Citrus Sinensis ID: 013058

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

MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK

ccHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHccHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHcccccccccccccEEEEcHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHccccccccccccccHHHHHHccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccEEEEccccccEEEccHHHHHHcccccccccccccEEEEEEccEEEEccccHHHHHHHHHHHHHHHcccccEEEEEcHHHHHHHHHccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHcccEEEcccEEccccccHHHHHHHHHHHHHccEEEEEcccccEEEEEccccHHHHHHHHHccc

ccccEEEHHcHHHHHHHccHHHHHHHHccHHHHHHHHHHccHHHHHHHHHHHHccccccHHHHHHHHcHHHHHHHHHHHHHHHcccEEEEccccccEEEEcHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHccccccccccccccHHHHHHHHccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHccEEEEEcccccccEcccEEEEEEcccccccccccccEEEEEEcEEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHHHHccccHHHHHHHHHHcccHHHHcccccccccHHHHHHHHHHHHccEEEcccEEEcccccHHHHHHHHHHHHHcccEEEEccccEEEEEccccHHHHHHHHHHccc

MPLVKIIAKNFMDMVASLTARdldrlyenpfICEAILRSLPPLAKKYVMQMFYIdgaipakmmeewvlpdgftkhRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLiyggalprepmpsgitarlptledLEAYAIGQWECFLLQLISstqaerptnfssSMMKVFQRGllsrrdkeaprltesGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLqqgrkenwfiptklatnlsmsltdssarkegFIVVETNFRMYAYSTSKLHCEILRLFSKVeyqlpnlivgAITKESLYNAFENGITAEQIISFLQqnahprvadrmpsvpenvCDQIRLWESDlnrvemtpahyydefpsrdvFEAACDYArdqsgllwedpkkMRLVVKAEIHMHMREFLRGQNK

MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVqlrlfseekkkettyrlnstfqsnLRKHLIYggalprepmpSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLatnlsmsltdssarkEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPahyydefpsrDVFEAACDYARdqsgllwedpkKMRLVVKAEIHMHMREFLRGQNK

***VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPRE*MPSGITARLPTLEDLEAYAIGQWECFLLQLIS**********************************ESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMR********

*********NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGAL**************TLEDLEAYAIGQWECFLLQL******************VFQ***************ESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT*****************VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPR*****PSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ**

*PLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGA****PMPSGI**RLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD***RKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ**

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		450	2.2.26 [Sep-21-2011]
P60027		462	General transcription fac	yes	no	0.982	0.956	0.340	5e-70
Q92759		462	General transcription fac	yes	no	0.982	0.956	0.340	5e-70
O70422		463	General transcription fac	yes	no	0.973	0.946	0.341	1e-69
Q6BZX4		467	RNA polymerase II transcr	yes	no	0.957	0.922	0.308	8e-63
Q54C29		483	General transcription fac	yes	no	0.942	0.877	0.320	7e-62
P87303		447	RNA polymerase II transcr	yes	no	0.882	0.888	0.328	5e-61
Q6BGW8		515	RNA polymerase II transcr	yes	no	0.884	0.772	0.304	1e-59
Q6CLR2		496	RNA polymerase II transcr	yes	no	0.926	0.840	0.300	6e-59
Q75B51		514	RNA polymerase II transcr	yes	no	0.913	0.799	0.297	8e-55
Q6FP41		504	RNA polymerase II transcr	yes	no	0.92	0.821	0.293	1e-52

>sp\|P60027\|TF2H4_PANTR General transcription factor IIH subunit 4 OS=Pan troglodytes GN=GTF2H4 PE=3 SV=1	Back alignment and function desciption

 Score =  265 bits (677), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 154/452 (34%), Positives = 250/452 (55%), Gaps = 10/452 (2%)

Query: 4   VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
           V +  +N  + +  L+   LDRLY +P  C A+ R LP LAK +VM+M +++  +P   +
Sbjct: 12  VHLQCRNLQEFLGGLSPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLEQPLPQAAV 71

Query: 64  EEWVLPDGFTKHRVAIDRLVQLRLFSEE--KKKETTYRLNSTFQSNLRKHLIYGG-ALPR 120
             WV  +       +   L  LR++  +          LN  F+ NLR  L+ GG A   
Sbjct: 72  ALWVKKEFSKAQEESTGLLSGLRIWHTQLLPGGLQGLILNPIFRQNLRIALLGGGKAWSD 131

Query: 121 EPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLL-SR 179
           +    G       +  L+ YA  +WE  L  ++ S  A    + +  +    Q GL+ S 
Sbjct: 132 DTSQLGPDKHARDVPSLDKYAEERWEVVLHFMVGSPSAAVSQDLAQLLS---QAGLMKST 188

Query: 180 RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEA 239
              E P +T +GFQFLL+DT AQLWY + +Y+  +Q RG++  +++SFL +LSF   G+ 
Sbjct: 189 EPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKD 248

Query: 240 YNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSA--RKEGFI 297
           Y++  +S+   + ++   + GLV  Q+ RK   + PT+LA NLS  ++ +     + GFI
Sbjct: 249 YSVEGMSDSLLNFLQHLREFGLV-FQRKRKSRRYYPTRLAINLSSGVSGAGGTVHQPGFI 307

Query: 298 VVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISF 357
           VVETN+R+YAY+ S+L   ++ LFS++ Y+ PN++V  +T+ES+  A  +GITA+QII F
Sbjct: 308 VVETNYRLYAYTESELQIALIALFSEMLYRFPNMVVAQVTRESVQQAIASGITAQQIIHF 367

Query: 358 LQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARD 417
           L+  AHP +  + P +P  + DQIRLWE + +R+  T    Y++F S+  FE    +AR+
Sbjct: 368 LRTRAHPVMLKQTPVLPPTITDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARE 427

Query: 418 QSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 449
              L++E+  K  +VV    H  ++ F + Q 
Sbjct: 428 LGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 459

Component of the core-TFIIH basal transcription factor involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.
Pan troglodytes (taxid: 9598)

>sp\|Q92759\|TF2H4_HUMAN General transcription factor IIH subunit 4 OS=Homo sapiens GN=GTF2H4 PE=2 SV=1	Back alignment and function description

>sp\|O70422\|TF2H4_MOUSE General transcription factor IIH subunit 4 OS=Mus musculus GN=Gtf2h4 PE=2 SV=1	Back alignment and function description

>sp\|Q6BZX4\|TFB2_YARLI RNA polymerase II transcription factor B subunit 2 OS=Yarrowia lipolytica (strain CLIB 122 / E 150) GN=TFB2 PE=3 SV=1	Back alignment and function description

>sp\|Q54C29\|TF2H4_DICDI General transcription factor IIH subunit 4 OS=Dictyostelium discoideum GN=gtf2h4 PE=3 SV=1	Back alignment and function description

>sp\|P87303\|TFB2_SCHPO RNA polymerase II transcription factor B subunit 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tfb2 PE=1 SV=2	Back alignment and function description

>sp\|Q6BGW8\|TFB2_DEBHA RNA polymerase II transcription factor B subunit 2 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=TFB2 PE=3 SV=2	Back alignment and function description

>sp\|Q6CLR2\|TFB2_KLULA RNA polymerase II transcription factor B subunit 2 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=TFB2 PE=3 SV=1	Back alignment and function description

>sp\|Q75B51\|TFB2_ASHGO RNA polymerase II transcription factor B subunit 2 OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=TFB2 PE=3 SV=1	Back alignment and function description

>sp\|Q6FP41\|TFB2_CANGA RNA polymerase II transcription factor B subunit 2 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=TFB2 PE=3 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		450
147854406		451	hypothetical protein VITISV_005315 [Viti	0.991	0.988	0.821	0.0
255556021		451	tfiih, polypeptide, putative [Ricinus co	0.995	0.993	0.795	0.0
449433857		451	PREDICTED: general transcription factor	0.995	0.993	0.797	0.0
224077128		449	predicted protein [Populus trichocarpa]	0.991	0.993	0.773	0.0
357461579		452	General transcription factor IIH subunit	0.995	0.991	0.760	0.0
358346685		451	General transcription factor IIH subunit	0.995	0.993	0.757	0.0
42566894		452	transcription initiation factor TFIIH su	1.0	0.995	0.75	0.0
334186626		482	transcription initiation factor TFIIH su	0.997	0.931	0.751	0.0
42572935		462	transcription initiation factor TFIIH su	1.0	0.974	0.75	0.0
51969958		452	unnamed protein product [Arabidopsis tha	1.0	0.995	0.75	0.0

>gi\|147854406\|emb\|CAN81292.1\| hypothetical protein VITISV_005315 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  788 bits (2034), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/448 (82%), Positives = 413/448 (92%), Gaps = 2/448 (0%)

Query: 1   MPLVKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPA 60
           MP VKIIAKNFMDMVASL A  LD LY N FICEAILRSLPPLAKKY++QM YID  + A
Sbjct: 1   MPQVKIIAKNFMDMVASLPAMKLDALYHNTFICEAILRSLPPLAKKYILQMLYIDVPVTA 60

Query: 61  KMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EKKKETTYRLNSTFQSNLRKHLIYGGAL 118
           K MEEWVL DGF+KHRVAIDRL+QLR+F+E  ++KKET+YRLN TFQ+NL+KHLIYGG L
Sbjct: 61  KAMEEWVLADGFSKHRVAIDRLIQLRVFTETSDRKKETSYRLNPTFQTNLQKHLIYGGVL 120

Query: 119 PREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLS 178
           PREPMPS IT RLP+L+DLEAYA+GQWECFLLQLISSTQ E+ TNFSSS+MKVFQRGLL+
Sbjct: 121 PREPMPSNITVRLPSLDDLEAYALGQWECFLLQLISSTQTEKLTNFSSSLMKVFQRGLLT 180

Query: 179 RRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238
           +R+KEAPRLTESGFQFLLMDTNAQLWYI+REYISNS+ERG++ ADLISFLLELSFHV GE
Sbjct: 181 QREKEAPRLTESGFQFLLMDTNAQLWYIMREYISNSEERGVDPADLISFLLELSFHVTGE 240

Query: 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIV 298
           AYN+NTL+E Q++ IKD  DLGLVKLQQGRKE+WFIPTKLATNLSMSL+D+S+RK+GF+V
Sbjct: 241 AYNINTLTEFQRNTIKDLVDLGLVKLQQGRKESWFIPTKLATNLSMSLSDTSSRKQGFVV 300

Query: 299 VETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 358
           VETNFR+YAYS+SKLHCEILRLFS+VEYQLPNLIVGAITKESLYNAFENGITAEQIISFL
Sbjct: 301 VETNFRLYAYSSSKLHCEILRLFSRVEYQLPNLIVGAITKESLYNAFENGITAEQIISFL 360

Query: 359 QQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQ 418
           QQNAHPRVA+R P+VPENV DQIRLWE+DLNRVE  P+H YDEFPSRDVFEAACD+AR+ 
Sbjct: 361 QQNAHPRVAERTPAVPENVTDQIRLWETDLNRVETMPSHLYDEFPSRDVFEAACDFAREY 420

Query: 419 SGLLWEDPKKMRLVVKAEIHMHMREFLR 446
            GLLWED KKMRLVVKAEIH+HMRE+LR
Sbjct: 421 GGLLWEDSKKMRLVVKAEIHLHMREYLR 448

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255556021\|ref\|XP_002519045.1\| tfiih, polypeptide, putative [Ricinus communis] gi\|223541708\|gb\|EEF43256.1\| tfiih, polypeptide, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449433857\|ref\|XP_004134713.1\| PREDICTED: general transcription factor IIH subunit 4-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|224077128\|ref\|XP_002305144.1\| predicted protein [Populus trichocarpa] gi\|222848108\|gb\|EEE85655.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|357461579\|ref\|XP_003601071.1\| General transcription factor IIH subunit [Medicago truncatula] gi\|355490119\|gb\|AES71322.1\| General transcription factor IIH subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|358346685\|ref\|XP_003637396.1\| General transcription factor IIH subunit [Medicago truncatula] gi\|355503331\|gb\|AES84534.1\| General transcription factor IIH subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|42566894\|ref\|NP_193435.2\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi\|51969678\|dbj\|BAD43531.1\| unnamed protein product [Arabidopsis thaliana] gi\|115646777\|gb\|ABJ17114.1\| At4g17020 [Arabidopsis thaliana] gi\|332658439\|gb\|AEE83839.1\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|334186626\|ref\|NP_001190745.1\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi\|332658440\|gb\|AEE83840.1\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|42572935\|ref\|NP_974564.1\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana] gi\|332658438\|gb\|AEE83838.1\| transcription initiation factor TFIIH subunit H4 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|51969958\|dbj\|BAD43671.1\| 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		450
ZFIN\|ZDB-GENE-030131-6779		466	gtf2h4 "general transcription	0.977	0.944	0.356	1.4e-71
UNIPROTKB\|A6H7G8		463	GTF2H4 "Uncharacterized protei	0.977	0.950	0.347	5.1e-67
UNIPROTKB\|Q767M2		463	TFIIH "Uncharacterized protein	0.977	0.950	0.347	5.1e-67
UNIPROTKB\|F1PGI3		463	GTF2H4 "Uncharacterized protei	0.977	0.950	0.345	1.1e-66
UNIPROTKB\|Q92759		462	GTF2H4 "General transcription	0.977	0.952	0.345	1.1e-66
UNIPROTKB\|P60027		462	GTF2H4 "General transcription	0.977	0.952	0.345	1.1e-66
RGD\|1303309		463	Gtf2h4 "general transcription	0.966	0.939	0.346	1.3e-66
MGI\|MGI:1338799		463	Gtf2h4 "general transcription	0.966	0.939	0.346	1.7e-66
DICTYBASE\|DDB_G0293228		483	gtf2h4 "TFIIH subunit" [Dictyo	0.777	0.724	0.339	1.3e-65
FB\|FBgn0261109		499	mrn "marionette" [Drosophila m	0.968	0.873	0.309	1e-59

ZFIN\|ZDB-GENE-030131-6779 gtf2h4 "general transcription factor IIH, polypeptide 4" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

 Score = 724 (259.9 bits), Expect = 1.4e-71, P = 1.4e-71
 Identities = 165/463 (35%), Positives = 254/463 (54%)

Query:     4 VKIIAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMM 63
             V++  KN  + +  LT   LDRLY +P  C A+ R LPPLAK YVM+M ++D  +P   +
Sbjct:     5 VQLQCKNLHEYLKELTPEILDRLYNHPATCLAVYRELPPLAKNYVMRMLFLDHPLPQAAV 64

Query:    64 EEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETT--YRLNSTFQSNLRKHLIYGGALP-- 119
               WV       H   +  L  LRL+  +  +     + LN  F+ NLR  L+ GG  P  
Sbjct:    65 ALWVKKGSQKDHDQCVSVLTGLRLWHSQHLQGGLQGFVLNPVFKDNLRIALL-GGGKPWA 123

Query:   120 REPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSR 179
              E    G       +E L+ YA+ +WE  L  ++ S  A    + +  ++   Q GL+  
Sbjct:   124 DEGANLGPDRHARDVESLDRYAMERWEVILHFMVGSPSAAVSQDLAQLLI---QAGLMKS 180

Query:   180 RDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEA 239
                EAP +T +GFQFLL+DT +QLWY   +Y+  +Q RG++  +++SFL +LSF   G  
Sbjct:   181 ETGEAPCITSAGFQFLLLDTASQLWYFTLQYLKTAQSRGMDLVEILSFLFQLSFSTLGRD 240

Query:   240 YNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKE----- 294
             Y++  +SE   + ++   + GLV  Q+ RK   + PT+LA  L+  +T + A        
Sbjct:   241 YSVEGMSESLLTFLQHLREFGLV-FQRKRKSRRYYPTRLAITLAAGVTANPASGSASSAL 299

Query:   295 ---------GFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAF 345
                      GFIVVETN+R+YAY+ S+L   ++ LFS++ Y+ PNL+V  +T+ES+  A 
Sbjct:   300 GAIPGTGDTGFIVVETNYRIYAYTNSELQIALVALFSEMLYRFPNLVVAQVTRESVQQAI 359

Query:   346 ENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSR 405
              NGITA+QII FL+  AHP +  + P +P  + DQIRLWE + +R++ T    Y++F S+
Sbjct:   360 SNGITAQQIIHFLRTRAHPVMLKQTPVLPPTITDQIRLWELEKDRLQFTEGVLYNQFLSQ 419

Query:   406 DVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQ 448
               FE   D A+    L+W++P    +VV    H  ++ F + Q
Sbjct:   420 ADFEVLRDRAQGLGVLVWQNPAHRVMVVTPHGHSEVKRFWKRQ 462

GO:0005634 "nucleus" evidence=IEA

GO:0004003 "ATP-dependent DNA helicase activity" evidence=IEA

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

GO:0000439 "core TFIIH complex" evidence=IEA

UNIPROTKB\|A6H7G8 GTF2H4 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q767M2 TFIIH "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|F1PGI3 GTF2H4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q92759 GTF2H4 "General transcription factor IIH subunit 4" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|P60027 GTF2H4 "General transcription factor IIH subunit 4" [Pan troglodytes (taxid:9598)]	Back alignment and assigned GO terms

RGD\|1303309 Gtf2h4 "general transcription factor II H, polypeptide 4" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

MGI\|MGI:1338799 Gtf2h4 "general transcription factor II H, polypeptide 4" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0293228 gtf2h4 "TFIIH subunit" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

FB\|FBgn0261109 mrn "marionette" [Drosophila melanogaster (taxid:7227)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P60027	TF2H4_PANTR	No assigned EC number	0.3407	0.9822	0.9567	yes	no
O70422	TF2H4_MOUSE	No assigned EC number	0.3415	0.9733	0.9460	yes	no
Q6CLR2	TFB2_KLULA	No assigned EC number	0.3002	0.9266	0.8407	yes	no
P87303	TFB2_SCHPO	No assigned EC number	0.3284	0.8822	0.8881	yes	no
Q92759	TF2H4_HUMAN	No assigned EC number	0.3407	0.9822	0.9567	yes	no
Q54C29	TF2H4_DICDI	No assigned EC number	0.3200	0.9422	0.8778	yes	no
Q6BZX4	TFB2_YARLI	No assigned EC number	0.3085	0.9577	0.9229	yes	no

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:
	estExt_fgenesh4_pg.C_LG_IV0538	hypothetical protein (449 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pg.C_LG_I000900	hypothetical protein (803 aa)	•	•	•	•	0.885
	eugene3.00020503	hypothetical protein (758 aa)	•	•	•	•	0.836
	gw1.V.5266.1	hypothetical protein (289 aa)		•	•	•	0.795
	estExt_fgenesh4_pm.C_1650003	hypothetical protein (413 aa)	•	•	•	•	0.744
	estExt_Genewise1_v1.C_1330021	hypothetical protein (334 aa)			•	•	0.573
	estExt_Genewise1_v1.C_LG_IX3069	SubName- Full=Putative uncharacterized protein; (117 aa)	•		•		0.494
	grail3.0014029901	hypothetical protein (52 aa)			•		0.479
	gw1.70.559.1	hypothetical protein (329 aa)			•	•	0.472
	gw1.IX.2304.1	hypothetical protein (321 aa)			•		0.442
	fgenesh4_pg.C_scaffold_82000017	hypothetical protein (603 aa)			•	•	0.432

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		450
pfam03849		365	pfam03849, Tfb2, Transcription factor Tfb2	1e-168
TIGR00625		448	TIGR00625, tfb2, Transcription factor tfb2	3e-99
COG5144		447	COG5144, TFB2, RNA polymerase II transcription ini	5e-87
pfam13625		128	pfam13625, Helicase_C_3, Helicase conserved C-term	2e-04

>gnl\|CDD\|217760 pfam03849, Tfb2, Transcription factor Tfb2	Back alignment and domain information

 Score =  477 bits (1229), Expect = e-168
 Identities = 149/368 (40%), Positives = 228/368 (61%), Gaps = 19/368 (5%)

Query: 13  DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGF 72
           D + SL    LDRLY++P  C AI R LPPLAK+++M+M ++D  +PA  +++WV P+  
Sbjct: 1   DYLESLPPTVLDRLYQSPATCLAIFRLLPPLAKQFIMRMLFVDQPVPAADLDKWVKPESK 60

Query: 73  TKHRVAIDRLVQLRLF--SEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGIT-A 129
            +H  AI RL  L +   +    K+ + RLN TF+ NLR+ L  GG      +PS     
Sbjct: 61  KQHEEAIKRLKSLHIITETPSGGKKQSIRLNPTFKKNLRRALTGGGVNNSFGVPSDEPDK 120

Query: 130 RLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTE 189
           +L  +  L++YA  +WE  L  ++ S++A+  T  S S++ + + G L  R     R+T 
Sbjct: 121 KLVDVAFLDSYAREKWETILHYMVGSSEAK--TQPSKSVLNLLKHGGLMERSDGGLRITN 178

Query: 190 SGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQ 249
            GFQFLL D NAQ+W ++ +Y+  ++ERG++  D++SFL  L F   G+AY+ + LSE Q
Sbjct: 179 EGFQFLLQDVNAQIWTLLLQYLKLAEERGMDPVDVLSFLFMLGFLELGKAYSTDGLSETQ 238

Query: 250 KSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSS-------------ARKEGF 296
           ++M++D  D GLV  ++ +   ++ PT+LAT L+   +                A  +GF
Sbjct: 239 RNMLQDLRDYGLVYQRKRKSRRFY-PTRLATTLTSDSSALRTASSAMEAATSSEAASKGF 297

Query: 297 IVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIIS 356
           I+VETNFR+YAY++S L   IL LF +++Y+ PNL+VG IT+ES+ NA ENGITA+QIIS
Sbjct: 298 IIVETNFRLYAYTSSPLQIAILALFVELKYRFPNLVVGQITRESIRNALENGITADQIIS 357

Query: 357 FLQQNAHP 364
           +L+ +AHP
Sbjct: 358 YLETHAHP 365

Length = 365

>gnl\|CDD\|233058 TIGR00625, tfb2, Transcription factor tfb2	Back alignment and domain information

>gnl\|CDD\|227473 COG5144, TFB2, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>gnl\|CDD\|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		450
TIGR00625		448	tfb2 Transcription factor tfb2. This family is bas	100.0
KOG3471		465	consensus RNA polymerase II transcription initiati	100.0
COG5144		447	TFB2 RNA polymerase II transcription initiation/nu	100.0
PF03849		366	Tfb2: Transcription factor Tfb2; InterPro: IPR0045	100.0
PF13625		129	Helicase_C_3: Helicase conserved C-terminal domain	99.61
TIGR00603		732	rad25 DNA repair helicase rad25. All proteins in t	97.08
PF08671		30	SinI: Anti-repressor SinI; InterPro: IPR010981 The	90.69
PRK05718		212	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	81.5

>TIGR00625 tfb2 Transcription factor tfb2	Back alignment and domain information

Probab=100.00  E-value=3.4e-147  Score=1140.35  Aligned_cols=433  Identities=33%  Similarity=0.611  Sum_probs=411.6

Q ss_pred             hHHHHHhcCCHHHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceee
Q 013058           10 NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFS   89 (450)
Q Consensus        10 ~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~   89 (450)
                      +++|||++||+.++++||++||||+||||+||||||+|||||||+++|||.++++.|+++++++++++|+++|.+||||+
T Consensus         1 ~~~~yL~~Lp~~~~~~LY~~PatclAIfR~Lp~lAK~~vmrlL~~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~   80 (448)
T TIGR00625         1 SLQEFLEGLPPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFNEQPVPLADVDLWVKKEFKKAQEESTGLLSGLHIWH   80 (448)
T ss_pred             ChHHHHHhCCHHHHHHHhCCcHHHHHHHHcCcHHHHHHHHHHHcCCCCCCHHHHHHHhCccchHHHHHHHHHHHhCEeEE
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec-CCCceeEEeCHHHHHHHHHHHhcCCC-----CCCCCCCCCCCCCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCC
Q 013058           90 EE-KKKETTYRLNSTFQSNLRKHLIYGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTN  163 (450)
Q Consensus        90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~  163 (450)
                      +. .+|.+.|.|||+||+|||.||+|||+     +|+..++++    .+++++||+||++|||+|||||||++..   ..
T Consensus        81 ~~~~~~~~~~~Ln~~F~~~lr~aL~g~~~~~s~~v~~~~~d~~----~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~  153 (448)
T TIGR00625        81 TQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGPDKH----AVDVDSLDKYAEERWETILHFMVGTPSA---KV  153 (448)
T ss_pred             ecCCCCceeEEECHHHHHHHHHHhcCCCCCCCCCCcccCCCCC----CCCHHHHHHHHHHHHHHHHHHHcCCCCc---CC
Confidence            73 33557899999999999999999997     677777776    8999999999999999999999998754   57


Q ss_pred             CChhHHHHHHhCCCccCC--CCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCcccc
Q 013058          164 FSSSMMKVFQRGLLSRRD--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYN  241 (450)
Q Consensus       164 ~s~~v~~lL~~~gL~~~~--~~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~  241 (450)
                      +|++|+++|+++|||+.+  ++.+.||++||||||+|+|+|+|+||++||+++|++|+|++|+|+|||+||++++|++|+
T Consensus       154 ~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~lG~~Y~  233 (448)
T TIGR00625       154 PSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYS  233 (448)
T ss_pred             CchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCccC
Confidence            899999999999999973  335899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCCC----cc--ccccceEEEeeCceEEeecCChhHH
Q 013058          242 LNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD----SS--ARKEGFIVVETNFRMYAYSTSKLHC  315 (450)
Q Consensus       242 ~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~~----~~--~~~~g~IIvETNFrvYAYT~S~lqi  315 (450)
                      +++||++|++||+||+|+||||++++++++|| |||||++|+++.++    ++  +.++|||||||||||||||+|||||
T Consensus       234 ~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~  312 (448)
T TIGR00625       234 VDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQI  312 (448)
T ss_pred             CCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHH
Confidence            99999999999999999999999999999999 99999999886542    11  2567999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCcccc-ccCCCCChhHHHHHHHHHHhcCceeee
Q 013058          316 EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRMPSVPENVCDQIRLWESDLNRVEMT  394 (450)
Q Consensus       316 aiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~-~~~~~lP~tV~dQIrLWe~Er~R~~~~  394 (450)
                      +||++||++.|||||||||+||||||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||++++
T Consensus       313 ~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~  392 (448)
T TIGR00625       313 ALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFT  392 (448)
T ss_pred             HHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEee
Confidence            9999999999999999999999999999999999999999999999999998 478999999999999999999999999


Q ss_pred             cceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 013058          395 PAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK  450 (450)
Q Consensus       395 ~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr~f~k~~~~  450 (450)
                      +||||++|+|++||+++++||+++|||+|+|+.||+|||+.+||++||+|||++|+
T Consensus       393 ~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~  448 (448)
T TIGR00625       393 EGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH  448 (448)
T ss_pred             cceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence            99999999999999999999999999999999999999999999999999999986

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

>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]	Back alignment and domain information

>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]	Back alignment and domain information

>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair	Back alignment and domain information

>PF13625 Helicase_C_3: Helicase conserved C-terminal domain	Back alignment and domain information

>TIGR00603 rad25 DNA repair helicase rad25	Back alignment and domain information

>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []	Back alignment and domain information

>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional	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		450
3dom_A		108	Crystal Structure Of The Complex Between Tfb5 And T		5e-04

>pdb|3DOM|A Chain A, Crystal Structure Of The Complex Between Tfb5 And The C-Terminal Domain Of Tfb2 Length = 108

Back alignment and structure

Iteration: 1

Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust. Identities = 25/83 (30%), Positives = 42/83 (50%) Query: 364 PRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLW 423 P + + +P V DQIRLW+ +L+RV Y +F + + YA+D LLW Sbjct: 19 PNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLW 78 Query: 424 EDPKKMRLVVKAEIHMHMREFLR 446 +D KK + + E + + +F + Sbjct: 79 KDDKKKKFFISKEGNSQVLDFAK 101

PyMOL of 3dom

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		450
3dom_A		108	RNA polymerase II transcription factor B subunit;	7e-37
3dgp_A		80	RNA polymerase II transcription factor B subunit;	1e-29

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae} Length = 108	Back alignment and structure

 Score =  130 bits (327), Expect = 7e-37
 Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 1/100 (1%)

Query: 351 AEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 410
           AE+ +   +    P   + +  +P  V DQIRLW+ +L+RV       Y +F +   +  
Sbjct: 7   AEEKLEK-KLELDPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNL 65

Query: 411 ACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 450
              YA+D   LLW+D KK +  +  E +  + +F + + K
Sbjct: 66  LSKYAQDIGVLLWKDDKKKKFFISKEGNSQVLDFAKRKLK 105

PyMOL of 3dom

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae} Length = 80	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		450
3dom_A		108	RNA polymerase II transcription factor B subunit;	99.98
3dgp_A		80	RNA polymerase II transcription factor B subunit;	99.97
3jth_A		98	Transcription activator HLYU; transcription factor	81.21
3f6o_A		118	Probable transcriptional regulator, ARSR family pr	80.87
3pqk_A		102	Biofilm growth-associated repressor; helix-turn-he	80.63

>3dom_A RNA polymerase II transcription factor B subunit; protein-protein complex, heterodimer, beta-alpha-beta split, strand addition; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

Probab=99.98  E-value=1.8e-33  Score=240.18  Aligned_cols=88  Identities=30%  Similarity=0.586  Sum_probs=72.4

Q ss_pred             CccccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHH
Q 013058          363 HPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMR  442 (450)
Q Consensus       363 Hp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr  442 (450)
                      .|+++...|+|||||+|||||||.|||||++++||||++|.|+++|+.+++||+++|||+|+|+.+|+|||+.+||++||
T Consensus        18 ~~~~~~~~p~lPpTVvDQIrLWE~ErnRl~~~~G~LY~dF~s~~efe~v~~yA~e~gvLlW~d~~kr~~~Vs~egh~~vk   97 (108)
T 3dom_A           18 DPNCKEPLQVLPPTVVDQIRLWQLELDRVITYEGSLYSDFETSQEYNLLSKYAQDIGVLLWKDDKKKKFFISKEGNSQVL   97 (108)
T ss_dssp             --------------CCCHHHHHHHHHTTCEEEEEEEEECCSCHHHHHHHHHHHHHHTCEEEEEGGGTEEEEEGGGHHHHH
T ss_pred             CcccccCCCCCCCcHHHHHHHHHHhhCceeccceEEEecCCCHHHHHHHHHHHHHcCeEEEecCCccEEEEeccchHHHH
Confidence            35556667999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccC
Q 013058          443 EFLRGQNK  450 (450)
Q Consensus       443 ~f~k~~~~  450 (450)
                      +|||++++
T Consensus        98 ~f~Kr~~~  105 (108)
T 3dom_A           98 DFAKRKLK  105 (108)
T ss_dssp             HHHHHHC-
T ss_pred             HHHHHHHh
Confidence            99999875

PyMOL of 3dom

>3dgp_A RNA polymerase II transcription factor B subunit; protein-protein complex, beta-alpha-beta spilt, heterodimer, damage, DNA excision; 1.80A {Saccharomyces cerevisiae}	Back alignment and structure

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}	Back alignment and structure

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}	Back alignment and structure

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		450
d1r1ta_		98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	87.29

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=87.29  E-value=1.2  Score=34.68  Aligned_cols=84  Identities=13%  Similarity=0.159  Sum_probs=64.3

Q ss_pred             hcCCHHHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeecCC-C
Q 013058           16 ASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKK-K   94 (450)
Q Consensus        16 ~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~~-~   94 (450)
                      +.++|++++.|       -.+|+.|.+-.|.-|+++|. +++....++..-..- +.......++.|++.+|+...+. .
T Consensus         3 ~~~~pe~~~~l-------a~~~kaL~~p~Rl~Il~~L~-~~~~~v~ela~~l~i-s~stvS~HL~~L~~aglV~~~r~G~   73 (98)
T d1r1ta_           3 QAIAPEVAQSL-------AEFFAVLADPNRLRLLSLLA-RSELCVGDLAQAIGV-SESAVSHQLRSLRNLRLVSYRKQGR   73 (98)
T ss_dssp             CCCCHHHHHHH-------HHHHHHHCCHHHHHHHHHHT-TCCBCHHHHHHHHTC-CHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             ccCCHHHHHHH-------HHHHHHhCCHHHHHHHHHHH-cCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCceEEEEECC
Confidence            34667666643       47899888888888899885 678999999988765 46788899999999999987543 4


Q ss_pred             ceeEEeCHHHHHHH
Q 013058           95 ETTYRLNSTFQSNL  108 (450)
Q Consensus        95 ~~~~~Ln~~F~~~l  108 (450)
                      ...|.||+..-..+
T Consensus        74 ~~~Y~l~~~~i~~l   87 (98)
T d1r1ta_          74 HVYYQLQDHHIVAL   87 (98)
T ss_dssp             EEEEEESSHHHHHH
T ss_pred             EEEEEEChHHHHHH
Confidence            46788987654444

PyMOL of d1r1ta_