Citrus Sinensis ID: 013514

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-

MDQEQPQQPQQTQTPTPSTTTTTTANTASSTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccc

ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccc

mdqeqpqqpqqtqtptpsttttttantasstvttsqitapssqppqqqqqtpptpstpssttiptstpttntpnpnpspspspappsrptsltpppprptsfsrpwqppqqhfshfsslpssssatpstsasppipspprggiaigvpaprptalspqpsppfsssfgqpfgglgrsgvnvpdsvrppaiqgmgvmgslgsssqmrpagisvqhhqprpvqqsslrpppsspssqspgtqnfqgqglmrvsqvgspgssspntsqsvqsfnqpwlssgsqgkpplappstyrpqmntpsmqqrshipqqhsplstnlqqqhlssvqpqqskpshqlpdhygqqfssprvpqssphqqqitrppgsatqkpsslalvqpnavqtgnqskiagtesdefgnrilTKRSIQELVnqidpserldpdvEDILVDIAEDFVESVSS

mdqeqpqqpqqtqtptpsttttttantassTVTTSQITAPSSQPPQQQQQTPPTPSTPSSTTIPTSTPTTNTPNPNPSPSPSPAPPSRPTSLTPPPPRPTSFSRPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSLGSSSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSPNTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVqtgnqskiagtesdefgnrILTKRSIQELvnqidpserldpdVEDILVDIAEDFVESVSS

MDQEqpqqpqqtqtptpsttttttantasstvttsqitapssqppqqqqqtpptpstpssttiptstpttntpnpnpspspspappsrptsltpppprptsFSRPWQPPQQHFSHFsslpssssatpstsasppipsppRGGIAIGVPAPRPTALspqpsppfsssfgqpfggLGRSGVNVPDSVRPPAIQgmgvmgslgsssqmRPAGISVQHHqprpvqqsslrpppsspssqspGTQNFQGQGLMRvsqvgspgssspntsqsvqsFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLqqqhlssvqpqqsKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS

***************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************VEDILVDIAED*******

****************************************************************************************************************************************SPPRGGIAIGVPAPRPTALSPQPSPPFSSSFGQPFGGLGRSGVNVPDSVRPPAIQGMGVMGSL******************************************FQGQGLMRV************************************PPSTYRPQM*****************************************************************************LALVQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS

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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

No hits with e-value below 0.001 by BLAST

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		441
359481991		496	PREDICTED: uncharacterized protein LOC10	0.736	0.655	0.613	3e-88
297740082		372	unnamed protein product [Vitis vinifera]	0.560	0.663	0.675	8e-75
224087397		497	predicted protein [Populus trichocarpa]	0.721	0.639	0.544	1e-66
356548409		507	PREDICTED: uncharacterized protein LOC10	0.634	0.552	0.524	3e-59
356537087		507	PREDICTED: uncharacterized protein LOC10	0.600	0.522	0.536	3e-58
449482360		511	PREDICTED: uncharacterized protein LOC10	0.648	0.559	0.546	6e-56
297833786		541	tata-associated factor II 58 [Arabidopsi	0.752	0.613	0.501	4e-54
449451128		511	PREDICTED: uncharacterized protein LOC10	0.648	0.559	0.530	7e-53
255575631		451	protein with unknown function [Ricinus c	0.444	0.434	0.609	3e-52
18398741		539	transcription initiation factor TFIID su	0.752	0.615	0.490	1e-51

>gi\|359481991\|ref\|XP_002277150.2\| PREDICTED: uncharacterized protein LOC100242486 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  332 bits (850), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 222/362 (61%), Positives = 255/362 (70%), Gaps = 37/362 (10%)

Query: 104 RPWQPPQQHFSHFSSLPSSSSATPSTSASPPIPSPP--------RGGIAIGVPAPRPTAL 155
           RPWQ  Q HF HFSS  SSSS++ ST +     S          RGGIAIGVPA +PT  
Sbjct: 44  RPWQQ-QSHFQHFSSNLSSSSSSSSTPSLSTSTSSSAVSAPPSQRGGIAIGVPAGQPT-- 100

Query: 156 SPQPSPPFSS----SFGQPFGGLGRSGVNVPDSVR-------PPAIQG---MGVMGSLGS 201
                 PFSS    +FGQ +GGLGRS VNVP+SV         P+IQG   MG+MG+LGS
Sbjct: 101 ------PFSSLNPPTFGQQYGGLGRSAVNVPESVANTNTSQVRPSIQGSQGMGMMGTLGS 154

Query: 202 SSQMRPAGISVQHHQPRPVQQSSLRPPPSSPSSQSPGTQNFQGQGLMRVSQVGSPGSSSP 261
            SQMRP GIS  HHQ RPVQ SSLRP  S+ ++QSP TQNFQG GL+R S VGSPG+ SP
Sbjct: 155 GSQMRPGGISA-HHQQRPVQ-SSLRPQ-STVNNQSPATQNFQGHGLLRASSVGSPGAPSP 211

Query: 262 NTSQSVQSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHS-PL-STNLQQ 319
           NTSQS+Q  NQPWLSSGSQGKPPL  PS +RPQM   S+ QRSHIPQQH  PL + + QQ
Sbjct: 212 NTSQSMQPHNQPWLSSGSQGKPPLPSPS-FRPQMTAQSLPQRSHIPQQHHHPLPTASQQQ 270

Query: 320 QHLSSVQPQQSKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALVQPN 379
           Q  ++ QPQQ   SHQ  +HYGQQF   RVPQS PH QQI R  GS  QKPSSLA+VQP+
Sbjct: 271 QMSTAQQPQQPLLSHQQQEHYGQQFPPSRVPQSLPHPQQIGRVQGSGNQKPSSLAIVQPS 330

Query: 380 AVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439
             Q G  S+ A  E+ E GNRIL+KRSI ELVNQIDPSE+LDP+VEDILVDIAEDFVES+
Sbjct: 331 TPQLGPHSRTASAEASESGNRILSKRSIHELVNQIDPSEKLDPEVEDILVDIAEDFVESI 390

Query: 440 SS 441
           ++
Sbjct: 391 TT 392

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297740082\|emb\|CBI30264.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224087397\|ref\|XP_002308150.1\| predicted protein [Populus trichocarpa] gi\|222854126\|gb\|EEE91673.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|356548409\|ref\|XP_003542594.1\| PREDICTED: uncharacterized protein LOC100787779 [Glycine max]	Back alignment and taxonomy information

>gi\|356537087\|ref\|XP_003537062.1\| PREDICTED: uncharacterized protein LOC100781682 [Glycine max]	Back alignment and taxonomy information

>gi\|449482360\|ref\|XP_004156257.1\| PREDICTED: uncharacterized protein LOC101226357 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|297833786\|ref\|XP_002884775.1\| tata-associated factor II 58 [Arabidopsis lyrata subsp. lyrata] gi\|297330615\|gb\|EFH61034.1\| tata-associated factor II 58 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|449451128\|ref\|XP_004143314.1\| PREDICTED: uncharacterized protein LOC101211513 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255575631\|ref\|XP_002528715.1\| protein with unknown function [Ricinus communis] gi\|223531809\|gb\|EEF33627.1\| protein with unknown function [Ricinus communis]	Back alignment and taxonomy information

>gi|18398741|ref|NP_566367.1| transcription initiation factor TFIID subunit D10 [Arabidopsis thaliana] gi|6143870|gb|AAF04417.1|AC010927_10 unknown protein [Arabidopsis thaliana] gi|13492646|gb|AAK28289.1|AF344878_1 putative TBP-associated 58 kDa subunit protein [Arabidopsis thaliana] gi|39545904|gb|AAR28015.1| TAF12 [Arabidopsis thaliana] gi|62320727|dbj|BAD95394.1| hypothetical protein [Arabidopsis thaliana] gi|332641335|gb|AEE74856.1| transcription initiation factor TFIID subunit D10 [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		441
TAIR\|locus:2100053		539	TAF12 "TBP-associated factor 1	0.736	0.602	0.358	5.7e-43
TAIR\|locus:2018861		683	EER4 "ENHANCED ETHYLENE RESPON	0.374	0.241	0.329	4.2e-14
UNIPROTKB\|Q5ZKX3		161	TAF12 "Uncharacterized protein	0.174	0.478	0.430	5.8e-11
UNIPROTKB\|G3MXQ4		161	G3MXQ4 "Uncharacterized protei	0.158	0.434	0.456	2e-10
MGI\|MGI:1913714		161	Taf12 "TAF12 RNA polymerase II	0.160	0.440	0.423	3.5e-10
RGD\|1592841		161	Taf12 "TAF12 RNA polymerase II	0.167	0.459	0.402	3.5e-10
UNIPROTKB\|Q3T174		161	TAF12 "Transcription initiatio	0.158	0.434	0.444	4.6e-10
UNIPROTKB\|E2QVZ3		161	TAF12 "Uncharacterized protein	0.174	0.478	0.392	6.2e-10
UNIPROTKB\|Q16514		161	TAF12 "Transcription initiatio	0.174	0.478	0.392	1.1e-09
ZFIN\|ZDB-GENE-031030-5		162	taf12 "TAF12 RNA polymerase II	0.163	0.444	0.435	1.4e-09

TAIR\|locus:2100053 TAF12 "TBP-associated factor 12" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 129/360 (35%), Positives = 159/360 (44%)

Query:   102 FSRPWQPPQQHFSHFXXXXXXXXXXXXXXXXXXXXX----XXRGGIAIGVPA-----PRP 152
             +SRPWQ     ++HF                           RGG+AIGVPA     P P
Sbjct:    95 YSRPWQQ-HSSYTHFSSASSPLLSSSSAPASSSSSLPISGQQRGGMAIGVPASPIPSPSP 153

Query:   153 TALXXXXXXXXXXXXXXXXXXLGRSGVNVPDSVR---PPAI------QXXXXXXXXXXXX 203
             T                    LGR  V + ++      P +      Q            
Sbjct:   154 TP-SQHSPSAFPGSFGQQYGGLGRGTVGMSEATSNTSSPQVRMMQGTQGIGMMGTLGSGS 212

Query:   204 XXRPAGISVQHHXXXXXXXXXXXXXXXXXXXXXXGTQNFQGQGLMRXXXXXX-XXXXXXX 262
               RP+G++ QH                         QNFQG  LMR              
Sbjct:   213 QIRPSGMT-QHQQRPTQSSLRPASSTSTQSPVA---QNFQGHSLMRPSPISSPNVQSTGA 268

Query:   263 XXXXXXXFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLXXXXX 322
                     NQPWLSS  QGKPPL PPS YRPQ+N+PSMQQR HIPQQH  +ST+      
Sbjct:   269 SQQSLQAINQPWLSSTPQGKPPLPPPS-YRPQVNSPSMQQRPHIPQQH--ISTS---AAT 322

Query:   323 XXXXXXXXKPSHQLPDHYGQQFSSPRVPQSSPHQQQITRPPGSATQKPSSLALV-QPNAV 381
                     +  HQ P    QQ  SP+ P + PHQ   TR  G   QK +S  +  QP   
Sbjct:   323 PQPQQQQSQQQHQ-PQEQLQQLRSPQQPLAHPHQP--TRVQGLVNQKVTSPVMPSQPPVA 379

Query:   382 QTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS 441
             Q GN +K    E++   +RIL KRSI EL+ QIDPSE+LDP+VEDIL DIAEDFVES+++
Sbjct:   380 QPGNHAKTVSAETEPSDDRILGKRSIHELLQQIDPSEKLDPEVEDILSDIAEDFVESITT 439

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0006352 "DNA-dependent transcription, initiation" evidence=IEA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

TAIR\|locus:2018861 EER4 "ENHANCED ETHYLENE RESPONSE 4" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZKX3 TAF12 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|G3MXQ4 G3MXQ4 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:1913714 Taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

RGD\|1592841 Taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3T174 TAF12 "Transcription initiation factor TFIID subunit 12" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QVZ3 TAF12 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|Q16514 TAF12 "Transcription initiation factor TFIID subunit 12" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-031030-5 taf12 "TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor" [Danio rerio (taxid:7955)]	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:
	GSVIVG00021654001	SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (351 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00032691001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (676 aa)	•	•	•		0.640
	GSVIVG00034077001	SubName- Full=Chromosome chr9 scaffold_7, whole genome shotgun sequence; (177 aa)	•	•			0.574
	GSVIVG00014940001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (712 aa)	•	•	•	•	0.551
	GSVIVG00018562001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (1798 aa)	•	•			0.456

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		441
cd07981		72	cd07981, TAF12, TATA Binding Protein (TBP) Associa	7e-18
pfam03847		67	pfam03847, TFIID_20kDa, Transcription initiation f	4e-17
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	2e-10
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	5e-08
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	8e-08
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	1e-07
PHA03247		3151	PHA03247, PHA03247, large tegument protein UL36; P	9e-07
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-07
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	9e-07
pfam04652		315	pfam04652, DUF605, Vta1 like	1e-06
pfam04652		315	pfam04652, DUF605, Vta1 like	7e-06
pfam04652		315	pfam04652, DUF605, Vta1 like	7e-06
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-05
PRK14950		585	PRK14950, PRK14950, DNA polymerase III subunits ga	1e-05
PRK14950		585	PRK14950, PRK14950, DNA polymerase III subunits ga	1e-05
PRK07994		647	PRK07994, PRK07994, DNA polymerase III subunits ga	1e-05
PRK14971		614	PRK14971, PRK14971, DNA polymerase III subunits ga	2e-05
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-05
PRK07994		647	PRK07994, PRK07994, DNA polymerase III subunits ga	3e-05
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	3e-05
PRK14950		585	PRK14950, PRK14950, DNA polymerase III subunits ga	4e-05
COG3889		872	COG3889, COG3889, Predicted solute binding protein	4e-05
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	8e-05
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	1e-04
PRK10856		331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	1e-04
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-04
pfam09770		804	pfam09770, PAT1, Topoisomerase II-associated prote	2e-04
PRK10856		331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	2e-04
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	2e-04
PRK12270		1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	2e-04
pfam04652		315	pfam04652, DUF605, Vta1 like	3e-04
PRK10856		331	PRK10856, PRK10856, cytoskeletal protein RodZ; Pro	3e-04
PRK11907		814	PRK11907, PRK11907, bifunctional 2',3'-cyclic nucl	3e-04
PRK14951		618	PRK14951, PRK14951, DNA polymerase III subunits ga	3e-04
PRK13042		291	PRK13042, PRK13042, superantigen-like protein; Rev	3e-04
pfam05539		408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	3e-04
pfam05086		910	pfam05086, Dicty_REP, Dictyostelium (Slime Mold) R	4e-04
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	5e-04
PRK12270		1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	5e-04
PHA02638		417	PHA02638, PHA02638, CC chemokine receptor-like pro	5e-04
PRK13335		356	PRK13335, PRK13335, superantigen-like protein; Rev	5e-04
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	6e-04
PRK12323		700	PRK12323, PRK12323, DNA polymerase III subunits ga	6e-04
PRK14971		614	PRK14971, PRK14971, DNA polymerase III subunits ga	7e-04
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	7e-04
pfam11725		1771	pfam11725, AvrE, Pathogenicity factor	8e-04
PRK14971		614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.001
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.001
pfam01034		207	pfam01034, Syndecan, Syndecan domain	0.001
PRK07994		647	PRK07994, PRK07994, DNA polymerase III subunits ga	0.002
PRK14971		614	PRK14971, PRK14971, DNA polymerase III subunits ga	0.002
PRK14948		620	PRK14948, PRK14948, DNA polymerase III subunits ga	0.002
PRK12270		1228	PRK12270, kgd, alpha-ketoglutarate decarboxylase;	0.002
PRK14951		618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.002
PLN02258		590	PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygen	0.002
PRK14951		618	PRK14951, PRK14951, DNA polymerase III subunits ga	0.003
pfam05539		408	pfam05539, Pneumo_att_G, Pneumovirinae attachment	0.003
pfam05086		910	pfam05086, Dicty_REP, Dictyostelium (Slime Mold) R	0.003
PRK07003		830	PRK07003, PRK07003, DNA polymerase III subunits ga	0.003
PHA03307		1352	PHA03307, PHA03307, transcriptional regulator ICP4	0.004
PRK07764		824	PRK07764, PRK07764, DNA polymerase III subunits ga	0.004

>gnl\|CDD\|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex	Back alignment and domain information

 Score = 77.3 bits (191), Expect = 7e-18
 Identities = 25/41 (60%), Positives = 35/41 (85%)

Query: 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS 441
           ILTKR +QEL+ +IDP E+LDPDVE++L++IA+DFV+ V  
Sbjct: 1   ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVE 41

The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF12 domain interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. Length = 72

>gnl\|CDD\|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID subunit A	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|226406 COG3889, COG3889, Predicted solute binding protein [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1	Back alignment and domain information

>gnl\|CDD\|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed	Back alignment and domain information

>gnl\|CDD\|218191 pfam04652, DUF605, Vta1 like	Back alignment and domain information

>gnl\|CDD\|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional	Back alignment and domain information

>gnl\|CDD\|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed	Back alignment and domain information

>gnl\|CDD\|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|183854 PRK13042, PRK13042, superantigen-like protein; Reviewed	Back alignment and domain information

>gnl\|CDD\|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G	Back alignment and domain information

>gnl\|CDD\|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed	Back alignment and domain information

>gnl\|CDD\|165021 PHA02638, PHA02638, CC chemokine receptor-like protein; Provisional	Back alignment and domain information

>gnl\|CDD\|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|221188 pfam11725, AvrE, Pathogenicity factor	Back alignment and domain information

>gnl\|CDD\|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|216257 pfam01034, Syndecan, Syndecan domain	Back alignment and domain information

>gnl\|CDD\|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|237030 PRK12270, kgd, alpha-ketoglutarate decarboxylase; Reviewed	Back alignment and domain information

>gnl\|CDD\|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED	Back alignment and domain information

>gnl\|CDD\|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau; Provisional	Back alignment and domain information

>gnl\|CDD\|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane glycoprotein G	Back alignment and domain information

>gnl\|CDD\|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein	Back alignment and domain information

>gnl\|CDD\|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

>gnl\|CDD\|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional	Back alignment and domain information

>gnl\|CDD\|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		441
KOG1142		258	consensus Transcription initiation factor TFIID, s	99.89
PF03847		68	TFIID_20kDa: Transcription initiation factor TFIID	99.46
COG5624		505	TAF61 Transcription initiation factor TFIID, subun	99.08
cd07981		72	TAF12 TATA Binding Protein (TBP) Associated Factor	99.05
PF00808		65	CBFD_NFYB_HMF: Histone-like transcription factor (	85.04

>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]	Back alignment and domain information

Probab=99.89  E-value=9.3e-24  Score=201.44  Aligned_cols=166  Identities=28%  Similarity=0.339  Sum_probs=114.5

Q ss_pred             cccCccccccCCCCCCCCCCCCCCCCCCCCcchhccccCcccCCCCcchhhhhhcccccCCCCCCCCCCccccccccCC-
Q 013514          268 QSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSS-  346 (441)
Q Consensus       268 Q~~nQ~WLss~~q~kppl~SP~s~R~Q~n~~slQQR~hipqQh~~~~t~lqqqqlsq~QqqQ~q~~hqqq~H~~QQl~q-  346 (441)
                      |..++.||+.+..+.++...+ +||+|++.+.+.+|.++.+|+-+..-..  .+.   ........+...+|+. ++.. 
T Consensus        25 q~~qq~~~~~~~~~~s~~~~~-s~~~q~~~~~~~~~~~~~qq~~s~~~~~--~~~---~n~~~~s~~~~~~~~~-~~~~~   97 (258)
T KOG1142|consen   25 QARQQQWLRQIQGIPSPESYP-SQRQQRFSPTCSIRENPNQQWISTGYPQ--PQV---SNGGPPSQALNQQDSQ-QSAIS   97 (258)
T ss_pred             HHHHhhhhccccCCCCCCCCh-hhccccCCCcccccCCCCccccccccCc--ccc---ccCCchHHhhhhhhHH-hhccc
Confidence            456889999999999888886 9999999999999988888875443321  011   0111111111112222 2211 


Q ss_pred             -CCCCCCCccccccCCCCCCCCCCcccccc-CCCCccccCCcccCCCcccCCCCCcccchhHHHHHHHhcCCCCCCChHH
Q 013514          347 -PRVPQSSPHQQQITRPPGSATQKPSSLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDV  424 (441)
Q Consensus       347 -~q~~q~l~qQqQ~~R~~g~a~qKp~SLtg-sQP~~~~~G~ttk~~~~~~~~~gnrVLtKrKLqELVrQVDP~e~LDpDV  424 (441)
                       .+.++....+....+++...+++...-.. ++......|++.++.....++++++||+|+||+|||++||.+++||+||
T Consensus        98 ~~q~P~~~~~q~~~~~~~~~~~~~~~~P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId~~~~LD~dV  177 (258)
T KOG1142|consen   98 QQQQPASSPSQGSSMSNQTSSVQKDPAPVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQIDGTTKLDDDV  177 (258)
T ss_pred             cCCCCccCCCCCCCccccCcccccCCCCCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhcCcccccHHH
Confidence             34444555566666667777766654433 2233333344455666677889999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhc
Q 013514          425 EDILVDIAEDFVESVS  440 (441)
Q Consensus       425 EElLLdLADDFVdSVv  440 (441)
                      |||||||||||||+|+
T Consensus       178 edlLleiADdFV~sii  193 (258)
T KOG1142|consen  178 EDLLLEIADDFVSSII  193 (258)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            9999999999999997

>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []	Back alignment and domain information

>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]	Back alignment and domain information

>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex	Back alignment and domain information

>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin	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		441
1h3o_B		76	Crystal Structure Of The Human Taf4-Taf12 (Tafii135		2e-07

>pdb|1H3O|B Chain B, Crystal Structure Of The Human Taf4-Taf12 (Tafii135-Tafii20) Complex Length = 76

Back alignment and structure

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/39 (56%), Positives = 34/39 (87%)
Query: 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439
           +LTK+ +Q+LV ++DP+E+LD DVE+ L+ IA+DF+ESV
Sbjct: 5   VLTKKKLQDLVREVDPNEQLDEDVEEXLLQIADDFIESV 43
  Database: pdbaa

PyMOL of 1h3o

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		441
1h3o_B		76	Transcription initiation factor TFIID 20/15 kDa su	5e-20
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	8e-11
1twf_A		1733	B220, DNA-directed RNA polymerase II largest subun	3e-08
3h0g_A		1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-09
3h0g_A		1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-08
3h0g_A		1752	DNA-directed RNA polymerase II subunit RPB1; trans	8e-07
3h0g_A		1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-06
3dzy_A		467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-06
3dzy_A		467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	1e-04
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-06
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	4e-06
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	6e-06
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	1e-05
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-05
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	3e-05
1m2v_B		926	SEC24, protein transport protein SEC24, SEC24P, SE	9e-05
3nwa_A		703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	1e-05
3nwa_A		703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	2e-04
3nwa_A		703	GB, GB-1, GB1, envelope glycoprotein B; coiled-coi	3e-04
1pk8_A		422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	2e-05
1pk8_A		422	RAT synapsin I; ATP binding, ATP grAsp, calcium (I	5e-05
3v1v_A		433	2-MIB synthase, 2-methylisoborneol synthase; class	2e-05
3v1v_A		433	2-MIB synthase, 2-methylisoborneol synthase; class	3e-05
3v1v_A		433	2-MIB synthase, 2-methylisoborneol synthase; class	5e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
2z73_A		448	Rhodopsin; visual pigment, GQ-type, G-protein coup	4e-05
3sv0_A		483	Casein kinase I-like; typical kinase domain fold,	1e-04

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3 Length = 76	Back alignment and structure

 Score = 82.9 bits (205), Expect = 5e-20
 Identities = 22/44 (50%), Positives = 37/44 (84%)

Query: 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS 441
            + +LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ESV +
Sbjct: 2   SHMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVT 45

PyMOL of 1h3o

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733	Back alignment and structure

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752	Back alignment and structure

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752	Back alignment and structure

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752	Back alignment and structure

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752	Back alignment and structure

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467	Back alignment and structure

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein, abnormal nuclear; zinc-finger, beta barrel, VWA domain, gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1 Length = 926	Back alignment and structure

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703	Back alignment and structure

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703	Back alignment and structure

>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane fusion, viral P glycoprotein B, HSV-1, membrane; HET: NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A* 3nwd_A* Length = 703	Back alignment and structure

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422	Back alignment and structure

>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A* Length = 422	Back alignment and structure

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433	Back alignment and structure

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433	Back alignment and structure

>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid cyclase fold, DDXXXXD motif, NDXXSXXXE MOT methylisoborneol biosynthesis; HET: GST; 1.80A {Streptomyces coelicolor} PDB: 3v1x_A* Length = 433	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

>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor, chromophore, glycoprotein, lipoprotein, membrane, palmitate phosphorylation; HET: BOG RET PLM TWT PC1; 2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A* Length = 448	Back alignment and structure

>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol, transferase; 2.00A {Oryza sativa japonica group} Length = 483	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		441
1h3o_B		76	Transcription initiation factor TFIID 20/15 kDa su	99.6
3b0c_W		76	CENP-W, centromere protein W; histone fold, DNA bi	93.99
1ku5_A		70	HPHA, archaeal histon; histone fold, DNA binding p	88.82
1id3_B		102	Histone H4; nucleosome core particle, chromatin, p	88.57
2hue_C		84	Histone H4; mini beta sheet, elongated beta sandwh	87.48
1b67_A		68	Protein (histone HMFA); DNA binding protein; 1.48A	86.65
1tzy_D		103	Histone H4-VI; histone-fold, tetramer-dimer-dimer,	84.63
2yfw_B		103	Histone H4, H4; cell cycle, kinetochore, centromer	83.25

>1h3o_B Transcription initiation factor TFIID 20/15 kDa subunits; transcription/TBP-associated factors, TBP-associated factors; 2.3A {Homo sapiens} SCOP: a.22.1.3	Back alignment and structure

Probab=99.60  E-value=4e-16  Score=125.17  Aligned_cols=44  Identities=50%  Similarity=0.908  Sum_probs=41.4

Q ss_pred             CCcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhcC
Q 013514          398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS  441 (441)
Q Consensus       398 gnrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVvS  441 (441)
                      ..+||+|++|+|||++|||++.||+||||+||+|||||||+|++
T Consensus         2 s~~vl~k~~L~~Lv~~idp~~~ld~~vee~ll~lADdFV~~V~~   45 (76)
T 1h3o_B            2 SHMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVT   45 (76)
T ss_dssp             -CCSSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999999999999999973

PyMOL of 1h3o

>3b0c_W CENP-W, centromere protein W; histone fold, DNA binding, DNA binding protein; HET: CIT; 2.20A {Gallus gallus} PDB: 3b0d_W* 3vh5_W 3vh6_W	Back alignment and structure

>1ku5_A HPHA, archaeal histon; histone fold, DNA binding protein; 2.30A {Pyrococcus horikoshii} SCOP: a.22.1.2	Back alignment and structure

>1id3_B Histone H4; nucleosome core particle, chromatin, protein/DNA interaction, nucleoprotein, supercoiled DNA; 3.10A {Saccharomyces cerevisiae} SCOP: a.22.1.1	Back alignment and structure

>2hue_C Histone H4; mini beta sheet, elongated beta sandwhich, DNA binding prote; 1.70A {Xenopus laevis} SCOP: a.22.1.1 PDB: 3nqj_B 1aoi_B 3kwq_B* 1hio_D 2yfv_B	Back alignment and structure

>1b67_A Protein (histone HMFA); DNA binding protein; 1.48A {Methanothermus fervidus} SCOP: a.22.1.2 PDB: 1hta_A 1a7w_A 1b6w_A 1bfm_A	Back alignment and structure

>1tzy_D Histone H4-VI; histone-fold, tetramer-dimer-dimer, DNA binding protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB: 1f66_B 1eqz_D 1hq3_D 1u35_B 2aro_D 2cv5_B* 2f8n_B 3nqu_B 3r45_B 3azg_B 3a6n_B 3an2_B 3av1_B 3av2_B 3ayw_B 3aze_B 3azf_B 3afa_B 3azh_B 3azk_B ...	Back alignment and structure

>2yfw_B Histone H4, H4; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.60A {Kluyveromyces lactis nrrl y-1140}	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		441
d1h3ob_		74	a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), hi	2e-21

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]} Length = 74	Back information, alignment and structure


class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.9 bits (213), Expect = 2e-21
 Identities = 22/43 (51%), Positives = 37/43 (86%)

Query: 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS 441
           + +LTK+ +Q+LV ++DP+E+LD DVE++L+ IA+DF+ESV +
Sbjct: 1   HMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVT 43

PyMOL of d1h3ob_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		441
d1h3ob_		74	TAF(II)-20, (TAF(II)-15, hTAF12), histone fold dom	99.6
d1htaa_		68	Archaeal histone {Archaeon Methanothermus fervidus	87.76
d1n1ja_		87	Nuclear transcription factor Y subunit beta (Nf-Yb	82.66
d1fx0a1		129	F1 ATP synthase alpha subunit, domain 3 {Spinach (	82.19
d1ku5a_		66	Archaeal histone {Archaeon (Pyrococcus horikoshii)	82.11

>d1h3ob_ a.22.1.3 (B:) TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: TBP-associated factors, TAFs
domain: TAF(II)-20, (TAF(II)-15, hTAF12), histone fold domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=2.2e-16  Score=124.52  Aligned_cols=42  Identities=52%  Similarity=0.936  Sum_probs=40.9

Q ss_pred             CcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514          399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS  440 (441)
Q Consensus       399 nrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv  440 (441)
                      |.||+|+||+|||++|||++.||+||||+||+|||||||+|+
T Consensus         1 ~~il~K~~L~eLv~~idp~~~ld~~vee~ll~iADdFV~~V~   42 (74)
T d1h3ob_           1 HMVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVV   42 (74)
T ss_dssp             CCSSCHHHHHHHHHHHCSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CccccHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            579999999999999999999999999999999999999997

PyMOL of d1h3ob_

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}	Back information, alignment and structure

>d1n1ja_ a.22.1.3 (A:) Nuclear transcription factor Y subunit beta (Nf-Yb3) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fx0a1 a.69.1.1 (A:373-501) F1 ATP synthase alpha subunit, domain 3 {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}	Back information, alignment and structure

>d1ku5a_ a.22.1.2 (A:) Archaeal histone {Archaeon (Pyrococcus horikoshii) [TaxId: 53953]}	Back information, alignment and structure