YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|187730326, gi...
Organism:	Shigella boydii CDC 3083-94
Length:	346 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|187730326, gi....

Description	E-value	Query Range	Subject Range
gi\|237707059, gi... - gi\|237707059\|ref\|ZP_04537540.1\| outer membrane protein A [Escherichia sp. 3_2_53FAA], gi\|226898269\|g... gi\|91210052, gi\|... - gi\|91210052\|ref\|YP_540038.1\| outer membrane protein A [Escherichia coli UTI89], gi\|91071626\|gb\|ABE06...	304.0	[0..1]	[346..30]
gi\|110342738, gi... - gi\|110641146\|ref\|YP_668876.1\| outer membrane protein A [Escherichia coli 536], gi\|110342738\|gb\|ABG68...	303.0	[0..1]	[346..1]
gi\|117623167, gi... - gi\|117623167\|ref\|YP_852080.1\| outer membrane protein A [Escherichia coli APEC O1], gi\|115512291\|gb\|A...	303.0	[0..1]	[346..25]
gi\|7188818 - gi\|7188818\|gb\|AAF37887.1\|AF234269_1 outer membrane protein A [Escherichia coli] gi\|218364624, gi... - gi\|218557855\|ref\|YP_002390768.1\| outer membrane protein A [Escherichia coli S88], gi\|218364624\|emb\|C...	302.0	[0..1]	[346..1]
gi\|46812309 - gi\|46812309\|gb\|AAT02227.1\| outer membrane protein A precursor [Shigella boydii]	300.0	[0..1]	[346..1]
gi\|26107378, gi\|... - gi\|26246978\|ref\|NP_753018.1\| outer membrane protein A [Escherichia coli CFT073], gi\|26107378\|gb\|AAN7...	295.0	[0..1]	[346..30]
OMPA_SHIDY - Outer membrane protein A OS=Shigella dysenteriae GN=ompA PE=3 SV=1	294.0	[0..1]	[346..1]
gi\|56413933, gi\|... - gi\|56413933\|ref\|YP_151008.1\| outer membrane protein A [Salmonella enterica subsp. enterica serovar P... gi\|197362856, gi... - gi\|197362856\|ref\|YP_002142493.1\| outer membrane protein A [Salmonella enterica subsp. enterica serov...	294.0	[0..1]	[346..1]

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Predicted Domain #1

Region A:
Residues: [1-206]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKKTAIAIAV ALAGFATVAQ AAPKDNTWYT GAKLGWSQYH DTGFINNNGP THENQLGAGA  60
   61 FGGYQVNPYV GFEMGYDWLG RMPYKGSVEN GAYKAQGVQL TAKLGYPITD DLDIYTRLGG 120
  121 MVWRADTKSN VYGKNHDTGV SPVFAGGVEY AITPEIATRL EYQWTNNIGD AHTIGTRPDN 180
  181 GMLSLGVSYR FGQGEAAPVV APAPAP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.09691
Match:	1qjpA
Description:	Outer membrane protein A (OMPA) transmembrane domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
porin activity	5.10991724700971	bayes_pls_golite062009
channel activity	4.78965126968592	bayes_pls_golite062009
passive transmembrane transporter activity	4.78965126968592	bayes_pls_golite062009
wide pore channel activity	3.92328965238944	bayes_pls_golite062009
transporter activity	2.94995161862691	bayes_pls_golite062009
transmembrane transporter activity	2.84443650880263	bayes_pls_golite062009
receptor activity	1.96745124806322	bayes_pls_golite062009
signal transducer activity	1.14131647544827	bayes_pls_golite062009
molecular transducer activity	1.14131647544827	bayes_pls_golite062009
binding	0.881171786743586	bayes_pls_golite062009
protein binding	0.251915221742479	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [207-346]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APEVQTKHFT LKSDVLFNFN KATLKPEGQA ALDQLYSQLS NLDPKDGSVV VLGYTDRIGS  60
   61 DAYNQGLSER RAQSVVDYLI SKGIPADKIS ARGMGESNPV TGNTCDNVKQ RAALIDCLAP 120
  121 DRRVEIEVKG IKDVVTQPQA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.09691
Match:	1r1mA
Description:	Structure of the OmpA-like domain of RmpM from Neisseria meningitidis
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.708705497872653	bayes_pls_golite062009
protein binding	0.0802304930997709	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:

Predicted functions: