YRC Public Data Repository - Protein Structure Prediction

Protein:	TFA1
Organism:	Saccharomyces cerevisiae
Length:	482 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for TFA1.

Description	E-value	Query Range	Subject Range
TFA1 - TFIIE large subunit, involved in recruitment of RNA polymerase II to the promoter, activation of TFI... T2EA_YEAST - Transcription initiation factor IIE subunit alpha OS=Saccharomyces cerevisiae (strain ATCC 204508 / ...	0.0	[1..462]	[1..462]
GTF2E1 - general transcription factor IIE, polypeptide 1, alpha 56kDa	8.0E-87	[5..387]	[10..365]
tfa1 - transcription factor TFIIE alpha subunit Tfa1 T2EA_SCHPO - Transcription initiation factor IIE subunit alpha OS=Schizosaccharomyces pombe (strain 972 / ATCC 24...	1.0E-85	[6..463]	[5..411]
T2EA_MOUSE - General transcription factor IIE subunit 1 OS=Mus musculus GN=Gtf2e1 PE=1 SV=1	4.0E-83	[5..345]	[10..335]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	2.0E-80	[5..341]	[10..326]
gi\|32412670, gi\|... - gi\|32412670\|ref\|XP_326815.1\| hypothetical protein ( (AL451017) related to transcription initiation f... gi\|85102867 - gi\|85102867\|ref\|XP_961408.1\| hypothetical protein NCU01322 [Neurospora crassa OR74A]	8.0E-72	[7..349]	[2..329]
gi\|20465667, gi\|... - gi\|39545888\|gb\|AAR28007.1\| TFIIE-alpha 1 [Arabidopsis thaliana], gi\|20465667\|gb\|AAM20302.1\| unknown ...	3.0E-66	[5..413]	[13..427]
TfIIEalpha-PA - The gene Transcription factor IIEÃ?Ã?Â± is referred to in FlyBase by the symbol Dmel\TfIIEÃ?&#... gi\|220952772, gi... - gi\|220952772\|gb\|ACL88929.1\| TfIIEalpha-PA [synthetic construct], gi\|220944528\|gb\|ACL84807.1\| TfIIEal...	3.0E-61	[5..299]	[24..289]

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Predicted Domain #1

Region A:
Residues: [1-219]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDRPIDDIVK NLLKFVVRGF YGGSFVLVLD AILFHSVLAE DDLKQLLSIN KTELGPLIAR  60
   61 LRSDRLISIH KQREYPPNSK SVERVYYYVK YPHAIDAIKW KVHQVVQRLK DDLDKNSEPN 120
  121 GYMCPICLTK YTQLEAVQLL NFDRTEFLCS LCDEPLVEDD SGKKNKEKQD KLNRLMDQIQ 180
  181 PIIDSLKKID DSRIEENTFE IALARLIPPQ NQSHAAYTY

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	96.420216
Match:	PF02002
Description:	TFIIE alpha subunit

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	5.67074370996647	bayes_pls_golite062009
transcription regulator activity	5.55329976718261	bayes_pls_golite062009
DNA binding	4.84466441605416	bayes_pls_golite062009
nucleic acid binding	4.57954522145536	bayes_pls_golite062009
transcription factor activity	4.12685284895733	bayes_pls_golite062009
binding	4.05190810999633	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.60738445921725	bayes_pls_golite062009
sequence-specific DNA binding	2.3918869755162	bayes_pls_golite062009
transcription activator activity	2.37668609508629	bayes_pls_golite062009
transcription repressor activity	2.22485867684613	bayes_pls_golite062009
DNA-directed RNA polymerase activity	1.82365519759474	bayes_pls_golite062009
RNA polymerase activity	1.82365519759474	bayes_pls_golite062009
protein binding	0.961087148890615	bayes_pls_golite062009
transcription factor binding	0.85714789329232	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	0.66743181561551	bayes_pls_golite062009
nucleotidyltransferase activity	0.237727660028553	bayes_pls_golite062009
RNA polymerase II transcription factor activity, enhancer binding	0.0360186926687502	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [220-482]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NPKKGSTMFR PGDSAPLPNL MGTALGNDSS RRAGANSQAT LHINITTASD EVAQRELQER  60
   61 QAEEKRKQNA VPEWHKQSTI GKTALGRLDN EEEFDPVVTA SAMDSINPDN EPAQETSYQN 120
  121 NRTLTEQEME ERENEKTLND YYAALAKKQA KLNKEEEEEE EEEEDEEEEE EEEMEDVMDD 180
  181 NDETARENAL EDEFEDVTDT AGTAKTESNT SNDVKQESIN DKTEDAVNAT ATASGPSANA 240
  241 KPNDGDDDDD DDDDEMDIEF EDV

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted functions:

Term	Confidence	Notes
general RNA polymerase II transcription factor activity	7.54088990789822	bayes_pls_golite062009
DNA-directed RNA polymerase activity	6.31798033897642	bayes_pls_golite062009
RNA polymerase activity	6.31798033897642	bayes_pls_golite062009
nucleotidyltransferase activity	3.73777657415367	bayes_pls_golite062009
transcription regulator activity	3.36253105801209	bayes_pls_golite062009
binding	2.58311326284197	bayes_pls_golite062009
transcription elongation regulator activity	2.03339710864117	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.95080397433956	bayes_pls_golite062009
nucleic acid binding	1.8086747972572	bayes_pls_golite062009
DNA binding	1.76634962183736	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.57988053581899	bayes_pls_golite062009
DNA primase activity	1.01743034310838	bayes_pls_golite062009
protein binding	0.764662055834369	bayes_pls_golite062009
catalytic activity	0.434839928397784	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [167-482]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EKQDKLNRLM DQIQPIIDSL KKIDDSRIEE NTFEIALARL IPPQNQSHAA YTYNPKKGST  60
   61 MFRPGDSAPL PNLMGTALGN DSSRRAGANS QATLHINITT ASDEVAQREL QERQAEEKRK 120
  121 QNAVPEWHKQ STIGKTALGR LDNEEEFDPV VTASAMDSIN PDNEPAQETS YQNNRTLTEQ 180
  181 EMEERENEKT LNDYYAALAK KQAKLNKEEE EEEEEEEDEE EEEEEEMEDV MDDNDETARE 240
  241 NALEDEFEDV TDTAGTAKTE SNTSNDVKQE SINDKTEDAV NATATASGPS ANAKPNDGDD 300
  301 DDDDDDDEMD IEFEDV

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: