Citrus Sinensis ID: 005629

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------
MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG
cccccccHHHccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHccccccccccccccccHHHHccccccccccccccccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEccccccccccEEEcccccccccccccccHHHHccccEEEEEEEcccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccccccccHHcccccHHHHHHHHHHHcccccccHHHHHcccHHHHHHHHHcccccccccccccEEccEEEEEcccccccccHHHHHHHcccccccccccccccc
cccccccccccccccccHHccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccEEEcccccccccccccccccccccccHHHcccccccccccccHccccccccccccccccccccccccccccEEEEEEcccHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHccccHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcEEEcccccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccccccEcccccccccccccccccccccccccEEEEEEEcccHHccccEEEEcccccccccccccccccccccccEEEEEEEccccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHcccccccccHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHccEEccccccccEEcccEEEccccEEEEccHHHHHHHccEEccccccEEEEcc
mrtrqdsktqkdqasgkestvrgalrdsesshnetgtlaetSREGVGKFLRHVnarsssrskkqdcAVGLTTSVLkvsgkqevdkrvtwsdvdahgcsrdamgntlreldegrlqdnvldggeemydsdwedgsipvacskenhpesdikgvtiefdaadsvtkkpvrrasAEDKELAELVHKVHLLCLLARgrlidsvcddplIQASLLSLLPSYLLKISEVSKLTANALSPivswfhdnfhvrssvstrrSFHSDLAHAlesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgggifnaptlmvakpeevlaspvksfscdkkenvcetsskgspeckysspksnntqskkspvscelssgnldpsssmacsdiseachpkeksqALKRKGDLEFEMQLEMALSATnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkvgaplYWAEVYcsgenltgkwvhvdaanaiIDGEQKVEAAAAACKTSLRYIVAFAgcgakdvtRRYCMKWYRIASKRVNSAWWDAVLAPlrelesgatgdlnvessakdsfvadrnsleDMELEtralteplptnqqaykNHQLYVIERWLNKYQilypkgpilgfcsghavyprscvQTLKTKERWLREALQVKanevpvkvcsg
mrtrqdsktqkdqasgkestvrgalrdsesshnetgtlaetsregvGKFLRHVnarsssrskkqdcavglttsvlkvsgkqevdkrvtwsdvdahgcsrdamgntlreldegrlQDNVLDGGEEMYDSDWEDGSIPVACSKenhpesdikgvtiefdaadsvtkkpVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHalesregtpEEIAALSVALFRALKLTTRFVSILDvaslkpeadknvssnqdssrvgGGIFNAPTLMVAKPEEVLASpvksfscdkkenvcetsskgspeckysspksnntqskksPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSAtnvatsksnicsdvkdlnsnsstvlpvkrlkkiesgesstsclgistavgsrkVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFagcgakdvTRRYCMKWYRIASKRVNSAWWDAVLAPLRELEsgatgdlnvessakdsfvadrNSLEDMELETralteplptnqqayKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREAlqvkanevpvkvcsg
MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQAsllsllpsyllKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG
*****************************************************************CAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGC*******************************************************************************LAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSV**********************EIAALSVALFRALKLTTRFVSILDVAS*********************IFNAPTLMV**********************************************************************************************************************************************CLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLREL********************************************AYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEV*******
*********************************************************************************************************************************WEDG********************************************AELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHV*************LAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVAS******************************************************************************************************************************************************************************************APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMEL***************YKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCS*
******************************************REGVGKFLRHV**************VGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAA**************DKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVR***********DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK**************RVGGGIFNAPTLMVAKPEEVLASPVKSFSCD**************************************************SDISEA**********KRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG
***************************************************************************************************************************EMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLK**************************************************************************************************************************************************************************************VGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MRTRQDSKTQKDQASGKESTVRGALRDSESSHNETGTLAETSREGVGKFLRHVNARSSSRSKKQDCAVGLTTSVLKVSGKQEVDKRVTWSDVDAHGCSRDAMGNTLRELDEGRLQDNVLDGGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG
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 ?
Query687 2.2.26 [Sep-21-2011]
P51612 930 DNA repair protein comple yes no 0.684 0.505 0.301 6e-43
Q01831 940 DNA repair protein comple yes no 0.256 0.187 0.359 4e-28
Q24595 1293 DNA repair protein comple yes no 0.264 0.140 0.345 8e-22
Q10445 638 DNA repair protein rhp41 yes no 0.263 0.283 0.290 2e-14
P14736 754 DNA repair protein RAD4 O yes no 0.241 0.220 0.254 1e-09
Q7F0R1447 Peptide-N(4)-(N-acetyl-be no no 0.096 0.147 0.319 3e-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 =  176 bits (446), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 167/553 (30%), Positives = 239/553 (43%), Gaps = 83/553 (15%)

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

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

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

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

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

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

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

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

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

Query: 675 VKANEVPVKVCSG 687
           V+  EVP K+  G
Sbjct: 690 VRLGEVPYKMVKG 702
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|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 ?
Query687
225453199 1103 PREDICTED: DNA repair protein complement 0.944 0.588 0.633 0.0
224079463 868 predicted protein [Populus trichocarpa] 0.874 0.692 0.603 0.0
255582247683 DNA repair protein xp-C / rad4, putative 0.754 0.758 0.653 0.0
356552017 926 PREDICTED: uncharacterized protein LOC10 0.944 0.700 0.545 0.0
449445198 923 PREDICTED: DNA repair protein complement 0.912 0.679 0.543 1e-166
449479948 923 PREDICTED: DNA repair protein complement 0.912 0.679 0.543 1e-165
22326854 865 xeroderma pigmentosum group C-complement 0.854 0.678 0.508 1e-157
297807689 868 DNA repair protein Rad4 family [Arabidop 0.867 0.686 0.505 1e-154
357141401 889 PREDICTED: DNA repair protein complement 0.812 0.627 0.481 1e-142
115476494 880 Os08g0427500 [Oryza sativa Japonica Grou 0.807 0.630 0.464 1e-137
>gi|225453199|ref|XP_002275277.1| PREDICTED: DNA repair protein complementing XP-C cells-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  771 bits (1990), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 427/674 (63%), Positives = 511/674 (75%), Gaps = 25/674 (3%)

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

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

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

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

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

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

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

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

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

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

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

Query: 671 EALQVKANEVPVKV 684
           E LQVKA+E P KV
Sbjct: 840 EGLQVKADEHPTKV 853

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224079463|ref|XP_002305874.1| predicted protein [Populus trichocarpa] gi|222848838|gb|EEE86385.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|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|356552017|ref|XP_003544368.1| PREDICTED: uncharacterized protein LOC100818100 [Glycine max] 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|22326854|ref|NP_197166.2| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|79327993|ref|NP_001031894.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|17065358|gb|AAL32833.1| Unknown protein [Arabidopsis thaliana] gi|34098839|gb|AAQ56802.1| At5g16630 [Arabidopsis thaliana] gi|332004936|gb|AED92319.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] gi|332004937|gb|AED92320.1| xeroderma pigmentosum group C-complementing protein [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|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|357141401|ref|XP_003572211.1| PREDICTED: DNA repair protein complementing XP-C cells homolog [Brachypodium distachyon] Back     alignment and taxonomy information
>gi|115476494|ref|NP_001061843.1| Os08g0427500 [Oryza sativa Japonica Group] gi|38175490|dbj|BAD01186.1| putative xeroderma pigmentosum group C protein [Oryza sativa Japonica Group] gi|38175770|dbj|BAD01464.1| putative xeroderma pigmentosum group C protein [Oryza sativa Japonica Group] gi|113623812|dbj|BAF23757.1| Os08g0427500 [Oryza sativa Japonica Group] 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 ?
Query687
TAIR|locus:2174160 865 RAD4 [Arabidopsis thaliana (ta 0.471 0.374 0.548 4.1e-149
MGI|MGI:103557 930 Xpc "xeroderma pigmentosum, co 0.950 0.702 0.252 2.2e-42
RGD|1305760 933 Xpc "xeroderma pigmentosum, co 0.806 0.593 0.270 3.6e-34
UNIPROTKB|Q01831 940 XPC "DNA repair protein comple 0.927 0.677 0.260 2.9e-31
UNIPROTKB|E9PH69 903 XPC "DNA repair protein-comple 0.740 0.563 0.271 1.2e-30
UNIPROTKB|E1BDJ1 932 XPC "Uncharacterized protein" 0.203 0.150 0.377 2.8e-30
UNIPROTKB|F1N806 826 Gga.54220 "Uncharacterized pro 0.698 0.581 0.278 1.3e-29
UNIPROTKB|F1SPI2 944 XPC "Uncharacterized protein" 0.206 0.150 0.360 1.5e-29
UNIPROTKB|E1BUG1 936 Gga.54220 "Uncharacterized pro 0.698 0.512 0.278 2.3e-29
UNIPROTKB|E2RCR3 949 XPC "Uncharacterized protein" 0.231 0.167 0.357 7.8e-28
TAIR|locus:2174160 RAD4 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 882 (315.5 bits), Expect = 4.1e-149, Sum P(2) = 4.1e-149
 Identities = 197/359 (54%), Positives = 242/359 (67%)

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

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

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

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

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

Query:   626 YVIERWLNKYQILYPKGPILGFCSGHAVYPRSCVQTLKTKERWLREALQVKANEVPVKV 684
             Y IE+WL+K QIL+PKGP+LGFCSGH VYPR+CVQTLKTKERWLR+ LQ+KANEVP K+
Sbjct:   560 YAIEKWLHKNQILHPKGPVLGFCSGHPVYPRTCVQTLKTKERWLRDGLQLKANEVPSKI 618
GO:0003677 "DNA binding" evidence=IEA
GO:0003684 "damaged DNA binding" evidence=IEA;ISS
GO:0005634 "nucleus" evidence=ISM;IEA;ISS
GO:0006289 "nucleotide-excision repair" evidence=IEA;ISS
GO:0009507 "chloroplast" evidence=IDA
MGI|MGI:103557 Xpc "xeroderma pigmentosum, complementation group C" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1305760 Xpc "xeroderma pigmentosum, complementation group C" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|Q01831 XPC "DNA repair protein complementing XP-C cells" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|E9PH69 XPC "DNA repair protein-complementing XP-C cells" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|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|F1SPI2 XPC "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|E1BUG1 Gga.54220 "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E2RCR3 XPC "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

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

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query687
TIGR00605 713 TIGR00605, rad4, DNA repair protein rad4 1e-33
pfam03835142 pfam03835, Rad4, Rad4 transglutaminase-like domain 8e-22
smart0103054 smart01030, BHD_1, Rad4 beta-hairpin domain 1 2e-18
pfam1040357 pfam10403, BHD_1, Rad4 beta-hairpin domain 1 2e-17
COG5535 650 COG5535, RAD4, DNA repair protein RAD4 [DNA replic 7e-15
pfam01841108 pfam01841, Transglut_core, Transglutaminase-like s 2e-04
pfam1040456 pfam10404, BHD_2, Rad4 beta-hairpin domain 2 8e-04
smart0103156 smart01031, BHD_2, Rad4 beta-hairpin domain 2 0.001
>gnl|CDD|233048 TIGR00605, rad4, DNA repair protein rad4 Back     alignment and domain information 
 Score =  136 bits (345), Expect = 1e-33
 Identities = 127/559 (22%), Positives = 182/559 (32%), Gaps = 78/559 (13%)

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

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

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

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

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

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

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

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

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

Query: 666 ERWLREALQVKANEVPVKV 684
           E+W ++   +K  E P KV
Sbjct: 538 EQWYKKGRVIKLGEQPYKV 556

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|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|227822 COG5535, RAD4, DNA repair protein RAD4 [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|216735 pfam01841, Transglut_core, Transglutaminase-like superfamily 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 687
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
PF03835145 Rad4: Rad4 transglutaminase-like domain; InterPro: 99.9
PF1040357 BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR01 99.79
KOG0909500 consensus Peptide:N-glycanase [Posttranslational m 99.76
TIGR00605 713 rad4 DNA repair protein rad4. This family is based 98.78
PF1040464 BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR01 98.29
KOG2179669 consensus Nucleotide excision repair complex XPC-H 97.29
PF01841113 Transglut_core: Transglutaminase-like superfamily; 96.54
COG5535650 RAD4 DNA repair protein RAD4 [DNA replication, rec 95.73
smart0046068 TGc Transglutaminase/protease-like homologues. Tra 95.69
COG1305319 Transglutaminase-like enzymes, putative cysteine p 93.05
smart0046068 TGc Transglutaminase/protease-like homologues. Tra 87.13
PF01841113 Transglut_core: Transglutaminase-like superfamily; 86.85
>TIGR00605 rad4 DNA repair protein rad4 Back     alignment and domain information 
Probab=100.00  E-value=7.3e-76  Score=670.31  Aligned_cols=430  Identities=23%  Similarity=0.327  Sum_probs=306.4

Q ss_pred             CCCCCCCCCccccCCCCCCCCCCCCCCCCCCeEEEEecCCcc------ccccccccCHHHHHHHHHHHHHHHHHHHHhhH
Q 005629          121 GGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSV------TKKPVRRASAEDKELAELVHKVHLLCLLARGR  194 (687)
Q Consensus       121 ~~deddd~dWEdV~~~~~~~~~~~p~~~~~~leI~l~~~~~~------kK~~~RR~s~~eKe~r~~~HKvHLLCLLah~~  194 (687)
                      ++++.+.+++|+|.+.....       .-++..++|.+....      .+...+-++.++|+.|+.||++||||||.|+.
T Consensus        90 ~~~~~~~~~~e~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~eR~~R~~iH~~~ll~ll~h~~  162 (713)
T TIGR00605        90 REEDYDSREFEDVYLSNLVA-------EFETISVEIKPSSKAESDDDAETLSRNVCSNEARKDRKYIHILYLLCLMVHLF  162 (713)
T ss_pred             cccccchhhhhhhhhccccc-------ccCcccccccccchhhhhhHHHHHHHhhccHHHHHHHHHHHHHHHHHHhhhhH
Confidence            34555677999987643111       122233333322111      11112237899999999999999999999999


Q ss_pred             HHHhhcCc-HHHHHHHhhcCchhhhcccCcc---------hhhHhhhhHHHHHhhhceeeccCCCcc-------------
Q 005629          195 LIDSVCDD-PLIQASLLSLLPSYLLKISEVS---------KLTANALSPIVSWFHDNFHVRSSVSTR-------------  251 (687)
Q Consensus       195 ~RN~wcnd-~~lqa~llSlLP~~~~~~~~~~---------~~~~~~L~~L~~Wf~~~F~vt~~~~~~-------------  251 (687)
                      +||.|||| +++|+.|..+||.++...+++.         ..+..+|+.|+.-|+..|+|+.+....             
T Consensus       163 ~RN~w~n~~~~~~~~L~~~~p~k~~~~l~p~~~~~~~~~s~s~~~~~~~l~~~~kk~~~it~~g~~~~~~~~~~~~~~~~  242 (713)
T TIGR00605       163 TRNEWSLSAPLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRKPLVEKLKKCMETWQKGLRKTTKGLLKLLNGGR  242 (713)
T ss_pred             hhhhhhCChHHHhHHHhhhCCHHHHHhcCccccccccccchhhhhhhHHHHHhhhhcchhcccccccCcccccccchhhH
Confidence            99999999 7999999999999998776542         235789999999999999999864111             


Q ss_pred             cch--HHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEEeeccccCCcccccccCCCCCCCCCCCCccCCCCccccC
Q 005629          252 RSF--HSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAK  329 (687)
Q Consensus       252 ~~~--~~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~SLqpl~lk~~~~k~~~~~~~~~~~~~~~~~~~~~~~~k  329 (687)
                      ..|  ..+|+.++.+++||||.||||||||||++|++|||||||||+||.+..+-.     ..+   ...+      +++
T Consensus       243 ~~~~~~~ef~~~a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~~~-----~~~---~~~~------~~~  308 (713)
T TIGR00605       243 YSRSKWEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDP-----EIS---SEGF------VPK  308 (713)
T ss_pred             HhhhhHHHHHHhhhccccccchhhhHHHHHHhhhcccccccccccccCcccCCCCc-----ccc---cccc------ccc
Confidence            011  467889999999999999999999999999999999999999998731100     000   0000      000


Q ss_pred             ccccccCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCcccC-CCcchhh
Q 005629          330 PEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEAC-HPKEKSQ  408 (687)
Q Consensus       330 ~~~~~~~p~k~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~s~~~~~s~~~~~~~~~~~~~~~~~s~~e~~-~s~~~~~  408 (687)
                      .          .       .+.                                     +...+..+ ..+. .+ ....
T Consensus       309 ~----------~-------~~~-------------------------------------~~q~~~~s-~~S~~~t-sR~~  332 (713)
T TIGR00605       309 L----------S-------ACN-------------------------------------ANQRLIMS-CESADRT-SRFR  332 (713)
T ss_pred             c----------c-------ccc-------------------------------------cccccccc-cCCCCcc-cccc
Confidence            0          0       000                                     00000000 0000 00 0000


Q ss_pred             hhhccCChHHHHHHHHHhhhccccccCCcccccccccCCCCCCccccccccccccCCCCccccCcccccCCCCCCCCceE
Q 005629          409 ALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYW  488 (687)
Q Consensus       409 ~~rR~g~~~fe~q~~~al~~t~~~~~~s~~~~~~~~~~~~~~~~~~~k~~kk~~~~~s~~~~~~~s~~~~~~~~~~P~fW  488 (687)
                      ..++.+.|.|.                              +++.+.+..+..         ........+.+++||+||
T Consensus       333 l~~~l~~P~fs------------------------------~~~~~~k~~~~~---------~~~~~~~~~~~~~~p~~W  373 (713)
T TIGR00605       333 MKKDPSLPGFS------------------------------AYSDMDKSPIFT---------CEEGDKFIDRWITYVDFW  373 (713)
T ss_pred             ccccCCCCCcc------------------------------ccccCCCCCccc---------hhcccccccccCCCCeeE
Confidence            11222222110                              000000111000         000111356789999999


Q ss_pred             EEEEeCcCCCCCceEEEeccc-Cccccch-hhHHhHhhcCCCeeEEEEEcCCC-cccchhhhhhhhhh-hccccCCHHHH
Q 005629          489 AEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-IASKRVNSAWW  564 (687)
Q Consensus       489 ~EV~~~~~~~~~kWI~VDpv~-~~V~~~~-~~Ep~~~~~~~~m~YVVAfd~dG-akDVT~RY~~~~~~-~~r~Rv~~~Ww  564 (687)
                      +|||++.   +++||||||++ ++++++. .|||    +.++|+|||||++|| |+|||+||+++|+. +++.|++..||
T Consensus       374 ~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~k~r~~Rv~~~w~  446 (713)
T TIGR00605       374 VEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYVKDVTRRYCDQWSTKVRKRRVEKADF  446 (713)
T ss_pred             EEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCceeechhhHhhhhhhhhheeeecccch
Confidence            9999987   48999999999 8888875 4554    459999999999998 99999999999996 56689998888


Q ss_pred             HHH-HHHhhccccCCCCCCcccccccCccccccChhHHHHHHHHhccCCCCCChhhhhcCchhHhhhhhhcccccCCC--
Q 005629          565 DAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK--  641 (687)
Q Consensus       565 ~~~-L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~~~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~--  641 (687)
                      ..+ |++|.+...             +.. ..+|..||.||.++.++||||+|+++|||||+|||||||++||+|||+  
T Consensus       447 ~~~w~~~~~~~~~-------------~r~-~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L~~~Evi~P~~~  512 (713)
T TIGR00605       447 GETWFRPIFGALH-------------KRK-RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKK  512 (713)
T ss_pred             HHHHHHHHhhhhc-------------cCc-cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhcccceeeccCCC
Confidence            887 777764321             111 227899999999999999999999999999999999999999999995  


Q ss_pred             CCcceeeccee-eeecCCccccccHHHHHHhccccCCCCeeeccccC
Q 005629          642 GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG  687 (687)
Q Consensus       642 a~~~G~~~gE~-VY~R~dV~~LkS~e~W~k~GR~VK~gE~P~K~Vkg  687 (687)
                      ++++|+++||+ ||+|+||++|||+++||++||+||+||+|||+|++
T Consensus       513 ~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~  559 (713)
T TIGR00605       513 ACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKA  559 (713)
T ss_pred             CCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEecc
Confidence            45789999998 99999999999999999999999999999999983

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
>PF03835 Rad4: Rad4 transglutaminase-like domain; InterPro: IPR018325 RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation Back     alignment and domain information
>PF10403 BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR018326 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome Back     alignment and domain information
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>TIGR00605 rad4 DNA repair protein rad4 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
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair] 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
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00460 TGc Transglutaminase/protease-like homologues Back     alignment and domain information
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism] 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 ?
Query687
2qsh_A 538 Crystal Structure Of Rad4-Rad23 Bound To A Mismatch 5e-10
2qsf_A 533 Crystal Structure Of The Rad4-Rad23 Complex Length 5e-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 = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 83/208 (39%), Gaps = 42/208 (20%)
Query: 482 VGAPLYWAEVYCSGENLTGKWVHVDAANA----IIDGEQKVEAAAAAC--KTSLRYIVAF 535
           V  P++W EV+   +  + KW+ VD  N      +    K+     AC  +  LRY++A+
Sbjct: 216 VKYPIFWCEVW---DKFSKKWITVDPVNLKTIEQVRLHSKLAPKGVACCERNMLRYVIAY 272
Query: 536 -AGCGAKDVTRRYCMKWY-------RIASKRVNSAWWDAVLAPLRELESGATGDLNVESS 587
               G +DVTRRY  +W        RI        W+  V+  L   +     D      
Sbjct: 273 DRKYGCRDVTRRYA-QWMNSKVRKRRITKDDFGEKWFRKVITALHHRKRTKIDDY----- 326
Query: 588 AKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGF 647
                       ED     R  +E +P + Q  KNH  YV+E+ + + QI+ P     G+
Sbjct: 327 ------------EDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGY 374
Query: 648 CSGHA-------VYPRSCVQTLKTKERW 668
              H        VY +  +  LK+  +W
Sbjct: 375 LKVHGKVGKVLKVYAKRDIADLKSARQW 402
>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 ?
Query687
2qsf_A 533 RAD4, DNA repair protein RAD4; alpha-beta structur 1e-36
2qsf_A533 RAD4, DNA repair protein RAD4; alpha-beta structur 1e-16
2f4m_A295 Peptide N-glycanase; glycoproteins, ubiquitin-depe 2e-22
1x3z_A335 Peptide: N-glycanase; hydrolase-hydrolase inhibito 1e-16
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 3e-07
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-06
>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 =  143 bits (362), Expect = 1e-36
 Identities = 51/225 (22%), Positives = 81/225 (36%), Gaps = 40/225 (17%)

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

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

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

Query: 647 FCSGHA-------VYPRSCVQTLKTKERWLREALQVKANEVPVKV 684
           +   H        VY +  +  LK+  +W      +K      KV
Sbjct: 369 YLKVHGKVGKVLKVYAKRDIADLKSARQWYMNGRILKTGSRCKKV 413
>2qsf_A RAD4, DNA repair protein RAD4; alpha-beta structure, beta hairpin, transglutaminase fold, DNA-damage recognition, DNA repair; HET: DNA; 2.35A {Saccharomyces cerevisiae} PDB: 2qsg_A* 2qsh_A* Length = 533 Back     alignment and structure
>2f4m_A Peptide N-glycanase; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: d.3.1.4 PDB: 2f4o_A* Length = 295 Back     alignment and structure
>1x3z_A Peptide: N-glycanase; hydrolase-hydrolase inhibitor complex; HET: SUC; 2.80A {Saccharomyces cerevisiae} SCOP: d.3.1.4 PDB: 1x3w_A* 3esw_A* Length = 335 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query687
2qsf_A 533 RAD4, DNA repair protein RAD4; alpha-beta structur 100.0
1x3z_A335 Peptide: N-glycanase; hydrolase-hydrolase inhibito 99.94
2f4m_A295 Peptide N-glycanase; glycoproteins, ubiquitin-depe 99.87
3isr_A293 Transglutaminase-like enzymes, putative cysteine; 95.58
3kd4_A506 Putative protease; structural genomics, joint cent 93.0
1ex0_A731 Coagulation factor XIII A chain; transglutaminase, 85.72
1vjj_A692 Protein-glutamine glutamyltransferase E; transglut 84.96
1g0d_A695 Protein-glutamine gamma-glutamyltransferase; tissu 84.08
2q3z_A687 Transglutaminase 2; transglutaminase 2, tissue tra 82.16
>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* Back     alignment and structure
Probab=100.00  E-value=5.5e-88  Score=755.24  Aligned_cols=356  Identities=21%  Similarity=0.353  Sum_probs=284.8

Q ss_pred             CCCCCeEEEEecCCc--cc--cccccccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCcHHHHHHHhhcCchhhhcccC
Q 005629          147 SDIKGVTIEFDAADS--VT--KKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISE  222 (687)
Q Consensus       147 ~~~~~leI~l~~~~~--~k--K~~~RR~s~~eKe~r~~~HKvHLLCLLah~~~RN~wcnd~~lqa~llSlLP~~~~~~~~  222 (687)
                      .+.++|+|||+.+..  .+  ++..+.+|++||++|+++|||||||||+||++||+||||++||++|+|+||.++.+.++
T Consensus         6 ~~~~~l~itl~~~~~~~~~~~~~~kk~~S~~ER~~R~~~Hk~hvl~LL~H~~~RN~W~nD~~lq~~L~sllP~~i~~~l~   85 (533)
T 2qsf_A            6 AGVEDISVEIKPSSKRNSDARRTSRNVCSNEERKRRKYFHMLYLVCLMVHGFIRNEWINSKRLSRKLSNLVPEKVFELLH   85 (533)
T ss_dssp             ---------------------CCCTTBCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHGGGSCHHHHHHTS
T ss_pred             CCCCCeEEEecCCccccchhhhccccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhhC
Confidence            356889999998632  21  12223489999999999999999999999999999999999999999999999976654


Q ss_pred             cc----------hhhHhhhhHHHHHhhhceeeccCCC---ccc----------------ch--HHHHHHHHHHhcCCHHH
Q 005629          223 VS----------KLTANALSPIVSWFHDNFHVRSSVS---TRR----------------SF--HSDLAHALESREGTPEE  271 (687)
Q Consensus       223 ~~----------~~~~~~L~~L~~Wf~~~F~vt~~~~---~~~----------------~~--~~~l~~~l~~~~GSrD~  271 (687)
                      +.          +.++++|++|+.||+.+|+|+++..   ...                .+  ..+|+.+|++++||+|+
T Consensus        86 p~~~~~~~~~~~~~~~~~Lk~L~~ww~~~F~it~p~~~~g~~~~~w~e~~~~~~~~~~f~~~~~~~f~~~~~~~~Gs~d~  165 (533)
T 2qsf_A           86 PQKDEELPLRSTRKLLDGLKKCMELWQKHWKITKKYDNEGLYMRTWKEIEMSANNKRKFKTLKRSDFLRAVSKGHGDPDI  165 (533)
T ss_dssp             CCCCSSCTHHHHHHHHHHHHHHHHHHHHHCCEECCCSSCTTSCCCHHHHHHTTTTCCCEECCCHHHHHHHHHHTEECHHH
T ss_pred             cCCCccccccchHHHHHHHHHHHHHHHhhEEEcCCccCCCccccCccccchhhccccccccccHHHHHHHHHhcCCChhH
Confidence            31          1246899999999999999998621   110                01  36899999999999999


Q ss_pred             HHHHHHHHHHhcCCceeEEEeeccccCCcccccccCCCCCCCCCCCCccCCCCccccCccccccCCCCcccccccccccc
Q 005629          272 IAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCE  351 (687)
Q Consensus       272 gAqLF~ALLRALgL~aRLV~SLqpl~lk~~~~k~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~p~k~~~~~~~~~~~~  351 (687)
                      +||||||||||||++||||+||||++|.+.  +..                            .++              
T Consensus       166 ~AqlF~aLlRalG~~aRlV~SLqP~~f~~~--k~~----------------------------~~~--------------  201 (533)
T 2qsf_A          166 SVQGFVAMLRACNVNARLIMSCQPPDFTNM--KID----------------------------TSL--------------  201 (533)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEECCCCTTCC--BSC----------------------------CCC--------------
T ss_pred             HHHHHHHHHHHCCCceEEEecccccccccc--ccc----------------------------cCc--------------
Confidence            999999999999999999999999998862  100                            000              


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCcccCCCcchhhhhhccCChHHHHHHHHHhhhccc
Q 005629          352 TSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNV  431 (687)
Q Consensus       352 ~~~~~~~~~~~~~~k~~~~~s~~~~~s~~~~~~~~~~~~~~~~~s~~e~~~s~~~~~~~rR~g~~~fe~q~~~al~~t~~  431 (687)
                                   .+                                  ...                            
T Consensus       202 -------------~k----------------------------------~~~----------------------------  206 (533)
T 2qsf_A          202 -------------NG----------------------------------NNA----------------------------  206 (533)
T ss_dssp             -------------C-------------------------------------C----------------------------
T ss_pred             -------------cc----------------------------------CCc----------------------------
Confidence                         00                                  000                            


Q ss_pred             cccCCcccccccccCCCCCCccccccccccccCCCCccccCcccccCCCCCCCCceEEEEEeCcCCCCCceEEEecccC-
Q 005629          432 ATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANA-  510 (687)
Q Consensus       432 ~~~~s~~~~~~~~~~~~~~~~~~~k~~kk~~~~~s~~~~~~~s~~~~~~~~~~P~fW~EV~~~~~~~~~kWI~VDpv~~-  510 (687)
                                                                    .+.++.||+||+|||++.   .++||||||+++ 
T Consensus       207 ----------------------------------------------~~~~~~~P~~W~EV~s~~---~~rWi~VDp~~~~  237 (533)
T 2qsf_A          207 ----------------------------------------------YKDMVKYPIFWCEVWDKF---SKKWITVDPVNLK  237 (533)
T ss_dssp             ----------------------------------------------HHHHTTSCSEEEEEEETT---TTEEEEEESSSSC
T ss_pred             ----------------------------------------------cccccCCCeEEEEEEEcC---CCeEEEEeccccc
Confidence                                                          011235899999999986   489999999985 


Q ss_pred             cc---ccchhhHHhH--hhcCCCeeEEEEEcCCC-cccchhhhhhhhhh-hccccCC-----HHHHHHHHHHhhccccCC
Q 005629          511 II---DGEQKVEAAA--AACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-IASKRVN-----SAWWDAVLAPLRELESGA  578 (687)
Q Consensus       511 ~V---~~~~~~Ep~~--~~~~~~m~YVVAfd~dG-akDVT~RY~~~~~~-~~r~Rv~-----~~Ww~~~L~~~~~~~~~~  578 (687)
                      +|   +.+..|||..  ..+.++|+|||||++|| |+|||+||+.+|.. +++.|+.     +.||.++|+.|+++    
T Consensus       238 ~id~~~~~~~~Ep~~~~~~~~~~m~YViAf~~d~~~kDVT~RY~~~~~~k~rr~Ri~~~~~~~~W~~~~L~~~~~~----  313 (533)
T 2qsf_A          238 TIEQVRLHSKLAPKGVACCERNMLRYVIAYDRKYGCRDVTRRYAQWMNSKVRKRRITKDDFGEKWFRKVITALHHR----  313 (533)
T ss_dssp             EEECCSSCCTTSCCSTTTTSSCCCCEEEEECTTCCEEECHHHHCTTCCCCCGGGSGGGSHHHHHHHHHHHHHHCCS----
T ss_pred             cccccccccccccccccccccCceeEEEEEcCCCceEecchhhhhchhhhhheeeecCCcchHHHHHHHHHHHhcC----
Confidence            44   3577899864  24679999999999987 99999999999984 4556764     78999999999863    


Q ss_pred             CCCCcccccccCccccccChhHHHHHHHHhccCCCCCChhhhhcCchhHhhhhhhcccccCCCCCcceeecc-------e
Q 005629          579 TGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG-------H  651 (687)
Q Consensus       579 ~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~~~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~a~~~G~~~g-------E  651 (687)
                                   ..+.+|..||.||+.+..+||||+|+++|||||+|||||||++||+|||+++++|+|+|       |
T Consensus       314 -------------~~~~~d~~Ed~el~~~~~~e~~P~s~~~fK~HP~yvLer~L~k~E~i~P~a~~~g~~~~~~k~~~~E  380 (533)
T 2qsf_A          314 -------------KRTKIDDYEDQYFFQRDESEGIPDSVQDLKNHPYYVLEQDIKQTQIVKPGCKECGYLKVHGKVGKVL  380 (533)
T ss_dssp             -------------CCCHHHHHHHHHHHHHHHHSCCCSSTGGGTTCSSEEEGGGSCTTEEECTTCCCSEEEECCSTTCCEE
T ss_pred             -------------CccccchhHHHHHHHHHhcCCCCccHHHHcCCcHhhhhhhhccceeeCCCCceeeEEecCcCCCccc
Confidence                         23577899999999999999999999999999999999999999999999999999987       9


Q ss_pred             eeeecCCccccccHHHHHHhccccCCCCeeeccccC
Q 005629          652 AVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG  687 (687)
Q Consensus       652 ~VY~R~dV~~LkS~e~W~k~GR~VK~gE~P~K~Vkg  687 (687)
                      +||+|+||++|||+++|+++||+||+||+|||+||+
T Consensus       381 ~VY~R~~V~~l~S~e~W~~~gR~vk~ge~P~K~v~~  416 (533)
T 2qsf_A          381 KVYAKRDIADLKSARQWYMNGRILKTGSRCKKVIKR  416 (533)
T ss_dssp             EEEEGGGEEECBCHHHHHTTTEEECSSCCCSEEECC
T ss_pred             ceeehhhhheeecHHHHHHcCCccCCCCeeeeEEec
Confidence            999999999999999999999999999999999975
>1x3z_A Peptide: N-glycanase; hydrolase-hydrolase inhibitor complex; HET: SUC; 2.80A {Saccharomyces cerevisiae} SCOP: d.3.1.4 PDB: 1x3w_A* 3esw_A* Back     alignment and structure
>2f4m_A Peptide N-glycanase; glycoproteins, ubiquitin-dependent protein degradation, NUCL excision repair, peptide:N-glycanase; 1.85A {Mus musculus} SCOP: d.3.1.4 PDB: 2f4o_A* Back     alignment and structure
>3isr_A Transglutaminase-like enzymes, putative cysteine; protease, hutchinsoni MCSG, structural genomics; 1.90A {Cytophaga hutchinsonii} Back     alignment and structure
>3kd4_A Putative protease; structural genomics, joint center for STR genomics, JCSG, protein structure initiative, PSI-2, hydrol; HET: MSE; 2.00A {Parabacteroides distasonis atcc 8503} Back     alignment and structure
>1ex0_A Coagulation factor XIII A chain; transglutaminase, blood coagulation, mutant, W279F, oxyanion, transferase; 2.00A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1evu_A 1fie_A 1f13_A 1ggt_A 1ggu_A 1ggy_A 1qrk_A Back     alignment and structure
>1vjj_A Protein-glutamine glutamyltransferase E; transglutaminase 3, X-RAY crystallography, metalloenzyme, calcium ION; HET: GDP; 1.90A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1sgx_A* 1l9m_A 1l9n_A* 1nud_A 1nuf_A 1nug_A 1rle_A* Back     alignment and structure
>1g0d_A Protein-glutamine gamma-glutamyltransferase; tissue transglutaminase,acyltransferase; 2.50A {Pagrus major} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 Back     alignment and structure
>2q3z_A Transglutaminase 2; transglutaminase 2, tissue transglutaminase, TG2, transferas; 2.00A {Homo sapiens} SCOP: b.1.18.9 b.1.5.1 b.1.5.1 d.3.1.4 PDB: 1kv3_A 3ly6_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 687
d1x3za1320 d.3.1.4 (A:8-327) Peptide:N-glycanase 1, PNG1 {Bak 2e-17
d2f4ma1287 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {M 1e-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 = 81.9 bits (202), Expect = 2e-17
 Identities = 23/123 (18%), Positives = 43/123 (34%), Gaps = 15/123 (12%)

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

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

Query: 603 ELE 605
           EL 
Sbjct: 315 ELI 317
>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 ?
Query687
d1x3za1320 Peptide:N-glycanase 1, PNG1 {Baker's yeast(Sacchar 99.88
d2f4ma1287 Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) 99.85
d1g0da4321 Transglutaminase catalytic domain {Red sea bream ( 81.08
d1vjja4321 Transglutaminase catalytic domain {Human (Homo sap 80.54
>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=99.88  E-value=1.4e-22  Score=210.15  Aligned_cols=106  Identities=20%  Similarity=0.316  Sum_probs=83.4

Q ss_pred             eEEEEEeCcCCCCCceEEEecccCccccchhhHHhHhhcCCCeeEEEEEcCCCcccchhhhhhhhhhhccccCCHHHHHH
Q 005629          487 YWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRIASKRVNSAWWDA  566 (687)
Q Consensus       487 fW~EV~~~~~~~~~kWI~VDpv~~~V~~~~~~Ep~~~~~~~~m~YVVAfd~dGakDVT~RY~~~~~~~~r~Rv~~~Ww~~  566 (687)
                      +|+|||++.+   ++||||||+.+.|++|..|+.   ++.++|+|||||+.||++|||+||+.+| .+++.|++..||..
T Consensus       212 vW~EVys~~~---kRWIhvDpce~~id~P~lye~---gw~k~msYVIAf~~dgv~DVT~RY~~k~-~~rR~rv~E~wl~~  284 (320)
T d1x3za1         212 VWCEYFSNFL---NRWVHVDSCEQSFDQPYIYSI---NWNKKMSYCIAFGKDGVVDVSKRYILQN-ELPRDQIKEEDLKF  284 (320)
T ss_dssp             EEEEEEETTT---TEEEEEETTTTEESCTHHHHT---TSCCCBCCEEEEETTEEEECHHHHCSSS-BCCCCSSCHHHHHH
T ss_pred             eEEEEeeccc---CeEEEEcCCCCccCCcceecc---CCCCceEEEEEecCCcceechhhhcccc-cCccccCCHHHHHH
Confidence            8999999864   899999999999999999875   5789999999999999999999999876 46678999999999


Q ss_pred             HHHHhhccccCCCCCCcccccccCccccccChhHHHHHH
Q 005629          567 VLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELE  605 (687)
Q Consensus       567 ~L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~  605 (687)
                      +|..+++......      +......+..||..|+.||.
T Consensus       285 ~L~~l~~~~r~~~------s~~e~~~L~~RD~~E~~ELl  317 (320)
T d1x3za1         285 LCQFITKRLRYSL------NDDEIYQLACRDEQEQIELI  317 (320)
T ss_dssp             HHHHHHHHHHTTS------CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccC------CHHHHHHHHHhHHHHHHHhc
Confidence            9999876432110      00112223456667777764
>d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1g0da4 d.3.1.4 (A:141-461) Transglutaminase catalytic domain {Red sea bream (Chrysophrys major) [TaxId: 143350]} Back     information, alignment and structure
>d1vjja4 d.3.1.4 (A:141-461) Transglutaminase catalytic domain {Human (Homo sapiens), TGase E3 [TaxId: 9606]} Back     information, alignment and structure