSNQDSSRVGGG-----------IFNAPTL-MVAKPEEVLAS 235
            V  L    LK    K   S++++S  G G             N PT     K EE L+ 
Sbjct: 311 LVLSLQPIPLKSAVTKGRKSSKETSVEGPGGSSELSSNSPESHNKPTTSRRIKEEETLSE 370

Query: 236 PVKSFSCDKKENVCETSSKG--SPECKYSSPKSNNTQ----SKKSPVSCELS-------- 281
                +   K       S+    P C          Q    ++K  V+ ++S        
Sbjct: 371 GRGKATARGKRGTGTAGSRQRRKPSCSEGEEAEQKVQGRPHARKRRVAAKVSYKEESESD 430

Query: 282 ----SGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNI 337
                 + +PSS        E C P  + Q  KR        Q   A S +   T + + 
Sbjct: 431 GAGSGSDFEPSSGEGQHSSDEDCEPGPRKQ--KRAS----APQRTKAGSKSASKTQRGSQ 484

Query: 338 CSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENL 397
           C +       SS+    KR KK+ SG         +  +  RK      W EVYC  +  
Sbjct: 485 C-EPSSFPEASSSSSGCKRGKKVSSG---------AEEMADRKPAGVDQWLEVYCEPQ-- 532

Query: 398 TGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIASK 456
             KWV VD  + ++   Q V     A K  + Y+V     G  +DVT+RY   W     K
Sbjct: 533 -AKWVCVDCVHGVVG--QPVACYKYATK-PMTYVVGIDSDGWVRDVTQRYDPAWMTATRK 588

Query: 457 -RVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTN 515
            RV++ WW   L P R                  S + +R   ED E + + L +PLPT+
Sbjct: 589 CRVDAEWWAETLRPYR------------------SLLTEREKKEDQEFQAKHLDQPLPTS 630

Query: 516 QQAYKNHQLYVIERWLNKYQILYPK-GPILGFCSGHAVYPRSCVQTLKTKERWLREALQV 574
              YKNH LY ++R L K+Q +YP+   +LG+C G AVY R CV TL +++ WL++A  V
Sbjct: 631 ISTYKNHPLYALKRHLLKFQAIYPETAAVLGYCRGEAVYSRDCVHTLHSRDTWLKQARVV 690

Query: 575 KANEVPVKVIKN-SSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPR 633
           +  EVP K++K  S++++K +  EP+ +D  D    + LYG WQ E  + P AV+G VPR
Sbjct: 691 RLGEVPYKMVKGFSNRARKARLSEPQLHDHND----LGLYGHWQTEEYQPPIAVDGKVPR 746

Query: 634 NERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVV 693
           NE G V ++    +P G V + LP +  VA++L ID   A+ GF+F  G   PV DG +V
Sbjct: 747 NEFGNVYLFLPSMMPVGCVQMTLPNLNRVARKLGIDCVQAITGFDFHGGYCHPVTDGYIV 806

Query: 694 CAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNS 749
           C EF+D +L A+  E+   E +EK+++E +A   W  L+  ++ R+RL   YG  S
Sbjct: 807 CEEFRDVLLAAWENEQAIIEKKEKEKKEKRALGNWKLLVRGLLIRERLKLRYGAKS 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		833
224079463		868	predicted protein [Populus trichocarpa]	0.960	0.921	0.651	0.0
225453199		1103	PREDICTED: DNA repair protein complement	0.986	0.745	0.659	0.0
356552017		926	PREDICTED: uncharacterized protein LOC10	0.947	0.852	0.616	0.0
255582247		683	DNA repair protein xp-C / rad4, putative	0.783	0.956	0.679	0.0
449445198		923	PREDICTED: DNA repair protein complement	0.967	0.873	0.590	0.0
449479948		923	PREDICTED: DNA repair protein complement	0.967	0.873	0.589	0.0
297807689		868	DNA repair protein Rad4 family [Arabidop	0.936	0.898	0.548	0.0
22326854		865	xeroderma pigmentosum group C-complement	0.936	0.901	0.552	0.0
357492015		1052	DNA repair protein complementing XP-C ce	0.786	0.622	0.623	0.0
357141401		889	PREDICTED: DNA repair protein complement	0.927	0.869	0.516	0.0

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

 Score = 1039 bits (2687), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 551/846 (65%), Positives = 639/846 (75%), Gaps = 46/846 (5%)

Query: 4   TLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEF-DAADSVT 62
           T  +LD    Q    +  +EM D DWEDGS  +    +NHP   I+ VTIEF ++ DS  
Sbjct: 53  TWNDLDARGFQTTFQESDQEMDDIDWEDGSSSILGHVKNHPGDGIREVTIEFSESPDSAK 112

Query: 63  KKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEV 122
           +KP+RRA+AE+K LAELVHKVHLLCLLARGR+ID  CDDPLIQASLLS+LP++L      
Sbjct: 113 RKPIRRATAEEKGLAELVHKVHLLCLLARGRIIDHACDDPLIQASLLSILPAHLSNTLGD 172

Query: 123 SKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRAL 182
            KL A ALSP+  WFH+NFHV SSVS +RSFHS L+ ALE+REGT EE+AALSVALFRAL
Sbjct: 173 PKLHAKALSPLAHWFHNNFHVASSVSEKRSFHSALSCALETREGTLEELAALSVALFRAL 232

Query: 183 KLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSC 242
           KLTTRFVSILDVAS+KP+ADK  S +Q +S++  GIFN  TLMV +P+EV   P KS SC
Sbjct: 233 KLTTRFVSILDVASIKPDADKYESLSQGTSKMHRGIFNTSTLMVDRPKEVFIPP-KSLSC 291

Query: 243 DKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHP 302
           ++K+N                      QS  SP + EL    +D     A ++ SE C  
Sbjct: 292 NEKKN--------------------KIQSNDSPPAVELKDKMVDTFPCEAQNNTSEECVT 331

Query: 303 KEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIES 362
           K KSQ  KRKGDLEFEMQL+MA+SAT VAT +SN   DVK+ +++S    P KR++KI +
Sbjct: 332 K-KSQGSKRKGDLEFEMQLQMAMSATAVAT-QSNKELDVKESSNSSDVSSPFKRIRKIAN 389

Query: 363 GESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAA 422
            ESS+   GISTA+GSRK+G+PLYWAEVYCSGENLTGKWVHVDA + I+DGEQKVEAAA 
Sbjct: 390 EESSSQ--GISTALGSRKIGSPLYWAEVYCSGENLTGKWVHVDAVHDIVDGEQKVEAAAD 447

Query: 423 ACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDL- 481
           ACKTSLRY+VAFAG GAKDVTRRYCMKWY+IAS+RVNS WWDAVLAPLRELESGATG + 
Sbjct: 448 ACKTSLRYVVAFAGLGAKDVTRRYCMKWYKIASQRVNSLWWDAVLAPLRELESGATGGMA 507

Query: 482 --------------NVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVI 527
                         NV +S  +SF A RN++EDMEL+TRALTEPLPTNQQAYKNH LY I
Sbjct: 508 HLEKPHADASNEHENVIASGLNSFAATRNTIEDMELQTRALTEPLPTNQQAYKNHLLYAI 567

Query: 528 ERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNS 587
           E+WL K QIL+PKGPILGFCSGH VYPR+CVQTL+TKERWLRE LQVK  E+P KV+K S
Sbjct: 568 EKWLTKCQILHPKGPILGFCSGHPVYPRACVQTLRTKERWLREGLQVKVKELPAKVVKQS 627

Query: 588 SKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCL 647
            K KK Q  E +DY E D+ G +ELYG WQLEPL+LP AVNGIVP+NERGQVDVWSEKCL
Sbjct: 628 GKLKKVQFSEDDDYGETDS-GVVELYGMWQLEPLQLPHAVNGIVPKNERGQVDVWSEKCL 686

Query: 648 PPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAE 707
           PPGTVHLRLPRV+ VAKRLEID APAMVGFEFRNGRS PVFDGIVVC EFKD ILEAYAE
Sbjct: 687 PPGTVHLRLPRVFYVAKRLEIDYAPAMVGFEFRNGRSVPVFDGIVVCNEFKDAILEAYAE 746

Query: 708 EEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNV 767
           EEE+R+AEEKKR EAQA SRWYQLLSSI+TRQRLNN YGN    Q  SN QN      +V
Sbjct: 747 EEERRDAEEKKRNEAQAISRWYQLLSSIITRQRLNNSYGNGLLPQMPSNVQNT-NNQPDV 805

Query: 768 GVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFT 827
            V S+Q      +Q D  D KL+APS   +++HEHV+L+EDQSFDEE S  TKRCHCGF+
Sbjct: 806 HVGSTQ---PPGHQKDAKDRKLNAPSMTLTDDHEHVFLVEDQSFDEETSTRTKRCHCGFS 862

Query: 828 IQVEEL 833
           +QVEEL
Sbjct: 863 VQVEEL 868

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|225453199\|ref\|XP_002275277.1\| PREDICTED: DNA repair protein complementing XP-C cells-like [Vitis vinifera]	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		833
TAIR\|locus:2174160		865	RAD4 [Arabidopsis thaliana (ta	0.684	0.658	0.527	2.8e-211
MGI\|MGI:103557		930	Xpc "xeroderma pigmentosum, co	0.840	0.752	0.283	2.1e-64
UNIPROTKB\|F1N806		826	Gga.54220 "Uncharacterized pro	0.755	0.761	0.303	4.8e-64
UNIPROTKB\|E1BUG1		936	Gga.54220 "Uncharacterized pro	0.755	0.672	0.303	3e-63
UNIPROTKB\|E1BDJ1		932	XPC "Uncharacterized protein"	0.301	0.269	0.365	3.1e-60
RGD\|1305760		933	Xpc "xeroderma pigmentosum, co	0.834	0.744	0.282	1.9e-56
UNIPROTKB\|E9PH69		903	XPC "DNA repair protein-comple	0.798	0.736	0.284	6.9e-56
UNIPROTKB\|Q01831		940	XPC "DNA repair protein comple	0.764	0.677	0.289	1.9e-55
UNIPROTKB\|F1SPI2		944	XPC "Uncharacterized protein"	0.345	0.305	0.327	1.1e-50
UNIPROTKB\|E2RCR3		949	XPC "Uncharacterized protein"	0.303	0.266	0.370	4.9e-50

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

 Score = 1484 (527.5 bits), Expect = 2.8e-211, Sum P(2) = 2.8e-211
 Identities = 322/610 (52%), Positives = 395/610 (64%)

Query:   245 KENVCETSSKGSPECKYSS--PKSNNTQSK-KSPVSCELSSGNLDPSSSMACSDISEACH 301
             K  +  TS+   P+ +  S  PK +++  K KSP   +   GN   S  +  + ++ +C 
Sbjct:   275 KHGIFRTSTLMVPKQQAISSYPKKSSSHVKNKSPFE-KPQLGNPLGSDQVQDNAVNSSCE 333

Query:   302 P--KEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKK 359
                  KS   +RKGD+EFE Q+ MALSAT          +D    N  SS V   K++++
Sbjct:   334 AGMSIKSDGTRRKGDVEFERQIAMALSAT----------AD----NQQSSQVNNTKKVRE 379

Query:   360 IE--SGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKV 417
             I   S  SS S   ISTA GS+KV +PL W EVYC+GEN+ GKWVHVDA N +ID EQ +
Sbjct:   380 ITKISNSSSVSDQVISTAFGSKKVDSPLCWLEVYCNGENMDGKWVHVDAVNGMIDAEQNI 439

Query:   418 EAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGA 477
             EAAAAACKT LRY+VAFA  GAKDVTRRYC KW+ I+SKRV+S WWD VLAPL  LESGA
Sbjct:   440 EAAAAACKTVLRYVVAFAAGGAKDVTRRYCTKWHTISSKRVSSVWWDMVLAPLVHLESGA 499

Query:   478 TGD----------LN-VES--SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQL 524
             T D          LN V S  S+  S    R++LEDMEL TRALTE LPTNQQAYK+H++
Sbjct:   500 THDEDIALRNFNGLNPVSSRASSSSSSFGIRSALEDMELATRALTESLPTNQQAYKSHEI 559

Query:   525 YVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEXXXXXX 584
             Y IE+WL+K QIL+PKGP+LGFCSGH VYPR+CVQTLKTKERWLR+ LQ+KANE      
Sbjct:   560 YAIEKWLHKNQILHPKGPVLGFCSGHPVYPRTCVQTLKTKERWLRDGLQLKANEVPSKIL 619

Query:   585 XXXXXXXXGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSE 644
                      +DFE  D +       +ELYGKWQ+EPL LP AVNGIVP+NERGQVDVWSE
Sbjct:   620 KRNSKFKKVKDFEDGDNNIKGGSSCMELYGKWQMEPLCLPPAVNGIVPKNERGQVDVWSE 679

Query:   645 KCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEA 704
             KCLPPGTVHLR PR+++VAKR  ID APAMVGFE+R+G +TP+F+GIVVC EFKDTILEA
Sbjct:   680 KCLPPGTVHLRFPRIFAVAKRFGIDYAPAMVGFEYRSGGATPIFEGIVVCTEFKDTILEA 739

Query:   705 YXXXXXXXXXXXXXXXXXQATSRWYQLLSSIVTRQRLNNCYGXXXXXXXXXXXXXVKKTN 764
             Y                 QA SRWYQLLSSI+TR+RL N Y                + N
Sbjct:   740 YAEEQEKKEEEERRRNEAQAASRWYQLLSSILTRERLKNRYANNSNDVEAKSL----EVN 795

Query:   765 SNVGVDSSQNDWQSPNQV-DRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCH 823
             S   V +         +V  RG+      S  + E HEHV+L E+++FDEE SV TKRC 
Sbjct:   796 SETVVKAKNVKAPEKQRVAKRGEKSRVRKSRNEDESHEHVFLDEEETFDEETSVKTKRCK 855

Query:   824 CGFTIQVEEL 833
             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\|E9PH69 XPC "DNA repair protein-complementing XP-C cells" [Homo sapiens (taxid:9606)]	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\|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		833
TIGR00605		713	TIGR00605, rad4, DNA repair protein rad4	2e-77
COG5535		650	COG5535, RAD4, DNA repair protein RAD4 [DNA replic	2e-43
pfam10405		75	pfam10405, BHD_3, Rad4 beta-hairpin domain 3	2e-34
smart01032		75	smart01032, BHD_3, Rad4 beta-hairpin domain 3	3e-33
pfam03835		142	pfam03835, Rad4, Rad4 transglutaminase-like domain	1e-21
smart01030		54	smart01030, BHD_1, Rad4 beta-hairpin domain 1	8e-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	6e-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 =  265 bits (678), Expect = 2e-77
 Identities = 189/722 (26%), Positives = 275/722 (38%), Gaps = 85/722 (11%)

Query: 63  KKPVRRASAED-KELAELVHKVHLLCLLARGRLIDSVCDDP--LIQASLLSLLPSYLLKI 119
           +  +RR        L EL H+V L+C L      D V   P  L  +  +          
Sbjct: 38  EPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSVPDSLSVSEEIPSREEDYD-S 96

Query: 120 SEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEE-----IAAL 174
            E   +    LS +V+ F          S   S   D A  L     + E         +
Sbjct: 97  REFEDVY---LSNLVAEFETISVEIKPSSKAES--DDDAETLSRNVCSNEARKDRKYIHI 151

Query: 175 SVALFRALKLTTRFVSILDVASLKPEADKNVSSNQD------SSRVGGGIFNAPTLMVAK 228
              L   + L TR    L  A LK     N+   +       S R    + +     + K
Sbjct: 152 LYLLCLMVHLFTRNEWSLS-APLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRK 210

Query: 229 P-EEVLASPVKSFSC-------DKKENVCETS---SKGSPECKYSSPKSNN----TQSKK 273
           P  E L   ++++            + +       SK     K S+ K       T  + 
Sbjct: 211 PLVEKLKKCMETWQKGLRKTTKGLLKLLNGGRYSRSKWEEIEKSSNRKLGGRKYRTLKRG 270

Query: 274 SPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATS 333
           S +        L  S  +           +  S+    K       Q  +    +   TS
Sbjct: 271 SILENLNVPTRLVFSDFLLSVSKGHNDP-EISSEGFVPKLSACNANQRLIMSCESADRTS 329

Query: 334 KSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCS 393
           +  +  D   L   S+     K                       R +    +W EV+  
Sbjct: 330 RFRMKKDPS-LPGFSAYSDMDKSPIFTCEEGDKFI---------DRWITYVDFWVEVFIE 379

Query: 394 GENLTGKWVHVDAANAIIDGEQKVEAAAAACKTS---LRYIVAF-AGCGAKDVTRRYCMK 449
            E    KWV VDA          V       + +   + Y+ A+      KDVTRRYC +
Sbjct: 380 QEE---KWVCVDAV-----HSGVVPKGVTCFEPATLMMTYVFAYDRDGYVKDVTRRYCDQ 431

Query: 450 WYRIASK-RVNSAWWD-AVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRA 507
           W     K RV  A +      P+     GA                     ED E   R 
Sbjct: 432 WSTKVRKRRVEKADFGETWFRPIF----GALHKRKRTIDDI----------EDQEFLRRH 477

Query: 508 LTEPLPTNQQAYKNHQLYVIERWLNKYQILYP--KGPILGFCSGHA-VYPRSCVQTLKTK 564
            +E +P + Q  KNH LYV+ER L K Q L P  K   LGF +G A VY R  V  LK+ 
Sbjct: 478 ESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSA 537

Query: 565 ERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 624
           E+W ++   +K  E P KV+K  ++++  +  + E  +E      + LY   Q E    P
Sbjct: 538 EQWYKKGRVIKLGEQPYKVVK--ARARTVRLPKGEAEEED-----LGLYSYEQTELYIPP 590

Query: 625 SAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRS 684
            AV+GIVP+N  G +D++    +P G VHLRLP     AK+L ID APA+ GF+F  G S
Sbjct: 591 PAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYS 650

Query: 685 TPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNC 744
            PV DGI+VC EF++ I  A+ E E+ +E +E+++   +A   W  LL  +  R+RL   
Sbjct: 651 KPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKET 710

Query: 745 YG 746
           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		833
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:	99.88
PF10403		57	BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR01	99.77
KOG0909		500	consensus Peptide:N-glycanase [Posttranslational m	99.72
PF10404		64	BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR01	99.64
TIGR00605		713	rad4 DNA repair protein rad4. This family is based	99.19
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	97.05
KOG2179		669	consensus Nucleotide excision repair complex XPC-H	95.98
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	95.58
TIGR00598		172	rad14 DNA repair protein. This family is based on	94.92
COG1305		319	Transglutaminase-like enzymes, putative cysteine p	92.96
COG5145		292	RAD14 DNA excision repair protein [DNA replication	87.95
KOG4017		274	consensus DNA excision repair protein XPA/XPAC/RAD	86.54
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	84.7
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	84.37

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

Probab=100.00  E-value=4.9e-122  Score=1070.74  Aligned_cols=544  Identities=29%  Similarity=0.446  Sum_probs=423.0

Q ss_pred             ccChHHHHHHHHHHHHHHHHHHhhhHHHHhhcCc-HHHHHHhhcccccccccccCcc---------cccccccchhhhhh
Q 003292           68 RASAEDKELAELVHKVHLLCLLARGRLIDSVCDD-PLIQASLLSLLPSYLLKISEVS---------KLTANALSPIVSWF  137 (833)
Q Consensus        68 R~t~~eKe~~~~~HKvHLLCLLAhg~~rN~~Cnd-~~lqa~llSllp~~~~~~~~~~---------~~~~~~L~~lv~Wf  137 (833)
                      -++.++|+.|+++|++||||||.|+.+||.|||| +++|+.|..++|.++....++.         ....++|..|+.-|
T Consensus       137 ~~~~~eR~~R~~iH~~~ll~ll~h~~~RN~w~n~~~~~~~~L~~~~p~k~~~~l~p~~~~~~~~~s~s~~~~~~~l~~~~  216 (713)
T TIGR00605       137 VCSNEARKDRKYIHILYLLCLMVHLFTRNEWSLSAPLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRKPLVEKL  216 (713)
T ss_pred             hccHHHHHHHHHHHHHHHHHHhhhhHhhhhhhCChHHHhHHHhhhCCHHHHHhcCccccccccccchhhhhhhHHHHHhh
Confidence            3789999999999999999999999999999999 7999999999999987654432         23467888999999


Q ss_pred             ccceeecccCccc---c----------ch--hhHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCcccc
Q 003292          138 HDNFHVRSSVSTR---R----------SF--HSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEAD  202 (833)
Q Consensus       138 ~~~F~v~~~~~~~---~----------~~--~~~l~~~l~~~~Gs~de~a~LF~aLlRaLgl~~RLV~sLqp~pLkp~~~  202 (833)
                      +..|.++..-...   .          .+  ..++..+..+++|||+.++||||||||++|+.+||||||||+|+.....
T Consensus       217 kk~~~it~~g~~~~~~~~~~~~~~~~~~~~~~~ef~~~a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~  296 (713)
T TIGR00605       217 KKCMETWQKGLRKTTKGLLKLLNGGRYSRSKWEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHN  296 (713)
T ss_pred             hhcchhcccccccCcccccccchhhHHhhhhHHHHHHhhhccccccchhhhHHHHHHhhhcccccccccccccCcccCCC
Confidence            9999998643100   0          00  2345667778899999999999999999999999999999998865311


Q ss_pred             cccCCCCCCCCcCCCccCCCCccccCccccccCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCcccccC
Q 003292          203 KNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSS  282 (833)
Q Consensus       203 k~~~~~~~~~~~~~~~~~~~~p~~~k~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~  282 (833)
                      ...                     +..+.  ..+ +...       +                     +    +    + 
T Consensus       297 ~~~---------------------~~~~~--~~~-~~~~-------~---------------------~----~----~-  315 (713)
T TIGR00605       297 DPE---------------------ISSEG--FVP-KLSA-------C---------------------N----A----N-  315 (713)
T ss_pred             Ccc---------------------ccccc--ccc-cccc-------c---------------------c----c----c-
Confidence            000                     00000  000 0000       0                     0    0    0 


Q ss_pred             CCCCCCCCcccCCCcccCCCccchhhhccCCChHHHHHHHHHhhccccccCCCCccccccccCCCCCCcccccccccccc
Q 003292          283 GNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIES  362 (833)
Q Consensus       283 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kr~g~~~~~~q~~~a~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~  362 (833)
                          +   .+..+ ..++.........++.+.|.|.                              +++.+.+..+.. .
T Consensus       316 ----q---~~~~s-~~S~~~tsR~~l~~~l~~P~fs------------------------------~~~~~~k~~~~~-~  356 (713)
T TIGR00605       316 ----Q---RLIMS-CESADRTSRFRMKKDPSLPGFS------------------------------AYSDMDKSPIFT-C  356 (713)
T ss_pred             ----c---ccccc-cCCCCccccccccccCCCCCcc------------------------------ccccCCCCCccc-h
Confidence                0   00000 0000000000012233332210                              000000100000 0


Q ss_pred             CCCCCccCCcccccCCccCCCCceEEEEEecCCCCCCceEEEeccc-cccccch-hhhHhHhhcCCCeeEEEEEcCCC-c
Q 003292          363 GESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-A  439 (833)
Q Consensus       363 ~~s~~~~~~~s~~~~~~~~~~P~fWvEV~~~~~~~~~kWI~VDPv~-~~Vd~~~-~~Ep~~~~~~~~msYVVAfd~dG-a  439 (833)
                      ++        .....+.+++||+||+|||++.   +++||||||++ ++++++. .+||    +.++|+|||||++|| |
T Consensus       357 ~~--------~~~~~~~~~~~p~~W~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~  421 (713)
T TIGR00605       357 EE--------GDKFIDRWITYVDFWVEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYV  421 (713)
T ss_pred             hc--------ccccccccCCCCeeEEEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCce
Confidence            00        0112346788999999999985   49999999999 8888875 3443    569999999999997 9


Q ss_pred             ccchhhhHhhHhh-hcccccCHHHHHHH-HhhhhhcccCCCCCCcccccccCcccccCCchHHHHHHHHhccCCCCcChH
Q 003292          440 KDVTRRYCMKWYR-IASKRVNSAWWDAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQ  517 (833)
Q Consensus       440 kDVTrRY~~~~~~-~~rkRv~~~Ww~~~-L~~~~~~~~~~~g~~~i~a~~~~~~~~~rd~~Ed~El~~~~~~e~mP~si~  517 (833)
                      +|||+||+++|++ +++.|++..||..+ |++|.+...             +.. ..+|..||.||.+++++||||+|++
T Consensus       422 kDVT~RY~~~~~~k~r~~Rv~~~w~~~~w~~~~~~~~~-------------~r~-~~~d~~Ed~el~~~~~~e~~P~si~  487 (713)
T TIGR00605       422 KDVTRRYCDQWSTKVRKRRVEKADFGETWFRPIFGALH-------------KRK-RTIDDIEDQEFLRRHESEGIPKSIQ  487 (713)
T ss_pred             eechhhHhhhhhhhhheeeecccchHHHHHHHHhhhhc-------------cCc-cchhhhhhhHhhhhhcccCCChhHH
Confidence            9999999999996 66789998888877 776653210             111 1267899999999999999999999


Q ss_pred             hhhcCCchhhhhhhccccccCCC--CCcceeeccee-eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCC
Q 003292          518 AYKNHQLYVIERWLNKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQ  594 (833)
Q Consensus       518 ~fKnHP~YvLerhL~k~EvI~P~--a~~~G~~~gE~-VY~R~dV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~  594 (833)
                      +|||||+|||||||++||+|||+  ++++|+++|++ ||+|+||++|||+++||++||+||+||+|+|+|+.+++..+. 
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            99999999999999999999995  46789999998 999999999999999999999999999999999987442211 


Q ss_pred             CCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeece
Q 003292          595 DFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAM  674 (833)
Q Consensus       595 ~~~~~~~~~~~~~~~~~LYg~wQTe~y~pPp~vdG~VPkN~yGNVdlf~p~MlP~G~vHi~~~~~~rvAkkLgIDyA~AV  674 (833)
                        ..++.    ..+.++|||+||||+|+|||++||+||||+|||||||+|+|||+|||||++++|.+||++||||||+||
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 003292          675 VGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN  747 (833)
Q Consensus       675 tGFeF~~g~a~PvidGIVV~ee~~e~l~~a~~~~~~~~~~~e~~k~e~~aL~~Wk~Ll~~L~IreRL~~~Yg~  747 (833)
                      |||+|++|+++|||+|||||+||+++|++||.++++.++++++++++++||++|++||++|||++||+.+||.
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		833
2qsh_A		538	Crystal Structure Of Rad4-Rad23 Bound To A Mismatch		5e-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 = 5e-18, Method: Compositional matrix adjust. Identities = 85/344 (24%), Positives = 140/344 (40%), Gaps = 54/344 (15%) Query: 381 VGAPLYWAEVYCSGENLTGKWVHVDAANAI----IDGEQKVEAAAAAC--KTSLRYIVAF 434 V P++W EV+ + + KW+ VD N + K+ AC + LRY++A+ Sbjct: 216 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 272 Query: 435 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 486 G +DVTRRY +W RI W+ V+ L + D Sbjct: 273 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 326 Query: 487 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 546 ED R +E +P + Q KNH YV+E+ + + QI+ P G+ Sbjct: 327 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 374 Query: 547 CSGHA-------VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPE 599 H VY + + LK+ +W +K G E E Sbjct: 375 LKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAE 431 Query: 600 DYDE-VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPR 658 + DE + + + ELY + PL ++ +G + +N G ++V++ +P + P Sbjct: 432 EEDERLYSFEDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPV 484 Query: 659 VYSVAKRLEIDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 701 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		833
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	1e-78
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	5e-16
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	9e-22
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	4e-16
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-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 =  263 bits (672), Expect = 1e-78
 Identities = 84/353 (23%), Positives = 134/353 (37%), Gaps = 52/353 (14%)

Query: 379 RKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEA------AAAACKTSLRYIV 432
             V  P++W EV+        KW+ VD  N     + ++ +       A   +  LRY++
Sbjct: 209 DMVKYPIFWCEVWDKFSK---KWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVI 265

Query: 433 AFAGCG-AKDVTRRYCMKW------YRIASKRVNSAWWDAVLAPLRELESGATGDLNVES 485
           A+      +DVTRRY           RI        W+  V+  L               
Sbjct: 266 AYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHH------------- 312

Query: 486 SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILG 545
                     +  ED     R  +E +P + Q  KNH  YV+E+ + + QI+ P     G
Sbjct: 313 ----RKRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECG 368

Query: 546 FCSGHA-------VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEP 598
           +   H        VY +  +  LK+  +W      +K      KVIK +    KG+  E 
Sbjct: 369 YLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEE 428

Query: 599 EDYDEVDARGNIELYGKWQLEPLRLPSA-VNGIVPRNERGQVDVWSEKCLPPGTVHLRLP 657
           +            LY     E    P A  +G + +N  G ++V++   +P     +  P
Sbjct: 429 D----------ERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENP 478

Query: 658 RVYSVAKRLEIDSAPAMVGFEFRNGRS-TPVFDGIVVCAEFKDTILEAYAEEE 709
                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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		833
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	99.86
3isr_A		293	Transglutaminase-like enzymes, putative cysteine;	96.13
3kd4_A		506	Putative protease; structural genomics, joint cent	94.41
1ex0_A		731	Coagulation factor XIII A chain; transglutaminase,	85.19
1g0d_A		695	Protein-glutamine gamma-glutamyltransferase; tissu	84.97
1vjj_A		692	Protein-glutamine glutamyltransferase E; transglut	84.82
2q3z_A		687	Transglutaminase 2; transglutaminase 2, tissue tra	83.53

>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=6e-122  Score=1051.67  Aligned_cols=469  Identities=22%  Similarity=0.378  Sum_probs=372.3

Q ss_pred             CCCcceEEEEecCcc--ccc--ccccccChHHHHHHHHHHHHHHHHHHhhhHHHHhhcCcHHHHHHhhcccccccccccC
Q 003292           46 SDIKGVTIEFDAADS--VTK--KPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISE  121 (833)
Q Consensus        46 ~~~~~v~Ie~~~~~~--~kk--k~~RR~t~~eKe~~~~~HKvHLLCLLAhg~~rN~~Cnd~~lqa~llSllp~~~~~~~~  121 (833)
                      .+..+|+|+|+....  .++  ++.+.+|+.||++|+++||+||||||+|+++||+||||++||++|+|+||.++....+
T Consensus         6 ~~~~~l~itl~~~~~~~~~~~~~~kk~~S~~ER~~R~~~Hk~hvl~LL~H~~~RN~W~nD~~lq~~L~sllP~~i~~~l~   85 (533)
T 2qsf_A            6 AGVEDISVEIKPSSKRNSDARRTSRNVCSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLH   85 (533)
T ss_dssp             ---------------------CCCTTBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHGGGSCHHHHHHTS
T ss_pred             CCCCCeEEEecCCccccchhhhccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhhC
Confidence            345678888876521  221  2234489999999999999999999999999999999999999999999998865433


Q ss_pred             cc----------cccccccchhhhhhccceeecccCc---cc-------------c---ch--hhHHHHHHHHhcCCHHH
Q 003292          122 VS----------KLTANALSPIVSWFHDNFHVRSSVS---TR-------------R---SF--HSDLAHALESREGTPEE  170 (833)
Q Consensus       122 ~~----------~~~~~~L~~lv~Wf~~~F~v~~~~~---~~-------------~---~~--~~~l~~~l~~~~Gs~de  170 (833)
                      +.          +...++|+.|+.||+.+|.|+++..   ..             .   .+  ..+|..++++++|++|+
T Consensus        86 p~~~~~~~~~~~~~~~~~Lk~L~~ww~~~F~it~p~~~~g~~~~~w~e~~~~~~~~~~f~~~~~~~f~~~~~~~~Gs~d~  165 (533)
T 2qsf_A           86 PQKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDI  165 (533)
T ss_dssp             CCCCSSCTHHHHHHHHHHHHHHHHHHHHHCCEECCCSSCTTSCCCHHHHHHTTTTCCCEECCCHHHHHHHHHHTEECHHH
T ss_pred             cCCCccccccchHHHHHHHHHHHHHHHhhEEEcCCccCCCccccCccccchhhccccccccccHHHHHHHHHhcCCChhH
Confidence            21          1124789999999999999987411   00             0   01  24688999999999999


Q ss_pred             HHHHHHHHHHhcCCceEEEEeeccccCCcccccccCCCCCCCCcCCCccCCCCccccCccccccCCCccccccccccccc
Q 003292          171 IAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCE  250 (833)
Q Consensus       171 ~a~LF~aLlRaLgl~~RLV~sLqp~pLkp~~~k~~~~~~~~~~~~~~~~~~~~p~~~k~~~~~~~~~k~~~~~~~~~~~~  250 (833)
                      +||||||||||||+.||||+||||+++....                           . .  .++              
T Consensus       166 ~AqlF~aLlRalG~~aRlV~SLqP~~f~~~k---------------------------~-~--~~~--------------  201 (533)
T 2qsf_A          166 SVQGFVAMLRACNVNARLIMSCQPPDFTNMK---------------------------I-D--TSL--------------  201 (533)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEECCCCTTCCB---------------------------S-C--CCC--------------
T ss_pred             HHHHHHHHHHHCCCceEEEeccccccccccc---------------------------c-c--cCc--------------
Confidence            9999999999999999999999998765310                           0 0  000              


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCcccCCCcccCCCccchhhhccCCChHHHHHHHHHhhcccc
Q 003292          251 TSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNV  330 (833)
Q Consensus       251 ~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kr~g~~~~~~q~~~a~~~t~~  330 (833)
                                                                           .     +  ...               
T Consensus       202 -----------------------------------------------------~-----k--~~~---------------  206 (533)
T 2qsf_A          202 -----------------------------------------------------N-----G--NNA---------------  206 (533)
T ss_dssp             -----------------------------------------------------C----------C---------------
T ss_pred             -----------------------------------------------------c-----c--CCc---------------
Confidence                                                                 0     0  000               


Q ss_pred             ccCCCCccccccccCCCCCCccccccccccccCCCCCccCCcccccCCccCCCCceEEEEEecCCCCCCceEEEecccc-
Q 003292          331 ATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANA-  409 (833)
Q Consensus       331 ~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~s~~~~~~~s~~~~~~~~~~P~fWvEV~~~~~~~~~kWI~VDPv~~-  409 (833)
                                                                    .+.++.+|+||+|||++.   +++||||||+++ 
T Consensus       207 ----------------------------------------------~~~~~~~P~~W~EV~s~~---~~rWi~VDp~~~~  237 (533)
T 2qsf_A          207 ----------------------------------------------YKDMVKYPIFWCEVWDKF---SKKWITVDPVNLK  237 (533)
T ss_dssp             ----------------------------------------------HHHHTTSCSEEEEEEETT---TTEEEEEESSSSC
T ss_pred             ----------------------------------------------cccccCCCeEEEEEEEcC---CCeEEEEeccccc
Confidence                                                          001234899999999975   599999999985 


Q ss_pred             ccc---cchhhhHhH--hhcCCCeeEEEEEcCCC-cccchhhhHhhHhh-hcccccC-----HHHHHHHHhhhhhcccCC
Q 003292          410 IID---GEQKVEAAA--AACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-IASKRVN-----SAWWDAVLAPLRELESGA  477 (833)
Q Consensus       410 ~Vd---~~~~~Ep~~--~~~~~~msYVVAfd~dG-akDVTrRY~~~~~~-~~rkRv~-----~~Ww~~~L~~~~~~~~~~  477 (833)
                      +++   .+..|||..  .++.++|+|||||+.|| |+|||+||+.+|.. +++.|+.     ++||+.+|+.|+++    
T Consensus       238 ~id~~~~~~~~Ep~~~~~~~~~~m~YViAf~~d~~~kDVT~RY~~~~~~k~rr~Ri~~~~~~~~W~~~~L~~~~~~----  313 (533)
T 2qsf_A          238 TIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHR----  313 (533)
T ss_dssp             EEECCSSCCTTSCCSTTTTSSCCCCEEEEECTTCCEEECHHHHCTTCCCCCGGGSGGGSHHHHHHHHHHHHHHCCS----
T ss_pred             cccccccccccccccccccccCceeEEEEEcCCCceEecchhhhhchhhhhheeeecCCcchHHHHHHHHHHHhcC----
Confidence            444   567899853  25779999999999986 99999999998874 4556764     78999999999853    


Q ss_pred             CCCCcccccccCcccccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCCCCCcceeecc-------e
Q 003292          478 TGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG-------H  550 (833)
Q Consensus       478 ~g~~~i~a~~~~~~~~~rd~~Ed~El~~~~~~e~mP~si~~fKnHP~YvLerhL~k~EvI~P~a~~~G~~~g-------E  550 (833)
                                   ....+|..||+||+.+..+||||+|+++|||||+|||||||++||+|||+++++|+|+|       |
T Consensus       314 -------------~~~~~d~~Ed~el~~~~~~e~~P~s~~~fK~HP~yvLer~L~k~E~i~P~a~~~g~~~~~~k~~~~E  380 (533)
T 2qsf_A          314 -------------KRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVL  380 (533)
T ss_dssp             -------------CCCHHHHHHHHHHHHHHHHSCCCSSTGGGTTCSSEEEGGGSCTTEEECTTCCCSEEEECCSTTCCEE
T ss_pred             -------------CccccchhHHHHHHHHHhcCCCCccHHHHcCCcHhhhhhhhccceeeCCCCceeeEEecCcCCCccc
Confidence                         23467889999999999999999999999999999999999999999999999999987       9


Q ss_pred             eeeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCC-CCC
Q 003292          551 AVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSA-VNG  629 (833)
Q Consensus       551 ~VY~R~dV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~~~~~~~~~~~~~~~~~~LYg~wQTe~y~pPp~-vdG  629 (833)
                      |||+|+||++|||+++|+++||+||+||+|+|+||.++.+..    .+++      ...++|||+||||+|+|||+ +||
T Consensus       381 ~VY~R~~V~~l~S~e~W~~~gR~vk~ge~P~K~v~~r~~~~~----~~~~------~~~~~Ly~~~QTe~y~Pp~~~~dG  450 (533)
T 2qsf_A          381 KVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPK----GEAE------EEDERLYSFEDTELYIPPLASASG  450 (533)
T ss_dssp             EEEEGGGEEECBCHHHHHTTTEEECSSCCCSEEECC----------------------CEEEBCGGGEEECCCCCCCTTC
T ss_pred             ceeehhhhheeecHHHHHHcCCccCCCCeeeeEEecccCCcc----cccc------cccccccCHHhCccccCCCCccCC
Confidence            999999999999999999999999999999999998764321    1111      25689999999999999999 999


Q ss_pred             CccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeeceeceeecCC-eeeeeEceEEEccccHHHHHHHHHHH
Q 003292          630 IVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNG-RSTPVFDGIVVCAEFKDTILEAYAEE  708 (833)
Q Consensus       630 ~VPkN~yGNVdlf~p~MlP~G~vHi~~~~~~rvAkkLgIDyA~AVtGFeF~~g-~a~PvidGIVV~ee~~e~l~~a~~~~  708 (833)
                      +||||+|||||||+|+|||+|||||++++++++||+||||||+|||||+|++| +++|||+|||||+||+++|++||++.
T Consensus       451 ~VPkN~yGNvd~~~p~m~P~G~vhi~~~~~~~~ar~L~Idya~Av~GFef~~g~~~~Pv~~GiVV~~e~~~~l~~a~~~~  530 (533)
T 2qsf_A          451 EITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGI  530 (533)
T ss_dssp             CCCCCTTSCEECSSGGGSCTTEEEEECTTHHHHHHHTTCCCEEEEEEECC------CEEEEEEEEETTSHHHHHHHHHTG
T ss_pred             cccccCCCCEEeccCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeeCCCCcceEEeCeEEEehHHHHHHHHHHHhh
Confidence            99999999999999999999999999999999999999999999999999976 57999999999999999999999764


Q ss_pred             H
Q 003292          709 E  709 (833)
Q Consensus       709 ~  709 (833)
                      +
T Consensus       531 ~  531 (533)
T 2qsf_A          531 E  531 (533)
T ss_dssp             G
T ss_pred             h
Confidence            3

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		833
d1x3za1		320	d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Bak	5e-17
d2f4ma1		287	d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {M	3e-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 = 5e-17
 Identities = 23/123 (18%), Positives = 43/123 (34%), Gaps = 15/123 (12%)

Query: 383 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDV 442
               W E + +      +WVHVD+     D               + Y +AF   G  DV
Sbjct: 209 EDHVWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSIN---WNKKMSYCIAFGKDGVVDV 262

Query: 443 TRRYCMKWYRIASKRVNSAWWDAVLAPL-RELESGATGDLNVESSAKDSFVADRNSLEDM 501
           ++RY ++   +   ++       +   + + L      D       +   +A R+  E +
Sbjct: 263 SKRYILQN-ELPRDQIKEEDLKFLCQFITKRLRYSLNDD-------EIYQLACRDEQEQI 314

Query: 502 ELE 504
           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		833
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=9.2e-23  Score=215.88  Aligned_cols=82  Identities=20%  Similarity=0.379  Sum_probs=73.9

Q ss_pred             ceEEEEEecCCCCCCceEEEeccccccccchhhhHhHhhcCCCeeEEEEEcCCCcccchhhhHhhHhhhcccccCHHHHH
Q 003292          385 LYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWD  464 (833)
Q Consensus       385 ~fWvEV~~~~~~~~~kWI~VDPv~~~Vd~~~~~Ep~~~~~~~~msYVVAfd~dGakDVTrRY~~~~~~~~rkRv~~~Ww~  464 (833)
                      ++|+|||++..   ++||||||+.+++|+|..|+.   .|.++|+|||||+.||++|||+||+.+| .+++.|+++.||.
T Consensus       211 hvW~EVys~~~---kRWIhvDpce~~id~P~lye~---gw~k~msYVIAf~~dgv~DVT~RY~~k~-~~rR~rv~E~wl~  283 (320)
T d1x3za1         211 HVWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSI---NWNKKMSYCIAFGKDGVVDVSKRYILQN-ELPRDQIKEEDLK  283 (320)
T ss_dssp             EEEEEEEETTT---TEEEEEETTTTEESCTHHHHT---TSCCCBCCEEEEETTEEEECHHHHCSSS-BCCCCSSCHHHHH
T ss_pred             ceEEEEeeccc---CeEEEEcCCCCccCCcceecc---CCCCceEEEEEecCCcceechhhhcccc-cCccccCCHHHHH
Confidence            48999999754   899999999999999999875   4889999999999999999999999875 4678899999999


Q ss_pred             HHHhhhhhc
Q 003292          465 AVLAPLREL  473 (833)
Q Consensus       465 ~~L~~~~~~  473 (833)
                      .+|..+++.
T Consensus       284 ~~L~~l~~~  292 (320)
T d1x3za1         284 FLCQFITKR  292 (320)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999998754

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