Citrus Sinensis ID: 006346

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-------65

MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEEcccccccccccHHHHHHHHccccEEEEEEEcccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHHccccHHHHHHHHHHHcccccccHHHHHccccHHHHHHHcccccccccccccEEEccEEEEEccccEEEcHHHHHHHHccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEEEccccHHHHHHHccccEEcccccEEEcccEEEEEEcEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEcc

ccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccEEEEEEEEccccccccEEEEcccccccccccccccccHcccccEEEEEEEcccccHHHHHHHHHHHHHHHHHccccccccccEEEEEEcccccccccEEEEEccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHccEEccccccccccccccEEccccEEEEccHHHHHHHccEcccccccEEEEcccccHcccHHHHHHHcccccccccccEEEccccccccccccccccccccccccEEEEcccccccccEEEccHHHHHHHHHHccccccEEEcEEccccccEEEEcEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccEEEEEEcc

mvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskkspvscelssgnldpsssmacsdiseachpkeksqALKRKGDLEFEMQLEMALSATnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkvgaplYWAEVYcsgenltgkwvhvdaanaiIDGEQKVEAAAAACKTSLRYIVAFAgcgakdvtRRYCMKWYRIASKRVNSAWWDAVLAPLrelesgatggmtqmEKRHVNASNILEALktsnylyrdsfpnhvslygdsdlnvessakdsfvadrnsleDMELEtralteplptnqqaykNHQLYVIERWLNKYQilypkgpilgfcsghavyprscvQTLKTKERWLREALQVKAnevpvkviknsskskkgqdfepedydevdargnielygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprvYSVAKRleidsapamvgfefrngrstpvfdgIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRlnncygnnstsqsssnfqnvkktnsnvgvdssqndwqspnqvdrgdtklhapspfqseehehvyliedqsfdeensvttkrchcgftiqveel

mvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskksPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSAtnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFagcgakdvTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETralteplptnqqayKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREAlqvkanevpvkviknsskskkgqdfepedydevdARGNIELygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKrreaqatsrwYQLLSSIVTRQRLNNCYGNnstsqsssnfqnVKKTNsnvgvdssqndwQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEvpvkviknsskskkGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYaeeeekreaeekkrreaQATSRWYQLLSSIVTRQRLNNCYGnnstsqsssnfqnVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

************************************************************************************************************************************************CLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLREL***************VNASNILEALKTSNYLYRDSFPNHVSLYG****************************************AYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV*********************DARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAY*********************RWYQLLSSIVTRQRLNNCY*********************************************************VYLIE*********VTTKRCHCGFTIQ****

*************************************************************************************************************************************************************GAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDME***************AYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV*************************NIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKR*********AQATSRWYQLLSSIVTRQRLNN********************************************************************************CGFTIQVEEL

*************KSFSCD**************************************************SDISEA**********KRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKN**************YDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAE*****************TSRWYQLLSSIVTRQRLNNCYGN***********NVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

***********************************************************************************************************************************************************KVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSS*****************ARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYG************************************************************EDQSFDEENSVTTKRCHCGFTIQVEEL

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MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

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		649	2.2.26 [Sep-21-2011]
P51612		930	DNA repair protein comple	yes	no	0.718	0.501	0.306	2e-53
Q01831		940	DNA repair protein comple	yes	no	0.517	0.357	0.342	4e-52
Q24595		1293	DNA repair protein comple	yes	no	0.516	0.259	0.309	4e-48
Q10445		638	DNA repair protein rhp41	yes	no	0.499	0.507	0.269	2e-27
P87235		686	DNA repair protein rhp42	no	no	0.530	0.501	0.262	7e-23
P14736		754	DNA repair protein RAD4 O	yes	no	0.402	0.346	0.266	5e-16
Q7F0R1		447	Peptide-N(4)-(N-acetyl-be	no	no	0.192	0.279	0.307	6e-06

>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 =  211 bits (537), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 169/551 (30%), Positives = 252/551 (45%), Gaps = 85/551 (15%)

Query: 17  SCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEAC 76
           SC + E   E   +G P  +     +  +  ++S      S  + +PSS        E C
Sbjct: 395 SCSEGEEA-EQKVQGRPHARKRRVAAKVSYKEESESDGAGSGSDFEPSSGEGQHSSDEDC 453

Query: 77  HPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKI 136
            P  + Q  KR        Q   A S +   T + + C +       SS+    KR KK+
Sbjct: 454 EPGPRKQ--KRAS----APQRTKAGSKSASKTQRGSQC-EPSSFPEASSSSSGCKRGKKV 506

Query: 137 ESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAA 196
            SG         +  +  RK      W EVYC  +    KWV VD  + ++   Q V   
Sbjct: 507 SSG---------AEEMADRKPAGVDQWLEVYCEPQ---AKWVCVDCVHGVVG--QPVACY 552

Query: 197 AAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGG 256
             A K  + Y+V     G           W R  ++R + AW                  
Sbjct: 553 KYATK-PMTYVVGIDSDG-----------WVRDVTQRYDPAW------------------ 582

Query: 257 MTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLED 316
           MT   K  V+A    E L+     YR                       S + +R   ED
Sbjct: 583 MTATRKCRVDAEWWAETLRP----YR-----------------------SLLTEREKKED 615

Query: 317 MELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK-GPILGFCSGHAVYPRSCVQ 375
            E + + L +PLPT+   YKNH LY ++R L K+Q +YP+   +LG+C G AVY R CV 
Sbjct: 616 QEFQAKHLDQPLPTSISTYKNHPLYALKRHLLKFQAIYPETAAVLGYCRGEAVYSRDCVH 675

Query: 376 TLKTKERWLREALQVKANEVPVKVIKN-SSKSKKGQDFEPEDYDEVDARGNIELYGKWQL 434
           TL +++ WL++A  V+  EVP K++K  S++++K +  EP+ +D  D    + LYG WQ 
Sbjct: 676 TLHSRDTWLKQARVVRLGEVPYKMVKGFSNRARKARLSEPQLHDHND----LGLYGHWQT 731

Query: 435 EPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFE 494
           E  + P AV+G VPRNE G V ++    +P G V + LP +  VA++L ID   A+ GF+
Sbjct: 732 EEYQPPIAVDGKVPRNEFGNVYLFLPSMMPVGCVQMTLPNLNRVARKLGIDCVQAITGFD 791

Query: 495 FRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTR 554
           F  G   PV DG +VC EF+D +L A+  E+   E +EK+++E +A   W  L+  ++ R
Sbjct: 792 FHGGYCHPVTDGYIVCEEFRDVLLAAWENEQAIIEKKEKEKKEKRALGNWKLLVRGLLIR 851

Query: 555 QRLNNCYGNNS 565
           +RL   YG  S
Sbjct: 852 ERLKLRYGAKS 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		649
224079463		868	predicted protein [Populus trichocarpa]	0.915	0.684	0.648	0.0
225453199		1103	PREDICTED: DNA repair protein complement	0.944	0.555	0.632	0.0
357492015		1052	DNA repair protein complementing XP-C ce	0.944	0.582	0.599	0.0
356552017		926	PREDICTED: uncharacterized protein LOC10	0.938	0.657	0.592	0.0
296087135		866	unnamed protein product [Vitis vinifera]	0.764	0.572	0.671	0.0
449445198		923	PREDICTED: DNA repair protein complement	0.933	0.656	0.577	0.0
449479948		923	PREDICTED: DNA repair protein complement	0.933	0.656	0.576	0.0
255582247		683	DNA repair protein xp-C / rad4, putative	0.747	0.710	0.642	0.0
297807689		868	DNA repair protein Rad4 family [Arabidop	0.807	0.603	0.568	1e-169
22326854		865	xeroderma pigmentosum group C-complement	0.807	0.605	0.571	1e-166

>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 =  788 bits (2034), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/649 (64%), Positives = 482/649 (74%), Gaps = 55/649 (8%)

Query: 1   MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGN 60
           MV +P+EV   P KS SC++K+N                      QS  SP + EL    
Sbjct: 275 MVDRPKEVFIPP-KSLSCNEKKN--------------------KIQSNDSPPAVELKDKM 313

Query: 61  LDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDL 120
           +D     A ++ SE C  K KSQ  KRKGDLEFEMQL+MA+SAT VAT +SN   DVK+ 
Sbjct: 314 VDTFPCEAQNNTSEECVTK-KSQGSKRKGDLEFEMQLQMAMSATAVAT-QSNKELDVKES 371

Query: 121 NSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHV 180
           +++S    P KR++KI + ESS+   GISTA+GSRK+G+PLYWAEVYCSGENLTGKWVHV
Sbjct: 372 SNSSDVSSPFKRIRKIANEESSSQ--GISTALGSRKIGSPLYWAEVYCSGENLTGKWVHV 429

Query: 181 DAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWD 240
           DA + I+DGEQKVEAAA ACKTSLRY+VAFAG GAKDVTRRYCMKWY+IAS+RVNS WWD
Sbjct: 430 DAVHDIVDGEQKVEAAADACKTSLRYVVAFAGLGAKDVTRRYCMKWYKIASQRVNSLWWD 489

Query: 241 AVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVE 300
           AVLAPLRELESGATGGM  +EK H +ASN  E                         NV 
Sbjct: 490 AVLAPLRELESGATGGMAHLEKPHADASNEHE-------------------------NVI 524

Query: 301 SSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPIL 360
           +S  +SF A RN++EDMEL+TRALTEPLPTNQQAYKNH LY IE+WL K QIL+PKGPIL
Sbjct: 525 ASGLNSFAATRNTIEDMELQTRALTEPLPTNQQAYKNHLLYAIEKWLTKCQILHPKGPIL 584

Query: 361 GFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEV 420
           GFCSGH VYPR+CVQTL+TKERWLRE LQVK  E+P KV+K S K KK Q  E +DY E 
Sbjct: 585 GFCSGHPVYPRACVQTLRTKERWLREGLQVKVKELPAKVVKQSGKLKKVQFSEDDDYGET 644

Query: 421 DARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAK 480
           D+ G +ELYG WQLEPL+LP AVNGIVP+NERGQVDVWSEKCLPPGTVHLRLPRV+ VAK
Sbjct: 645 DS-GVVELYGMWQLEPLQLPHAVNGIVPKNERGQVDVWSEKCLPPGTVHLRLPRVFYVAK 703

Query: 481 RLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQA 540
           RLEID APAMVGFEFRNGRS PVFDGIVVC EFKD ILEAYAEEEE+R+AEEKKR EAQA
Sbjct: 704 RLEIDYAPAMVGFEFRNGRSVPVFDGIVVCNEFKDAILEAYAEEEERRDAEEKKRNEAQA 763

Query: 541 TSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDR 600
            SRWYQLLSSI+TRQRLNN YGN    Q  SN QN      +V V S+Q      +Q D 
Sbjct: 764 ISRWYQLLSSIITRQRLNNSYGNGLLPQMPSNVQNT-NNQPDVHVGSTQ---PPGHQKDA 819

Query: 601 GDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 649
            D KL+APS   +++HEHV+L+EDQSFDEE S  TKRCHCGF++QVEEL
Sbjct: 820 KDRKLNAPSMTLTDDHEHVFLVEDQSFDEETSTRTKRCHCGFSVQVEEL 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\|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\|356552017\|ref\|XP_003544368.1\| PREDICTED: uncharacterized protein LOC100818100 [Glycine max]	Back alignment and taxonomy information

>gi\|296087135\|emb\|CBI33509.3\| unnamed protein product [Vitis vinifera]	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\|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\|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

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		649
TAIR\|locus:2174160		865	RAD4 [Arabidopsis thaliana (ta	0.530	0.397	0.565	3.9e-153
UNIPROTKB\|E2RCR3		949	XPC "Uncharacterized protein"	0.389	0.266	0.370	3.5e-55
UNIPROTKB\|E1BDJ1		932	XPC "Uncharacterized protein"	0.386	0.269	0.365	1.4e-53
MGI\|MGI:103557		930	Xpc "xeroderma pigmentosum, co	0.389	0.272	0.362	1.5e-52
UNIPROTKB\|F1N806		826	Gga.54220 "Uncharacterized pro	0.389	0.306	0.376	4.1e-51
UNIPROTKB\|E9PH69		903	XPC "DNA repair protein-comple	0.383	0.275	0.376	6.8e-51
UNIPROTKB\|Q01831		940	XPC "DNA repair protein comple	0.383	0.264	0.376	8.5e-51
UNIPROTKB\|E1BUG1		936	Gga.54220 "Uncharacterized pro	0.389	0.270	0.376	9e-51
RGD\|1305760		933	Xpc "xeroderma pigmentosum, co	0.386	0.269	0.361	4.6e-49
UNIPROTKB\|F1SPI2		944	XPC "Uncharacterized protein"	0.383	0.263	0.352	2e-47

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

 Score = 999 (356.7 bits), Expect = 3.9e-153, Sum P(2) = 3.9e-153
 Identities = 198/350 (56%), Positives = 240/350 (68%)

Query:   301 SSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPIL 360
             SS+  SF   R++LEDMEL TRALTE LPTNQQAYK+H++Y IE+WL+K QIL+PKGP+L
Sbjct:   521 SSSSSSF-GIRSALEDMELATRALTESLPTNQQAYKSHEIYAIEKWLHKNQILHPKGPVL 579

Query:   361 GFCSGHAVYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPEDYDEV 420
             GFCSGH VYPR+CVQTLKTKERWLR+ LQ+KANE               +DFE  D +  
Sbjct:   580 GFCSGHPVYPRTCVQTLKTKERWLRDGLQLKANEVPSKILKRNSKFKKVKDFEDGDNNIK 639

Query:   421 DARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAK 480
                  +ELYGKWQ+EPL LP AVNGIVP+NERGQVDVWSEKCLPPGTVHLR PR+++VAK
Sbjct:   640 GGSSCMELYGKWQMEPLCLPPAVNGIVPKNERGQVDVWSEKCLPPGTVHLRFPRIFAVAK 699

Query:   481 RLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYXXXXXXXXXXXXXXXXXQA 540
             R  ID APAMVGFE+R+G +TP+F+GIVVC EFKDTILEAY                 QA
Sbjct:   700 RFGIDYAPAMVGFEYRSGGATPIFEGIVVCTEFKDTILEAYAEEQEKKEEEERRRNEAQA 759

Query:   541 TSRWYQLLSSIVTRQRLNNCYGXXXXXXXXXXXXXVKKTNSNVGVDSSQNDWQSPNQV-D 599
              SRWYQLLSSI+TR+RL N Y                + NS   V +         +V  
Sbjct:   760 ASRWYQLLSSILTRERLKNRYANNSNDVEAKSL----EVNSETVVKAKNVKAPEKQRVAK 815

Query:   600 RGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 649
             RG+      S  + E HEHV+L E+++FDEE SV TKRC CGF+++VE++
Sbjct:   816 RGEKSRVRKSRNEDESHEHVFLDEEETFDEETSVKTKRCKCGFSVEVEQM 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

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

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

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\|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\|E1BUG1 Gga.54220 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	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\|F1SPI2 XPC "Uncharacterized protein" [Sus scrofa (taxid:9823)]	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		649
TIGR00605		713	TIGR00605, rad4, DNA repair protein rad4	3e-67
COG5535		650	COG5535, RAD4, DNA repair protein RAD4 [DNA replic	4e-37
pfam10405		75	pfam10405, BHD_3, Rad4 beta-hairpin domain 3	1e-34
smart01032		75	smart01032, BHD_3, Rad4 beta-hairpin domain 3	3e-33
pfam03835		142	pfam03835, Rad4, Rad4 transglutaminase-like domain	2e-21
smart01030		54	smart01030, BHD_1, Rad4 beta-hairpin domain 1	1e-17
pfam10403		57	pfam10403, BHD_1, Rad4 beta-hairpin domain 1	8e-17
pfam10404		56	pfam10404, BHD_2, Rad4 beta-hairpin domain 2	2e-10
smart01031		56	smart01031, BHD_2, Rad4 beta-hairpin domain 2	1e-08

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

 Score =  233 bits (595), Expect = 3e-67
 Identities = 133/452 (29%), Positives = 189/452 (41%), Gaps = 87/452 (19%)

Query: 120 LNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVH 179
           L   S+     K                       R +    +W EV+   E    KWV 
Sbjct: 339 LPGFSAYSDMDKSPIFTCEEGDKFI---------DRWITYVDFWVEVFIEQEE---KWVC 386

Query: 180 VDAANAIIDGEQKVEAAAAACKTS---LRYIVAF-AGCGAKDVTRRYCMKWYRIASK-RV 234
           VDA          V       + +   + Y+ A+      KDVTRRYC +W     K RV
Sbjct: 387 VDAV-----HSGVVPKGVTCFEPATLMMTYVFAYDRDGYVKDVTRRYCDQWSTKVRKRRV 441

Query: 235 NSAWWD-AVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYG 293
             A +      P+             + KR     +I +                     
Sbjct: 442 EKADFGETWFRPI----------FGALHKRKRTIDDIEDQ-------------------- 471

Query: 294 DSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQIL 353
                                   E   R  +E +P + Q  KNH LYV+ER L K Q L
Sbjct: 472 ------------------------EFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQAL 507

Query: 354 YP--KGPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQ 410
            P  K   LGF +G A VY R  V  LK+ E+W ++   +K  E P KV+K  ++++  +
Sbjct: 508 KPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVK--ARARTVR 565

Query: 411 DFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHL 470
             + E  +E      + LY   Q E    P AV+GIVP+N  G +D++    +P G VHL
Sbjct: 566 LPKGEAEEED-----LGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHL 620

Query: 471 RLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREA 530
           RLP     AK+L ID APA+ GF+F  G S PV DGI+VC EF++ I  A+ E E+ +E 
Sbjct: 621 RLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEE 680

Query: 531 EEKKRREAQATSRWYQLLSSIVTRQRLNNCYG 562
           +E+++   +A   W  LL  +  R+RL   YG
Sbjct: 681 KEQEKHRKRALGNWKTLLKGLRIRERLKETYG 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		649
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	99.78
PF10404		64	BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR01	99.67
KOG0909		500	consensus Peptide:N-glycanase [Posttranslational m	99.52
TIGR00598		172	rad14 DNA repair protein. This family is based on	97.35
COG5145		292	RAD14 DNA excision repair protein [DNA replication	94.54
KOG4017		274	consensus DNA excision repair protein XPA/XPAC/RAD	93.26
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	91.64
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	89.44

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

Probab=100.00  E-value=1.2e-100  Score=865.49  Aligned_cols=343  Identities=36%  Similarity=0.634  Sum_probs=306.0

Q ss_pred             CCCCCCCCceEEEEEeCCCCCCCceEEEeccc-Ccccccc-hhhhhHhhcCCCeeEEEEEcCCC-cccchhhhHhHHHH-
Q 006346          153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-  228 (649)
Q Consensus       153 ~~~~~~~P~fWvEV~~~~~~~~~rWI~VDPi~-~~Vd~~~-~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~~~-  228 (649)
                      ..++++||+||+|||++.   .++||||||++ ++++++. .+||    +.++|+|||||++|| |+|||+||+++|+. 
T Consensus       363 ~~~~~~~p~~W~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~k  435 (713)
T TIGR00605       363 IDRWITYVDFWVEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYVKDVTRRYCDQWSTK  435 (713)
T ss_pred             ccccCCCCeeEEEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCceeechhhHhhhhhhh
Confidence            346789999999999974   58999999999 8898876 4554    569999999999997 99999999999996 


Q ss_pred             hhhccCCHHHHHHH-HHhhhhcccCcCCCCcchhhhccchhhhHHHhhhccccccCCCCCcccccCCCCccccccccCcc
Q 006346          229 IASKRVNSAWWDAV-LAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSF  307 (649)
Q Consensus       229 ~~rkRv~~~Ww~~~-L~~l~~~~sga~~g~~~~~kr~~~~~~i~~~~~~~~~~~~d~f~~~v~~~g~~~~~~~~~~~~~~  307 (649)
                      +++.|++..||..+ |+++....                        .                             ...
T Consensus       436 ~r~~Rv~~~w~~~~w~~~~~~~~------------------------~-----------------------------~r~  462 (713)
T TIGR00605       436 VRKRRVEKADFGETWFRPIFGAL------------------------H-----------------------------KRK  462 (713)
T ss_pred             hheeeecccchHHHHHHHHhhhh------------------------c-----------------------------cCc
Confidence            66789999999988 76653200                        0                             000


Q ss_pred             cccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCCC--CCcceeeccee-eeecCCccccccHHHHH
Q 006346          308 VADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWL  384 (649)
Q Consensus       308 ~~~rd~~Ed~EL~~~~~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P~--~~~~G~~~GEp-VY~RsdV~~LkS~e~W~  384 (649)
                       ..+|..||.||.+++++|+||+|+++|||||+|||||||++||+|||+  ++++|+++|++ ||+|+||++|||+++||
T Consensus       463 -~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~  541 (713)
T TIGR00605       463 -RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWY  541 (713)
T ss_pred             -cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhcccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHH
Confidence             125789999999999999999999999999999999999999999994  46789999998 99999999999999999


Q ss_pred             HhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCCCCCcccCCCCCceEeecCCCCC
Q 006346          385 REALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLP  464 (649)
Q Consensus       385 r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~wQTe~y~pPp~vdG~VPkN~yGNIDlf~psMlP  464 (649)
                      ++||+||+||+|+|+|+.+++..+.   ..++.    ..+.++|||+|||++|+|||++||+||||+|||||||+|+|||
T Consensus       542 ~~GR~VK~ge~P~K~vk~r~r~~~~---~~~~~----~~~~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP  614 (713)
T TIGR00605       542 KKGRVIKLGEQPYKVVKARARTVRL---PKGEA----EEEDLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIP  614 (713)
T ss_pred             HcCCccCCCCccceEeccccccccc---ccccc----cccccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCC
Confidence            9999999999999999987543221   11111    1247999999999999999999999999999999999999999


Q ss_pred             CceEEecCccHHHHHHHcCCCEeeeeeeeeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006346          465 PGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRW  544 (649)
Q Consensus       465 ~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeFk~G~a~PvidGIVV~~E~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~W  544 (649)
                      +|||||++++++++|++||||||+|||||+|++|+++|||+|||||+||+++|++||.++++.++++++++++++||++|
T Consensus       615 ~G~vhi~~~~~~rvak~LgIDyA~AVtGFeF~~g~~~Pv~~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~W  694 (713)
T TIGR00605       615 KGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNW  694 (713)
T ss_pred             CCcEEecCccHHHHHHHhCCCeeeeeeceeecCCceeEeeceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhhhcC
Q 006346          545 YQLLSSIVTRQRLNNCYGN  563 (649)
Q Consensus       545 k~Llk~LrIreRL~~~Yg~  563 (649)
                      ++||++|||++||+++||.
T Consensus       695 k~ll~~LrIr~Rl~~~Yg~  713 (713)
T TIGR00605       695 KTLLKGLRIRERLKETYGK  713 (713)
T ss_pred             HHHHHHHHHHHHHHHHhCc
Confidence            9999999999999999994

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

>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

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

>TIGR00598 rad14 DNA repair protein	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		649
2qsh_A		538	Crystal Structure Of Rad4-Rad23 Bound To A Mismatch		6e-10
2qsf_A		533	Crystal Structure Of The Rad4-Rad23 Complex Length		7e-10

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

Back alignment and structure

Iteration: 1

Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust. Identities = 54/215 (25%), Positives = 93/215 (43%), Gaps = 19/215 (8%) Query: 312 NSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHA---- 367 + ED R +E +P + Q KNH YV+E+ + + QI+ P G+ H Sbjct: 324 DDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGK 383 Query: 368 ---VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPEDYDE-VDAR 423 VY + + LK+ +W +K G E E+ DE + + Sbjct: 384 VLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAEEEDERLYSF 440 Query: 424 GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLE 483 + ELY + PL ++ +G + +N G ++V++ +P + P A+ L Sbjct: 441 EDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLG 493 Query: 484 IDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 517 ++ APA+ F+F G + PV GIVV ++ I Sbjct: 494 VEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAI 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		649
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	5e-71
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	1e-16
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	2e-13

>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 =  238 bits (608), Expect = 5e-71
 Identities = 84/387 (21%), Positives = 140/387 (36%), Gaps = 80/387 (20%)

Query: 155 RKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEA------AAAACKTSLRYIV 208
             V  P++W EV+        KW+ VD  N     + ++ +       A   +  LRY++
Sbjct: 209 DMVKYPIFWCEVWDKFSK---KWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVI 265

Query: 209 AFAGCG-AKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNA 267
           A+      +DVTRRY               W ++ +   R         +T+ +      
Sbjct: 266 AYDRKYGCRDVTRRYA-------------QWMNSKVRKRR---------ITKDDFGEKWF 303

Query: 268 SNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEP 327
             ++ AL                                     +  ED     R  +E 
Sbjct: 304 RKVITALH-----------------------------HRKRTKIDDYEDQYFFQRDESEG 334

Query: 328 LPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHA-------VYPRSCVQTLKTK 380
           +P + Q  KNH  YV+E+ + + QI+ P     G+   H        VY +  +  LK+ 
Sbjct: 335 IPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSA 394

Query: 381 ERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 440
            +W      +K      KVIK +    KG+  E +            LY     E    P
Sbjct: 395 RQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEED----------ERLYSFEDTELYIPP 444

Query: 441 SA-VNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGR 499
            A  +G + +N  G ++V++   +P     +  P     A+ L ++ APA+  F+F  G 
Sbjct: 445 LASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGS 504

Query: 500 S-TPVFDGIVVCAEFKDTILEAYAEEE 525
           +  PV  GIVV    ++ I  A    E
Sbjct: 505 TVKPVLSGIVVAKWLREAIETAIDGIE 531

PyMOL of 2qsf

>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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		649
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	100.0
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	99.8
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	99.63

>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=1.7e-93  Score=790.73  Aligned_cols=356  Identities=25%  Similarity=0.351  Sum_probs=285.6

Q ss_pred             hhhhhhhccCcHHHHHHHHHHHHhhhhhhcccCcc--CccCCCCCCCCCcccchhhhhcccCCCCCCcCCcccccCCCCC
Q 006346           80 EKSQALKRKGDLEFEMQLEMALSATNVATSKSNIC--SDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKV  157 (649)
Q Consensus        80 ~~~~~~krkgd~~~e~q~~ma~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~st~~~~~~~  157 (649)
                      .-....+|+|+-++-+||=.||   +++.+-.++.  +-++.+........+             ++..    .....++
T Consensus       152 f~~~~~~~~Gs~d~~AqlF~aL---lRalG~~aRlV~SLqP~~f~~~k~~~~-------------~~k~----~~~~~~~  211 (533)
T 2qsf_A          152 FLRAVSKGHGDPDISVQGFVAM---LRACNVNARLIMSCQPPDFTNMKIDTS-------------LNGN----NAYKDMV  211 (533)
T ss_dssp             HHHHHHHTEECHHHHHHHHHHH---HHHTTCCEEEEEEECCCCTTCCBSCCC-------------CC-------CHHHHT
T ss_pred             HHHHHHhcCCChhHHHHHHHHH---HHHCCCceEEEeccccccccccccccC-------------cccC----Ccccccc
Confidence            3456788999999877776655   4556655552  323333321111000             0000    0112457


Q ss_pred             CCCceEEEEEeCCCCCCCceEEEecccC-cc---cccchhhhhH--hhcCCCeeEEEEEcCCC-cccchhhhHhHHHH-h
Q 006346          158 GAPLYWAEVYCSGENLTGKWVHVDAANA-II---DGEQKVEAAA--AACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-I  229 (649)
Q Consensus       158 ~~P~fWvEV~~~~~~~~~rWI~VDPi~~-~V---d~~~~~Ep~~--~~~~~~msYVVAfd~dG-akDVTrRYa~~~~~-~  229 (649)
                      .+|+||+|||++.   .++||||||+++ ++   +.+.+|||..  .++.++|+|||||+.|| |+|||+||+.+|+. +
T Consensus       212 ~~P~~W~EV~s~~---~~rWi~VDp~~~~~id~~~~~~~~Ep~~~~~~~~~~m~YViAf~~d~~~kDVT~RY~~~~~~k~  288 (533)
T 2qsf_A          212 KYPIFWCEVWDKF---SKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKV  288 (533)
T ss_dssp             TSCSEEEEEEETT---TTEEEEEESSSSCEEECCSSCCTTSCCSTTTTSSCCCCEEEEECTTCCEEECHHHHCTTCCCCC
T ss_pred             CCCeEEEEEEEcC---CCeEEEEeccccccccccccccccccccccccccCceeEEEEEcCCCceEecchhhhhchhhhh
Confidence            8999999999864   689999999985 44   4678899853  25789999999999986 99999999999984 4


Q ss_pred             hhccCC-----HHHHHHHHHhhhhcccCcCCCCcchhhhccchhhhHHHhhhccccccCCCCCcccccCCCCcccccccc
Q 006346          230 ASKRVN-----SAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAK  304 (649)
Q Consensus       230 ~rkRv~-----~~Ww~~~L~~l~~~~sga~~g~~~~~kr~~~~~~i~~~~~~~~~~~~d~f~~~v~~~g~~~~~~~~~~~  304 (649)
                      ++.|++     ..||..+|++|++.                                                       
T Consensus       289 rr~Ri~~~~~~~~W~~~~L~~~~~~-------------------------------------------------------  313 (533)
T 2qsf_A          289 RKRRITKDDFGEKWFRKVITALHHR-------------------------------------------------------  313 (533)
T ss_dssp             GGGSGGGSHHHHHHHHHHHHHHCCS-------------------------------------------------------
T ss_pred             heeeecCCcchHHHHHHHHHHHhcC-------------------------------------------------------
Confidence            556764     78999999988631                                                       


Q ss_pred             CcccccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCCCCCcceeecc-------eeeeecCCcccc
Q 006346          305 DSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG-------HAVYPRSCVQTL  377 (649)
Q Consensus       305 ~~~~~~rd~~Ed~EL~~~~~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P~~~~~G~~~G-------EpVY~RsdV~~L  377 (649)
                        ...++|..||+||+.+..+||||+|+++|||||+|||||||++||+|||+++++|+|+|       ||||+|+||++|
T Consensus       314 --~~~~~d~~Ed~el~~~~~~e~~P~s~~~fK~HP~yvLer~L~k~E~i~P~a~~~g~~~~~~k~~~~E~VY~R~~V~~l  391 (533)
T 2qsf_A          314 --KRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADL  391 (533)
T ss_dssp             --CCCHHHHHHHHHHHHHHHHSCCCSSTGGGTTCSSEEEGGGSCTTEEECTTCCCSEEEECCSTTCCEEEEEEGGGEEEC
T ss_pred             --CccccchhHHHHHHHHHhcCCCCccHHHHcCCcHhhhhhhhccceeeCCCCceeeEEecCcCCCcccceeehhhhhee
Confidence              01245778999999999999999999999999999999999999999999999999987       999999999999


Q ss_pred             ccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCC-CCCcccCCCCCceE
Q 006346          378 KTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSA-VNGIVPRNERGQVD  456 (649)
Q Consensus       378 kS~e~W~r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~wQTe~y~pPp~-vdG~VPkN~yGNID  456 (649)
                      ||+++|+++||+||+||+|+|+|+.++.+..    .++      ...+++|||+||||+|+|||+ +||+||||+|||||
T Consensus       392 ~S~e~W~~~gR~vk~ge~P~K~v~~r~~~~~----~~~------~~~~~~Ly~~~QTe~y~Pp~~~~dG~VPkN~yGNvd  461 (533)
T 2qsf_A          392 KSARQWYMNGRILKTGSRCKKVIKRTVGRPK----GEA------EEEDERLYSFEDTELYIPPLASASGEITKNTFGNIE  461 (533)
T ss_dssp             BCHHHHHTTTEEECSSCCCSEEECC----------------------CEEEBCGGGEEECCCCCCCTTCCCCCCTTSCEE
T ss_pred             ecHHHHHHcCCccCCCCeeeeEEecccCCcc----ccc------ccccccccCHHhCccccCCCCccCCcccccCCCCEE
Confidence            9999999999999999999999997653211    111      125689999999999999999 99999999999999


Q ss_pred             eecCCCCCCceEEecCccHHHHHHHcCCCEeeeeeeeeecCC-eeeeeEceEEEccccHHHHHHHHHHHH
Q 006346          457 VWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNG-RSTPVFDGIVVCAEFKDTILEAYAEEE  525 (649)
Q Consensus       457 lf~psMlP~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeFk~G-~a~PvidGIVV~~E~~e~l~~a~~e~~  525 (649)
                      ||+|+|||+|||||++++++++||+||||||+|||||+|++| +++|||+|||||+||+++|++||++.+
T Consensus       462 ~~~p~m~P~G~vhi~~~~~~~~ar~L~Idya~Av~GFef~~g~~~~Pv~~GiVV~~e~~~~l~~a~~~~~  531 (533)
T 2qsf_A          462 VFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIE  531 (533)
T ss_dssp             CSSGGGSCTTEEEEECTTHHHHHHHTTCCCEEEEEEECC------CEEEEEEEEETTSHHHHHHHHHTGG
T ss_pred             eccCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeeCCCCcceEEeCeEEEehHHHHHHHHHHHhhh
Confidence            999999999999999999999999999999999999999976 579999999999999999999997543

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

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		649
d1x3za1		320	d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Bak	8e-15
d2f4ma1		287	d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {M	1e-12

>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 = 73.8 bits (181), Expect = 8e-15
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 7/89 (7%)

Query: 159 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDV 218
               W E + +      +WVHVD+     D               + Y +AF   G  DV
Sbjct: 209 EDHVWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSIN---WNKKMSYCIAFGKDGVVDV 262

Query: 219 TRRYCMKWYRIASKRVNSAWWDAVLAPLR 247
           ++RY ++   +   ++       +   + 
Sbjct: 263 SKRYILQN-ELPRDQIKEEDLKFLCQFIT 290

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		649
d1x3za1		320	Peptide:N-glycanase 1, PNG1 {Baker's yeast(Sacchar	99.78
d2f4ma1		287	Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus)	99.72

>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=99.78  E-value=2.2e-20  Score=192.21  Aligned_cols=84  Identities=19%  Similarity=0.378  Sum_probs=75.9

Q ss_pred             CCCceEEEEEeCCCCCCCceEEEecccCcccccchhhhhHhhcCCCeeEEEEEcCCCcccchhhhHhHHHHhhhccCCHH
Q 006346          158 GAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSA  237 (649)
Q Consensus       158 ~~P~fWvEV~~~~~~~~~rWI~VDPi~~~Vd~~~~~Ep~~~~~~~~msYVVAfd~dGakDVTrRYa~~~~~~~rkRv~~~  237 (649)
                      ..+|+|+|||++.   .+|||||||+.+++|+|..|+.   +|+++|+|||||+.||++|||+||+.++ .+++.|+++.
T Consensus       208 ~~DhvW~EVys~~---~kRWIhvDpce~~id~P~lye~---gw~k~msYVIAf~~dgv~DVT~RY~~k~-~~rR~rv~E~  280 (320)
T d1x3za1         208 REDHVWCEYFSNF---LNRWVHVDSCEQSFDQPYIYSI---NWNKKMSYCIAFGKDGVVDVSKRYILQN-ELPRDQIKEE  280 (320)
T ss_dssp             TTTEEEEEEEETT---TTEEEEEETTTTEESCTHHHHT---TSCCCBCCEEEEETTEEEECHHHHCSSS-BCCCCSSCHH
T ss_pred             CCCceEEEEeecc---cCeEEEEcCCCCccCCcceecc---CCCCceEEEEEecCCcceechhhhcccc-cCccccCCHH
Confidence            3589999999975   5899999999999999999985   6899999999999999999999999885 4677899999


Q ss_pred             HHHHHHHhhhh
Q 006346          238 WWDAVLAPLRE  248 (649)
Q Consensus       238 Ww~~~L~~l~~  248 (649)
                      ||..+|.+++.
T Consensus       281 wl~~~L~~l~~  291 (320)
T d1x3za1         281 DLKFLCQFITK  291 (320)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999999864

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