YRC Public Data Repository - Protein Structure Prediction

Protein:	SSB_SHEON
Organism:	Shewanella oneidensis MR-1
Length:	238 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 SSB_SHEON.

Description	E-value	Query Range	Subject Range
gi\|47019183, gi\|... - gi\|47092406\|ref\|ZP_00230196.1\| single-strand binding protein subfamily [Listeria monocytogenes str. ...	169.0	[0..6]	[165..2]
gi\|212012365, gi... - gi\|212218103\|ref\|YP_002304890.1\| single-strand DNA binding protein [Coxiella burnetii CbuK_Q154], gi... gi\|164601569, gi... - gi\|164686023\|ref\|ZP_01947649.2\| single-stranded DNA-binding protein [Coxiella burnetii 'MSU Goat Q17... SSB_COXBU - Single-stranded DNA-binding protein OS=Coxiella burnetii (strain RSA 493 / Nine Mile phase I) GN=ssb... gi\|94490838, gi\|... - gi\|94490838\|ref\|ZP_01298066.1\| hypothetical protein CburD_01002058 [Coxiella burnetii Dugway 7E9-12]... SSB_COXBU - Single-stranded DNA-binding protein OS=Coxiella burnetii GN=ssb PE=1 SV=1	169.0	[0..3]	[165..2]
SSB_BUCAP - Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Schizaphis graminum (strain Sg) GN... SSB_BUCAP - Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Schizaphis graminum GN=ssb PE=3 SV...	164.0	[0..1]	[129..1]
gi\|30410826 - gi\|30410826\|ref\|NP_660857.2\| single-strand binding protein [Buchnera aphidicola str. Sg (Schizaphis ...	164.0	[0..1]	[129..15]
gi\|207088673 - gi\|207088673\|gb\|EDZ65945.1\| single-strand binding protein [Nitrosococcus oceani AFC27] gi\|224409019, gi... - gi\|254435562\|ref\|ZP_05049069.1\| single-strand binding protein [Nitrosococcus oceani AFC27], gi\|22440... gi\|77166470, gi\|... - gi\|77166470\|ref\|YP_344995.1\| single-strand binding protein [Nitrosococcus oceani ATCC 19707], gi\|768...	163.0	[0..1]	[165..1]
gi\|311086266\|gb\|... - single-strand binding protein [Buchnera aphidicola str. LL01 (Acyrthosiphon pisum)] gi\|311087920\|gb\|... - single-strand binding protein [Buchnera aphidicola str. JF98 (Acyrthosiphon pisum)] SSB_BUCAI - Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Acyrthosiphon pisum GN=ssb PE=3 SV... gi\|311087430\|gb\|... - single-strand binding protein [Buchnera aphidicola str. JF99 (Acyrthosiphon pisum)] SSB_BUCAI - Single-stranded DNA-binding protein OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) G... gi\|219682445, gi... - gi\|219682445\|ref\|YP_002468829.1\| single-strand binding protein [Buchnera aphidicola str. Tuc7 (Acyrt... gi\|257471595\|ref... - single-strand binding protein [Buchnera aphidicola str. LSR1 (Acyrthosiphon pisum)] gi\|25294289 - gi\|25294289\|pir\|\|E84993 single-strand binding protein [imported] - Buchnera sp. (strain APS) gi\|311086841\|gb\|... - single-strand binding protein [Buchnera aphidicola str. TLW03 (Acyrthosiphon pisum)] gi\|219681890, gi... - gi\|219681890\|ref\|YP_002468276.1\| single-strand binding protein [Buchnera aphidicola str. 5A (Acyrtho...	163.0	[0..1]	[131..1]
gi\|254938251 - gi\|254938251\|ref\|ZP_05269948.1\| hypothetical protein LmonF6_14026 [Listeria monocytogenes F6900] gi\|47097485, gi\|... - gi\|47097485\|ref\|ZP_00235027.1\| single-strand binding protein subfamily [Listeria monocytogenes str. ... gi\|254900924, gi... - gi\|254900924\|ref\|ZP_05260848.1\| hypothetical protein LmonJ_13956 [Listeria monocytogenes J0161], gi\|... gi\|254913862, gi... - gi\|254913862\|ref\|ZP_05263874.1\| hypothetical protein LmonJ2_13736 [Listeria monocytogenes J2818], gi...	162.0	[0..6]	[165..2]
SSB2_LISMO - Single-stranded DNA-binding protein 2 OS=Listeria monocytogenes GN=ssb2 PE=3 SV=1 SSB2_LISMO - Single-stranded DNA-binding protein 2 OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / ... gi\|47096011, gi\|... - gi\|47096011\|ref\|ZP_00233613.1\| single-strand binding protein subfamily [Listeria monocytogenes str. ... gi\|254937196 - gi\|254937196\|ref\|ZP_05268893.1\| hypothetical protein LmonF6_08711 [Listeria monocytogenes F6900] gi\|255025273 - gi\|255025273\|ref\|ZP_05297259.1\| hypothetical protein LmonocytFSL_01287 [Listeria monocytogenes FSL J...	161.0	[0..6]	[165..2]
gi\|5823662, gi\|1... - gi\|5823662\|emb\|CAB53850.1\| putative SSB protein [Listeria phage A118], gi\|16798847\|ref\|NP_463525.1\| ... gi\|157325471, gi... - gi\|66733476\|gb\|AAY53290.1\| gp53 [Listeria phage A006], gi\|157325471\|ref\|YP_001468893.1\| gp53 [Lister...	161.0	[0..6]	[165..2]
gi\|9954964, gi\|9... - gi\|9954966\|pdb\|1EYG\|D Chain D, Crystal Structure Of Chymotryptic Fragment Of E. Coli Ssb Bound To Tw...	161.0	[0..1]	[112..1]

Back

Predicted Domain #1

Region A:
Residues: [1-165]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MASRGVNKVI LVGNLGQDPE VRYMPNGNAV ANITVATSES WKDQQGQQQE RTEWHRVVLF  60
   61 GKLAEITGEY LRKGSQVYLE GKLQTRKWKD QSGQDRYSTE VVIDQSGSMQ MLGSRNQGGQ 120
  121 GAPMGGMPQN GGYQSAPQQA APAQNQYAPA PQAAPAYQAP APQPQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.522879
Match:	1eqqA
Description:	SINGLE STRANDED DNA BINDING PROTEIN AND SSDNA COMPLEX
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	2.26271782657431	bayes_pls_golite062009
binding	2.01819468874386	bayes_pls_golite062009
DNA binding	1.81052012500635	bayes_pls_golite062009
single-stranded DNA binding	1.38758756313423	bayes_pls_golite062009
structure-specific DNA binding	1.30327082958682	bayes_pls_golite062009
transcription regulator activity	0.537716356194117	bayes_pls_golite062009
structural constituent of ribosome	0.0989196136046104	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [166-238]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGYNQPPAQQ SYGQQQAQPH VQPHAQPQQG GYAPKPAAPA YQAPAAPAQR PAPQPQQNFT  60
   61 PDLDDGWDDD IPF

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	1.17
Match:	1eqqA
Description:	SINGLE STRANDED DNA BINDING PROTEIN AND SSDNA COMPLEX
Matching Structure (courtesy of the PDB):

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: