Citrus Sinensis ID: 007298

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-------61

MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEEEccccccccccccHHHHHHccccEEEEEEEcccccccccHHcccccHHcccccccHHHHHHHHHHHHHccccccccccccccccccHHHHccHHHHHHHHHHHccccccccHHHHHccccHHHHHHHcccccccccccccEEEccEEEEEccccEEEcHHHHHHHHccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccEEEEccccHHHHHHHccccEEcccccEEEcccEEEEEEcEEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccEEEEccc

ccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccEEEEEEEcccHHccccEEEEcccccccccccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHccEEccccccccEEcccEEEccccEEEEccHHHHHHHHcEEccccccEEEEccccccccccHccHHccccccccccccEEEEcccccccccccccccccccccccEEEEcccccccccEEEccHHHHHHHHHHccccccEEEEEEcccccccEEEcEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccEEEEcccccEEEEEEcc

mvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskkspvscelssgnldpsssmacsdiseachpkeksqALKRKGDLEFEMQLEMALSATnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkvgaplYWAEVYcsgenltgkwvhvdaanaiIDGEQKVEAAAAACKTSLRYIVAFAgcgakdvtRRYCMKWYRIASKRVNSAWWDAVLAPlrelesgatgdlnvessakdsfvadrnsleDMELEtralteplptnqqaykNHQLYVIERWLNKYQilypkgpilgfcsghavyprscvQTLKTKERWLREALQVKAnevpvkviknsskskkgqdfepedydevdargnielygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprvYSVAKRleidsapamvgfefrngrstpvfdgIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRlnncygnnstsqsssnfqnvkktnsnvgvdssqndwqspnqvdrgdtklhapspfqseehehvyliedqsfdeensvttkrchcgftiqveel

mvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskksPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSAtnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFagcgakdvTRRYCMKWYRIASKRVNSAWWDAVLAPLRELEsgatgdlnvessakdsfvadrNSLEDMELETralteplptnqqayKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREAlqvkanevpvkviknsskskkgqdfepedydevdARGNIELygkwqleplrlpsavngivprnergqvdvwsekclppgtvhlrlprVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKrreaqatsrwYQLLSSIVTRQRLNNCYGNnstsqsssnfqnVKKTNsnvgvdssqndwQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEvpvkviknsskskkGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYaeeeekreaeekkrreaQATSRWYQLLSSIVTRQRLNNCYGnnstsqsssnfqnVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

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

**************************************************************************************************************************************************************APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRA*****PTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV************************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKR*********AQATSRWYQLLSSIVTRQRLNN******************************************************************************CHCGFTIQVEEL

*************KSFSCD**************************************************SDISEA**********KRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKN**************YDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAE*****************TSRWYQLLSSIVTRQRLNNCYGN***********NVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

***********************************************************************************************************************************************************KVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELE*****D**VE*S**DSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNS********************GNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYG***********************************************************IEDQSFDEENSVTTKRCHCGFTIQVEEL

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MVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxWYQLLSSIVTRQRLNNCYGNNSTSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL

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		609	2.2.26 [Sep-21-2011]
P51612		930	DNA repair protein comple	yes	no	0.761	0.498	0.329	2e-60
Q01831		940	DNA repair protein comple	yes	no	0.550	0.356	0.376	2e-59
Q24595		1293	DNA repair protein comple	yes	no	0.551	0.259	0.344	6e-54
Q10445		638	DNA repair protein rhp41	yes	no	0.532	0.507	0.295	9e-33
P87235		686	DNA repair protein rhp42	no	no	0.558	0.495	0.279	3e-25
P14736		754	DNA repair protein RAD4 O	yes	no	0.582	0.470	0.258	2e-24
Q7F0R1		447	Peptide-N(4)-(N-acetyl-be	no	no	0.108	0.147	0.319	5e-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 =  234 bits (596), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 169/513 (32%), Positives = 251/513 (48%), Gaps = 49/513 (9%)

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 AAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIASK-RVNSAWWDAVLAPLRELESGAT 254
             A K  + Y+V     G  +DVT+RY   W     K RV++ WW   L P R       
Sbjct: 553 KYATK-PMTYVVGIDSDGWVRDVTQRYDPAWMTATRKCRVDAEWWAETLRPYR------- 604

Query: 255 GDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILY 314
                      S + +R   ED E + + L +PLPT+   YKNH LY ++R L K+Q +Y
Sbjct: 605 -----------SLLTEREKKEDQEFQAKHLDQPLPTSISTYKNHPLYALKRHLLKFQAIY 653

Query: 315 PK-GPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKN-SSKSKKGQDF 372
           P+   +LG+C G AVY R CV TL +++ WL++A  V+  EVP K++K  S++++K +  
Sbjct: 654 PETAAVLGYCRGEAVYSRDCVHTLHSRDTWLKQARVVRLGEVPYKMVKGFSNRARKARLS 713

Query: 373 EPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRL 432
           EP+ +D  D    + LYG WQ E  + P AV+G VPRNE G V ++    +P G V + L
Sbjct: 714 EPQLHDHND----LGLYGHWQTEEYQPPIAVDGKVPRNEFGNVYLFLPSMMPVGCVQMTL 769

Query: 433 PRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEE 492
           P +  VA++L ID   A+ GF+F  G   PV DG +VC EF+D +L A+  E+   E +E
Sbjct: 770 PNLNRVARKLGIDCVQAITGFDFHGGYCHPVTDGYIVCEEFRDVLLAAWENEQAIIEKKE 829

Query: 493 KKRREAQATSRWYQLLSSIVTRQRLNNCYGNNS 525
           K+++E +A   W  L+  ++ R+RL   YG  S
Sbjct: 830 KEKKEKRALGNWKLLVRGLLIRERLKLRYGAKS 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		609
224079463		868	predicted protein [Populus trichocarpa]	0.950	0.667	0.660	0.0
225453199		1103	PREDICTED: DNA repair protein complement	0.990	0.546	0.656	0.0
357492015		1052	DNA repair protein complementing XP-C ce	0.991	0.574	0.626	0.0
356552017		926	PREDICTED: uncharacterized protein LOC10	0.985	0.647	0.620	0.0
296087135		866	unnamed protein product [Vitis vinifera]	0.786	0.553	0.689	0.0
449445198		923	PREDICTED: DNA repair protein complement	0.975	0.643	0.603	0.0
449479948		923	PREDICTED: DNA repair protein complement	0.975	0.643	0.602	0.0
255582247		683	DNA repair protein xp-C / rad4, putative	0.784	0.699	0.681	0.0
297807689		868	DNA repair protein Rad4 family [Arabidop	0.839	0.588	0.592	1e-171
10176972		856	unnamed protein product [Arabidopsis tha	0.839	0.596	0.596	1e-168

>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 =  774 bits (1999), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/624 (66%), Positives = 472/624 (75%), Gaps = 45/624 (7%)

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 AVLAPLRELESGATGDL---------------NVESSAKDSFVADRNSLEDMELETRALT 285
           AVLAPLRELESGATG +               NV +S  +SF A RN++EDMEL+TRALT
Sbjct: 490 AVLAPLRELESGATGGMAHLEKPHADASNEHENVIASGLNSFAATRNTIEDMELQTRALT 549

Query: 286 EPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLR 345
           EPLPTNQQAYKNH LY IE+WL K QIL+PKGPILGFCSGH VYPR+CVQTL+TKERWLR
Sbjct: 550 EPLPTNQQAYKNHLLYAIEKWLTKCQILHPKGPILGFCSGHPVYPRACVQTLRTKERWLR 609

Query: 346 EALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNG 405
           E LQVK  E+P KV+K S K KK Q  E +DY E D+ G +ELYG WQLEPL+LP AVNG
Sbjct: 610 EGLQVKVKELPAKVVKQSGKLKKVQFSEDDDYGETDS-GVVELYGMWQLEPLQLPHAVNG 668

Query: 406 IVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFD 465
           IVP+NERGQVDVWSEKCLPPGTVHLRLPRV+ VAKRLEID APAMVGFEFRNGRS PVFD
Sbjct: 669 IVPKNERGQVDVWSEKCLPPGTVHLRLPRVFYVAKRLEIDYAPAMVGFEFRNGRSVPVFD 728

Query: 466 GIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGNNS 525
           GIVVC EFKD ILEAYAEEEE+R+AEEKKR EAQA SRWYQLLSSI+TRQRLNN YGN  
Sbjct: 729 GIVVCNEFKDAILEAYAEEEERRDAEEKKRNEAQAISRWYQLLSSIITRQRLNNSYGNGL 788

Query: 526 TSQSSSNFQNVKKTNSNVGVDSSQNDWQSPNQVDRGDTKLHAPSPFQSEEHEHVYLIEDQ 585
             Q  SN QN      +V V S+Q      +Q D  D KL+APS   +++HEHV+L+EDQ
Sbjct: 789 LPQMPSNVQNT-NNQPDVHVGSTQ---PPGHQKDAKDRKLNAPSMTLTDDHEHVFLVEDQ 844

Query: 586 SFDEENSVTTKRCHCGFTIQVEEL 609
           SFDEE S  TKRCHCGF++QVEEL
Sbjct: 845 SFDEETSTRTKRCHCGFSVQVEEL 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\|10176972\|dbj\|BAB10190.1\| unnamed protein product [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		609
TAIR\|locus:2174160		865	RAD4 [Arabidopsis thaliana (ta	0.935	0.658	0.527	3.4e-154
UNIPROTKB\|E2RCR3		949	XPC "Uncharacterized protein"	0.415	0.266	0.370	3.5e-55
UNIPROTKB\|E1BDJ1		932	XPC "Uncharacterized protein"	0.412	0.269	0.365	1.4e-53
UNIPROTKB\|F1N806		826	Gga.54220 "Uncharacterized pro	0.415	0.306	0.376	1.7e-52
UNIPROTKB\|E1BUG1		936	Gga.54220 "Uncharacterized pro	0.415	0.270	0.376	3.7e-52
UNIPROTKB\|F1SPI2		944	XPC "Uncharacterized protein"	0.472	0.305	0.327	6.2e-51
MGI\|MGI:103557		930	Xpc "xeroderma pigmentosum, co	0.472	0.309	0.341	9.1e-46
ZFIN\|ZDB-GENE-030131-8461		879	xpc "xeroderma pigmentosum, co	0.408	0.283	0.350	5.9e-45
UNIPROTKB\|Q01831		940	XPC "DNA repair protein comple	0.472	0.306	0.344	1.3e-44
UNIPROTKB\|E9PH69		903	XPC "DNA repair protein-comple	0.472	0.318	0.344	1e-42

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

 Score = 1484 (527.5 bits), Expect = 3.4e-154, Sum P(2) = 3.4e-154
 Identities = 322/610 (52%), Positives = 395/610 (64%)

Query:    21 KENVCETSSKGSPECKYSS--PKSNNTQSK-KSPVSCELSSGNLDPSSSMACSDISEACH 77
             K  +  TS+   P+ +  S  PK +++  K KSP   +   GN   S  +  + ++ +C 
Sbjct:   275 KHGIFRTSTLMVPKQQAISSYPKKSSSHVKNKSPFE-KPQLGNPLGSDQVQDNAVNSSCE 333

Query:    78 P--KEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKK 135
                  KS   +RKGD+EFE Q+ MALSAT          +D    N  SS V   K++++
Sbjct:   334 AGMSIKSDGTRRKGDVEFERQIAMALSAT----------AD----NQQSSQVNNTKKVRE 379

Query:   136 IE--SGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKV 193
             I   S  SS S   ISTA GS+KV +PL W EVYC+GEN+ GKWVHVDA N +ID EQ +
Sbjct:   380 ITKISNSSSVSDQVISTAFGSKKVDSPLCWLEVYCNGENMDGKWVHVDAVNGMIDAEQNI 439

Query:   194 EAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGA 253
             EAAAAACKT LRY+VAFA  GAKDVTRRYC KW+ I+SKRV+S WWD VLAPL  LESGA
Sbjct:   440 EAAAAACKTVLRYVVAFAAGGAKDVTRRYCTKWHTISSKRVSSVWWDMVLAPLVHLESGA 499

Query:   254 TGD----------LN-VES--SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQL 300
             T D          LN V S  S+  S    R++LEDMEL TRALTE LPTNQQAYK+H++
Sbjct:   500 THDEDIALRNFNGLNPVSSRASSSSSSFGIRSALEDMELATRALTESLPTNQQAYKSHEI 559

Query:   301 YVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEXXXXXX 360
             Y IE+WL+K QIL+PKGP+LGFCSGH VYPR+CVQTLKTKERWLR+ LQ+KANE      
Sbjct:   560 YAIEKWLHKNQILHPKGPVLGFCSGHPVYPRTCVQTLKTKERWLRDGLQLKANEVPSKIL 619

Query:   361 XXXXXXXXGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSE 420
                      +DFE  D +       +ELYGKWQ+EPL LP AVNGIVP+NERGQVDVWSE
Sbjct:   620 KRNSKFKKVKDFEDGDNNIKGGSSCMELYGKWQMEPLCLPPAVNGIVPKNERGQVDVWSE 679

Query:   421 KCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEA 480
             KCLPPGTVHLR PR+++VAKR  ID APAMVGFE+R+G +TP+F+GIVVC EFKDTILEA
Sbjct:   680 KCLPPGTVHLRFPRIFAVAKRFGIDYAPAMVGFEYRSGGATPIFEGIVVCTEFKDTILEA 739

Query:   481 YXXXXXXXXXXXXXXXXXQATSRWYQLLSSIVTRQRLNNCYGXXXXXXXXXXXXXVKKTN 540
             Y                 QA SRWYQLLSSI+TR+RL N Y                + N
Sbjct:   740 YAEEQEKKEEEERRRNEAQAASRWYQLLSSILTRERLKNRYANNSNDVEAKSL----EVN 795

Query:   541 SNVGVDSSQNDWQSPNQV-DRGDTKLHAPSPFQSEEHEHVYLIEDQSFDEENSVTTKRCH 599
             S   V +         +V  RG+      S  + E HEHV+L E+++FDEE SV TKRC 
Sbjct:   796 SETVVKAKNVKAPEKQRVAKRGEKSRVRKSRNEDESHEHVFLDEEETFDEETSVKTKRCK 855

Query:   600 CGFTIQVEEL 609
             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

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

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\|F1SPI2 XPC "Uncharacterized protein" [Sus scrofa (taxid:9823)]	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

ZFIN\|ZDB-GENE-030131-8461 xpc "xeroderma pigmentosum, complementation group C" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

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

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

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		609
TIGR00605		713	TIGR00605, rad4, DNA repair protein rad4	7e-73
COG5535		650	COG5535, RAD4, DNA repair protein RAD4 [DNA replic	5e-44
pfam10405		75	pfam10405, BHD_3, Rad4 beta-hairpin domain 3	1e-34
smart01032		75	smart01032, BHD_3, Rad4 beta-hairpin domain 3	2e-33
pfam03835		142	pfam03835, Rad4, Rad4 transglutaminase-like domain	2e-21
smart01030		54	smart01030, BHD_1, Rad4 beta-hairpin domain 1	1e-17
pfam10403		57	pfam10403, BHD_1, Rad4 beta-hairpin domain 1	7e-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 =  247 bits (632), Expect = 7e-73
 Identities = 134/412 (32%), Positives = 187/412 (45%), Gaps = 47/412 (11%)

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-AVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQ 293
             A +      P+     GA                     ED E   R  +E +P + Q
Sbjct: 442 EKADFGETWFRPIF----GALHKRKRTIDDI----------EDQEFLRRHESEGIPKSIQ 487

Query: 294 AYKNHQLYVIERWLNKYQILYP--KGPILGFCSGHA-VYPRSCVQTLKTKERWLREALQV 350
             KNH LYV+ER L K Q L P  K   LGF +G A VY R  V  LK+ E+W ++   +
Sbjct: 488 DLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVI 547

Query: 351 KANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRN 410
           K  E P KV+K  ++++  +  + E  +E      + LY   Q E    P AV+GIVP+N
Sbjct: 548 KLGEQPYKVVK--ARARTVRLPKGEAEEED-----LGLYSYEQTELYIPPPAVDGIVPKN 600

Query: 411 ERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVC 470
             G +D++    +P G VHLRLP     AK+L ID APA+ GF+F  G S PV DGI+VC
Sbjct: 601 AYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVC 660

Query: 471 AEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYG 522
            EF++ I  A+ E E+ +E +E+++   +A   W  LL  +  R+RL   YG
Sbjct: 661 EEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKETYG 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		609
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:	99.89
PF10403		57	BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR01	99.79
PF10404		64	BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR01	99.66
KOG0909		500	consensus Peptide:N-glycanase [Posttranslational m	99.6
TIGR00598		172	rad14 DNA repair protein. This family is based on	97.43
COG5145		292	RAD14 DNA excision repair protein [DNA replication	94.86
KOG4017		274	consensus DNA excision repair protein XPA/XPAC/RAD	93.2
smart00460		68	TGc Transglutaminase/protease-like homologues. Tra	92.79
PF01841		113	Transglut_core: Transglutaminase-like superfamily;	92.64

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

Probab=100.00  E-value=2.7e-100  Score=857.27  Aligned_cols=343  Identities=36%  Similarity=0.634  Sum_probs=305.5

Q ss_pred             CCCCCCCCceEEEEEeCCCCCCCceEEEeccc-ccccCcc-hhhhhHHhcCCCceEEEEEcCCC-cccchhhhHhhHHH-
Q 007298          153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-  228 (609)
Q Consensus       153 ~~~~~~~P~fWvEVy~~~e~~~~rWI~VDPv~-~~vd~p~-~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~~k-  228 (609)
                      ...+++||+||+|||++.   .++||||||++ ++++++. .+|+    +.++|+|||||++|| |+|||+||+.+|+. 
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            345799999999999975   68999999999 8898876 4454    469999999999987 99999999999985 


Q ss_pred             hhhccCCHHHHHHH-HhhhhhcccCCCCCccccccccCcccccCCchHHHHHHHHhccCCCCCChhhhccCCceeehhcc
Q 007298          229 IASKRVNSAWWDAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWL  307 (609)
Q Consensus       229 ~~rkRv~~~Ww~~~-L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~~~~~~e~iPtsi~~fKnHP~YVLer~L  307 (609)
                      +++.|++..||..+ |+++...-.             ++. ..+|..||.||.++.++|+||+|+++|||||+|||||||
T Consensus       436 ~r~~Rv~~~w~~~~w~~~~~~~~~-------------~r~-~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L  501 (713)
T TIGR00605       436 VRKRRVEKADFGETWFRPIFGALH-------------KRK-RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHL  501 (713)
T ss_pred             hheeeecccchHHHHHHHHhhhhc-------------cCc-cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhc
Confidence            77889998888777 666542110             111 127899999999999999999999999999999999999


Q ss_pred             ccccccCCC--CCcceeeccee-eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCcccccccc
Q 007298          308 NKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARG  384 (609)
Q Consensus       308 kk~EvI~P~--~~v~G~~~GEp-VY~RsdV~~LkS~e~W~r~GR~VK~gE~PlK~vk~~~~~~k~~~~~~~~~~e~~~~~  384 (609)
                      ++||+|||+  ++++|+++|++ ||+|+||+.|||+++|+++||+||+||+|+|+|+.+++..+.   ..++.    ...
T Consensus       502 ~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~r~r~~~~---~~~~~----~~~  574 (713)
T TIGR00605       502 KKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKARARTVRL---PKGEA----EEE  574 (713)
T ss_pred             ccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEeccccccccc---ccccc----ccc
Confidence            999999994  46789999998 999999999999999999999999999999999977432211   11111    124


Q ss_pred             ccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCceeeecCccHHHHHHHcCCCeeeeeeeeeecCCeeeeee
Q 007298          385 NIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVF  464 (609)
Q Consensus       385 ~~~LYg~wQTe~y~pPpvvdG~VPkN~yGNIDlf~p~MlP~G~VHI~~~~i~kvAkkLgIDyA~AVtGFeFk~G~a~Pvi  464 (609)
                      .++|||+|||++|+|||++||+||||+|||||||+|+|||+|||||++++|+++|++||||||+|||||+|++|+++|||
T Consensus       575 ~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP~G~vhi~~~~~~rvak~LgIDyA~AVtGFeF~~g~~~Pv~  654 (713)
T TIGR00605       575 DLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVL  654 (713)
T ss_pred             ccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeecCCceeEee
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 007298          465 DGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN  523 (609)
Q Consensus       465 dGIVV~~e~~~~l~~a~~e~~e~~~~~e~~~~e~~aL~~Wk~Ll~~L~Ir~RL~~~Yg~  523 (609)
                      +|||||+||+++|++||.++++.++++++++++++||.+|++||++|||++||+++||.
T Consensus       655 ~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~Wk~ll~~LrIr~Rl~~~Yg~  713 (713)
T TIGR00605       655 DGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKETYGK  713 (713)
T ss_pred             ceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            99999999999999999999999999999999999999999999999999999999994

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		609
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		6e-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 = 89.4 bits (220), Expect = 5e-18, Method: Compositional matrix adjust. Identities = 85/344 (24%), Positives = 140/344 (40%), Gaps = 54/344 (15%) Query: 157 VGAPLYWAEVYCSGENLTGKWVHVDAANAI----IDGEQKVEAAAAAC--KTSLRYIVAF 210 V P++W EV+ + + KW+ VD N + K+ AC + LRY++A+ Sbjct: 216 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 272 Query: 211 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 262 G +DVTRRY +W RI W+ V+ L + D Sbjct: 273 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 326 Query: 263 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 322 ED R +E +P + Q KNH YV+E+ + + QI+ P G+ Sbjct: 327 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 374 Query: 323 CSGHA-------VYPRSCVQTLKTKERWLREALQVKANEXXXXXXXXXXXXXXGQDFEPE 375 H VY + + LK+ +W +K G E E Sbjct: 375 LKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKG---EAE 431 Query: 376 DYDE-VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPR 434 + DE + + + ELY + PL ++ +G + +N G ++V++ +P + P Sbjct: 432 EEDERLYSFEDTELY----IPPL---ASASGEITKNTFGNIEVFAPTMIPGNCCLVENPV 484 Query: 435 VYSVAKRLEIDSAPAMVGFEFRNGRST-PVFDGIVVCAEFKDTI 477 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		609
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	3e-79
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	2e-21
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	6e-16

>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 =  259 bits (662), Expect = 3e-79
 Identities = 84/353 (23%), Positives = 134/353 (37%), Gaps = 52/353 (14%)

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

Query: 209 AFAGCG-AKDVTRRYCMKW------YRIASKRVNSAWWDAVLAPLRELESGATGDLNVES 261
           A+      +DVTRRY           RI        W+  V+  L               
Sbjct: 266 AYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHH------------- 312

Query: 262 SAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILG 321
                     +  ED     R  +E +P + Q  KNH  YV+E+ + + QI+ P     G
Sbjct: 313 ----RKRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECG 368

Query: 322 FCSGHA-------VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEP 374
           +   H        VY +  +  LK+  +W      +K      KVIK +    KG+  E 
Sbjct: 369 YLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPKGEAEEE 428

Query: 375 EDYDEVDARGNIELYGKWQLEPLRLPSA-VNGIVPRNERGQVDVWSEKCLPPGTVHLRLP 433
           +            LY     E    P A  +G + +N  G ++V++   +P     +  P
Sbjct: 429 D----------ERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENP 478

Query: 434 RVYSVAKRLEIDSAPAMVGFEFRNGRS-TPVFDGIVVCAEFKDTILEAYAEEE 485
                A+ L ++ APA+  F+F  G +  PV  GIVV    ++ I  A    E
Sbjct: 479 VAIKAARFLGVEFAPAVTSFKFERGSTVKPVLSGIVVAKWLREAIETAIDGIE 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		609
2qsf_A		533	RAD4, DNA repair protein RAD4; alpha-beta structur	100.0
1x3z_A		335	Peptide: N-glycanase; hydrolase-hydrolase inhibito	99.81
2f4m_A		295	Peptide N-glycanase; glycoproteins, ubiquitin-depe	99.63
3isr_A		293	Transglutaminase-like enzymes, putative cysteine;	80.84

>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=1.8e-93  Score=785.87  Aligned_cols=355  Identities=25%  Similarity=0.364  Sum_probs=286.8

Q ss_pred             hhhhhhccCcHHHHHHHHHHHHhhhhhhcccCcc--CcccCCCCCCCCcccchhhhhcccCCCCCCCCCCccccCCCCCC
Q 007298           81 KSQALKRKGDLEFEMQLEMALSATNVATSKSNIC--SDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVG  158 (609)
Q Consensus        81 ~~~~~krkgd~~~e~q~~ma~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~st~~~~~~~~  158 (609)
                      .+...+|+|+-++-+||=.||   +++.+..++.  +-++.+++......+             +  ....  ....++.
T Consensus       153 ~~~~~~~~Gs~d~~AqlF~aL---lRalG~~aRlV~SLqP~~f~~~k~~~~-------------~--~k~~--~~~~~~~  212 (533)
T 2qsf_A          153 LRAVSKGHGDPDISVQGFVAM---LRACNVNARLIMSCQPPDFTNMKIDTS-------------L--NGNN--AYKDMVK  212 (533)
T ss_dssp             HHHHHHTEECHHHHHHHHHHH---HHHTTCCEEEEEEECCCCTTCCBSCCC-------------C--C-----CHHHHTT
T ss_pred             HHHHHhcCCChhHHHHHHHHH---HHHCCCceEEEeccccccccccccccC-------------c--ccCC--ccccccC
Confidence            456778999999777775555   5666666653  333333322111000             0  0000  1123578


Q ss_pred             CCceEEEEEeCCCCCCCceEEEecccc-cc---cCcchhhhhH--HhcCCCceEEEEEcCCC-cccchhhhHhhHH-Hhh
Q 007298          159 APLYWAEVYCSGENLTGKWVHVDAANA-II---DGEQKVEAAA--AACKTSLRYIVAFAGCG-AKDVTRRYCMKWY-RIA  230 (609)
Q Consensus       159 ~P~fWvEVy~~~e~~~~rWI~VDPv~~-~v---d~p~~~Ep~~--~~~~~~msYVVAfd~dG-akDVTrRYa~~~~-k~~  230 (609)
                      +|+||+|||++.   +++||||||+++ ++   +.+.+|||..  .++.++|+|||||+.|| |+|||+||+.+|. +++
T Consensus       213 ~P~~W~EV~s~~---~~rWi~VDp~~~~~id~~~~~~~~Ep~~~~~~~~~~m~YViAf~~d~~~kDVT~RY~~~~~~k~r  289 (533)
T 2qsf_A          213 YPIFWCEVWDKF---SKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVR  289 (533)
T ss_dssp             SCSEEEEEEETT---TTEEEEEESSSSCEEECCSSCCTTSCCSTTTTSSCCCCEEEEECTTCCEEECHHHHCTTCCCCCG
T ss_pred             CCeEEEEEEEcC---CCeEEEEeccccccccccccccccccccccccccCceeEEEEEcCCCceEecchhhhhchhhhhh
Confidence            999999999864   689999999985 44   4678899853  24779999999999976 9999999999997 455


Q ss_pred             hccCC-----HHHHHHHHhhhhhcccCCCCCccccccccCcccccCCchHHHHHHHHhccCCCCCChhhhccCCceeehh
Q 007298          231 SKRVN-----SAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIER  305 (609)
Q Consensus       231 rkRv~-----~~Ww~~~L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~~~~~~e~iPtsi~~fKnHP~YVLer  305 (609)
                      +.|+.     +.||..+|+.|++.                 ...++|..||+||+.+.++||||+|+++|||||+|||||
T Consensus       290 r~Ri~~~~~~~~W~~~~L~~~~~~-----------------~~~~~d~~Ed~el~~~~~~e~~P~s~~~fK~HP~yvLer  352 (533)
T 2qsf_A          290 KRRITKDDFGEKWFRKVITALHHR-----------------KRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQ  352 (533)
T ss_dssp             GGSGGGSHHHHHHHHHHHHHHCCS-----------------CCCHHHHHHHHHHHHHHHHSCCCSSTGGGTTCSSEEEGG
T ss_pred             eeeecCCcchHHHHHHHHHHHhcC-----------------CccccchhHHHHHHHHHhcCCCCccHHHHcCCcHhhhhh
Confidence            66764     78999999988742                 234578899999999999999999999999999999999


Q ss_pred             ccccccccCCCCCcceeecc-------eeeeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCcc
Q 007298          306 WLNKYQILYPKGPILGFCSG-------HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYD  378 (609)
Q Consensus       306 ~Lkk~EvI~P~~~v~G~~~G-------EpVY~RsdV~~LkS~e~W~r~GR~VK~gE~PlK~vk~~~~~~k~~~~~~~~~~  378 (609)
                      ||++||+|||+++++|+|+|       ||||+|+||++|||+++|+++||+||+||+|+|+|+.++.+..    .++   
T Consensus       353 ~L~k~E~i~P~a~~~g~~~~~~k~~~~E~VY~R~~V~~l~S~e~W~~~gR~vk~ge~P~K~v~~r~~~~~----~~~---  425 (533)
T 2qsf_A          353 DIKQTQIVKPGCKECGYLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKRTVGRPK----GEA---  425 (533)
T ss_dssp             GSCTTEEECTTCCCSEEEECCSTTCCEEEEEEGGGEEECBCHHHHHTTTEEECSSCCCSEEECC----------------
T ss_pred             hhccceeeCCCCceeeEEecCcCCCcccceeehhhhheeecHHHHHHcCCccCCCCeeeeEEecccCCcc----ccc---
Confidence            99999999999999999987       9999999999999999999999999999999999987653211    111   


Q ss_pred             ccccccccccccccccccCCCCCC-CCCCccCCCCCceEeecCCCCCCceeeecCccHHHHHHHcCCCeeeeeeeeeecC
Q 007298          379 EVDARGNIELYGKWQLEPLRLPSA-VNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRN  457 (609)
Q Consensus       379 e~~~~~~~~LYg~wQTe~y~pPpv-vdG~VPkN~yGNIDlf~p~MlP~G~VHI~~~~i~kvAkkLgIDyA~AVtGFeFk~  457 (609)
                         ....++|||+||||+|+|||+ +||+||||+|||||||+|+|||+|||||++++++++||+||||||+|||||+|++
T Consensus       426 ---~~~~~~Ly~~~QTe~y~Pp~~~~dG~VPkN~yGNvd~~~p~m~P~G~vhi~~~~~~~~ar~L~Idya~Av~GFef~~  502 (533)
T 2qsf_A          426 ---EEEDERLYSFEDTELYIPPLASASGEITKNTFGNIEVFAPTMIPGNCCLVENPVAIKAARFLGVEFAPAVTSFKFER  502 (533)
T ss_dssp             ------CEEEBCGGGEEECCCCCCCTTCCCCCCTTSCEECSSGGGSCTTEEEEECTTHHHHHHHTTCCCEEEEEEECC--
T ss_pred             ---ccccccccCHHhCccccCCCCccCCcccccCCCCEEeccCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeeCC
Confidence               135789999999999999999 9999999999999999999999999999999999999999999999999999997


Q ss_pred             C-eeeeeeceEEEccccHHHHHHHHHHHH
Q 007298          458 G-RSTPVFDGIVVCAEFKDTILEAYAEEE  485 (609)
Q Consensus       458 G-~a~PvidGIVV~~e~~~~l~~a~~e~~  485 (609)
                      | +++|||+|||||+||+++|++||++.+
T Consensus       503 g~~~~Pv~~GiVV~~e~~~~l~~a~~~~~  531 (533)
T 2qsf_A          503 GSTVKPVLSGIVVAKWLREAIETAIDGIE  531 (533)
T ss_dssp             ----CEEEEEEEEETTSHHHHHHHHHTGG
T ss_pred             CCcceEEeCeEEEehHHHHHHHHHHHhhh
Confidence            5 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

>3isr_A Transglutaminase-like enzymes, putative cysteine; protease, hutchinsoni MCSG, structural genomics; 1.90A {Cytophaga hutchinsonii}	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		609
d1x3za1		320	d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Bak	7e-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 = 79.6 bits (196), Expect = 7e-17
 Identities = 21/122 (17%), Positives = 42/122 (34%), Gaps = 13/122 (10%)

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

Query: 219 TRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDME 278
           ++RY ++   +   ++       +   + +            +  +   +A R+  E +E
Sbjct: 263 SKRYILQN-ELPRDQIKEEDLKFLCQFITKRLR------YSLNDDEIYQLACRDEQEQIE 315

Query: 279 LE 280
           L 
Sbjct: 316 LI 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		609
d1x3za1		320	Peptide:N-glycanase 1, PNG1 {Baker's yeast(Sacchar	99.77
d2f4ma1		287	Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus)	99.74

>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=99.77  E-value=5e-20  Score=188.27  Aligned_cols=83  Identities=19%  Similarity=0.387  Sum_probs=75.7

Q ss_pred             CCceEEEEEeCCCCCCCceEEEecccccccCcchhhhhHHhcCCCceEEEEEcCCCcccchhhhHhhHHHhhhccCCHHH
Q 007298          159 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAW  238 (609)
Q Consensus       159 ~P~fWvEVy~~~e~~~~rWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~dGakDVTrRYa~~~~k~~rkRv~~~W  238 (609)
                      ..|+|+|||++.   .++|||||||++++|+|.+|+.+   |+++|+|||||+.||++|||+||+.+| .+++.|+.+.|
T Consensus       209 ~DhvW~EVys~~---~kRWIhvDpce~~id~P~lye~g---w~k~msYVIAf~~dgv~DVT~RY~~k~-~~rR~rv~E~w  281 (320)
T d1x3za1         209 EDHVWCEYFSNF---LNRWVHVDSCEQSFDQPYIYSIN---WNKKMSYCIAFGKDGVVDVSKRYILQN-ELPRDQIKEED  281 (320)
T ss_dssp             TTEEEEEEEETT---TTEEEEEETTTTEESCTHHHHTT---SCCCBCCEEEEETTEEEECHHHHCSSS-BCCCCSSCHHH
T ss_pred             CCceEEEEeecc---cCeEEEEcCCCCccCCcceeccC---CCCceEEEEEecCCcceechhhhcccc-cCccccCCHHH
Confidence            468999999975   58999999999999999999876   899999999999999999999999985 46788899999


Q ss_pred             HHHHHhhhhh
Q 007298          239 WDAVLAPLRE  248 (609)
Q Consensus       239 w~~~L~~l~~  248 (609)
                      |..+|..++.
T Consensus       282 l~~~L~~l~~  291 (320)
T d1x3za1         282 LKFLCQFITK  291 (320)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999998875

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