YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213973981
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. AG3
Length:	288 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 gi|213973981.

Description	E-value	Query Range	Subject Range
gi\|197244088, gi... - gi\|197265833\|ref\|ZP_03165907.1\| transcription activator, effector binding [Salmonella enterica subsp... gi\|205331279, gi... - gi\|205331279\|gb\|EDZ18043.1\| transcription activator, effector binding [Salmonella enterica subsp. en... gi\|16421731, gi\|... - gi\|16766475\|ref\|NP_462090.1\| putative regulatory protein [Salmonella typhimurium LT2], gi\|16421731\|g... lcl\|NC_016856.1_... - [gene=STM14_3847] [protein=putative regulatory protein] [protein_id=YP_005239346.1] [location=comple...	2.0E-66	[1..288]	[1..288]
gi\|56129373, gi\|... - gi\|56415116\|ref\|YP_152191.1\| AraC family transcription regulator [Salmonella enterica subsp. enteric... gi\|197364045, gi... - gi\|197364045\|ref\|YP_002143682.1\| possible AraC-family transcriptional regulator [Salmonella enterica...	2.0E-66	[1..288]	[1..288]
gi\|62129322, gi\|... - gi\|62181689\|ref\|YP_218106.1\| AraC family regulatory protein [Salmonella enterica subsp. enterica ser... gi\|224584975, gi... - gi\|224584975\|ref\|YP_002638774.1\| possible AraC-family transcriptional regulator [Salmonella enterica... gi\|194446792, gi... - gi\|194446792\|ref\|YP_002042440.1\| transcription activator, effector binding [Salmonella enterica subs...	3.0E-66	[1..288]	[1..288]
gi\|34499596, gi\|... - gi\|34499596\|ref\|NP_903811.1\| AraC family transcription regulator [Chromobacterium violaceum ATCC 124...	1.0E-62	[6..288]	[4..286]
gi\|228655231, gi... - gi\|229128372\|ref\|ZP_04257353.1\| AraC-family transcriptional regulator [Bacillus cereus BDRD-Cer4], g... gi\|29896701, gi\|... - gi\|30021148\|ref\|NP_832779.1\| AraC family transcriptional regulator [Bacillus cereus ATCC 14579], gi\|...	3.0E-61	[11..287]	[12..293]
gi\|114552714, gi... - gi\|114776628\|ref\|ZP_01451671.1\| probable AraC-family transcriptional regulator [Mariprofundus ferroo...	2.0E-60	[1..288]	[1..288]
gi\|88917694, gi\|... - gi\|88935599\|ref\|ZP_01141229.1\| Helix-turn-helix, AraC type [Geobacter uraniumreducens Rf4], gi\|88917...	5.0E-60	[6..288]	[6..288]
gi\|78485568, gi\|... - gi\|78485568\|ref\|YP_391493.1\| AraC family transcriptional regulator [Thiomicrospira crunogena XCL-2],...	8.0E-60	[12..287]	[12..287]
gi\|42782144, gi\|... - gi\|42782144\|ref\|NP_979391.1\| AraC family transcriptional regulator [Bacillus cereus ATCC 10987], gi\|...	9.0E-60	[11..287]	[12..293]
gi\|163940775, gi... - gi\|89207155\|ref\|ZP_01185702.1\| Helix-turn-helix, AraC type:Bacterial transcription activator, effect...	1.0E-59	[11..287]	[12..293]

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Predicted Domain #1

Region A:
Residues: [1-288]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNDLISAAYS ERLRRVCDHI ERHLDEPLSL EALSRMAHSS PFHFHRQFTV WSGLPLYRYI  60
   61 QWLRLRRASW RLAFNPQDKV IDIALDAGFQ NPESFTRAFK TAFGQSPCRF RQSPDWLAWH 120
  121 QRVPKLALQE QHVMDVKIVE FPPTRVAMLT HLGHPDKVNA SAAKFIAWRR ETGQSPIASS 180
  181 QTFGIAWHDP QTTPPAQFRF DICGSVRQPI AENDVGVVNS EIPGGRCAVV RHQGSLDSLP 240
  241 ESVWYLFREW LPASGETLRD FPVFFQYLNF VHEVAEHELL TDIYLPLR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.09691
Match:	1d5yA
Description:	Rob transcription factor, N-terminal domain; Rob transcription factor, C-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.57523737355937	bayes_pls_golite062009
DNA binding	3.00143272905695	bayes_pls_golite062009
nucleic acid binding	2.89825020286436	bayes_pls_golite062009
transcription factor activity	2.53664874743748	bayes_pls_golite062009
binding	1.68817361068715	bayes_pls_golite062009
sequence-specific DNA binding	0.46503550280898	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.24108783215685	bayes_pls_golite062009
transcription repressor activity	0.20862059645422	bayes_pls_golite062009
protein binding	0.111941607625758	bayes_pls_golite062009

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: