YRC Public Data Repository - Protein Structure Prediction

Protein:	SO0859
Organism:	Shewanella oneidensis
Length:	1765 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 SO0859.

Description	E-value	Query Range	Subject Range
gi\|117921856, gi... - gi\|78684566\|ref\|ZP_00849349.1\| PAS [Shewanella sp. ANA-3], gi\|78507503\|gb\|EAP21013.1\| PAS [Shewanell...	900.0	[0..1]	[1765..1]
gi\|113890238, gi... - gi\|78690356\|ref\|ZP_00855004.1\| PAS [Shewanella sp. MR-7], gi\|78510268\|gb\|EAP23642.1\| PAS [Shewanella...	898.0	[0..1]	[1761..1]
gi\|82405384, gi\|... - gi\|82496616\|ref\|ZP_00882182.1\| PAS [Shewanella sp. MR-4], gi\|82405384\|gb\|EAP46058.1\| PAS [Shewanella...	897.0	[0..1]	[1761..1]
gi\|77809063, gi\|... - gi\|77815974\|ref\|ZP_00815187.1\| PAS [Shewanella putrefaciens CN-32], gi\|77809063\|gb\|EAO93472.1\| PAS [...	870.0	[0..1]	[1761..1]
gi\|68543356, gi\|... - gi\|68543356\|ref\|ZP_00583064.1\| PAS [Shewanella baltica OS155], gi\|68518944\|gb\|EAN42495.1\| PAS [Shewa...	854.0	[0..1]	[1764..1]
gi\|113948910, gi... - gi\|160873991\|ref\|YP_001553307.1\| multi-sensor hybrid histidine kinase [Shewanella baltica OS195], gi...	851.0	[0..1]	[1764..1]
gi\|68516760, gi\|... - gi\|68545731\|ref\|ZP_00585281.1\| PAS [Shewanella amazonensis SB2B], gi\|68516760\|gb\|EAN40471.1\| PAS [Sh...	842.0	[0..5]	[1762..7]
gi\|78366316, gi\|... - gi\|78366316\|ref\|ZP_00836597.1\| PAS [Shewanella sp. PV-4], gi\|78361632\|gb\|EAP03455.1\| PAS [Shewanella...	811.0	[0..1]	[1760..1]
gi\|108805455, gi... - gi\|108805455\|ref\|YP_645392.1\| multi-sensor hybrid histidine kinase [Rubrobacter xylanophilus DSM 994...	602.0	[0..397]	[1688..14]
gi\|34102933, gi\|... - gi\|34497076\|ref\|NP_901291.1\| sensor/response regulatory hybrid protein [Chromobacterium violaceum AT...	600.0	[0..33]	[1761..37]

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Predicted Domain #1

Region A:
Residues: [1-294]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDKSKLRTFR SKILSHIALP LILIMATVYG ITSWFNYLSI EKRLYENLAQ ESSHSASRLQ  60
   61 FLLEHAQANT QGLSDFIGLL ADKDDINNPE KLKTVLTNRI QRNPDFFGSA IAFKPNTFPN 120
  121 KKLFSPYVYR SGSGFNYLDI GADGYDYTDG NWDWWSKAIN QVGGYWSKAY FDEGAGNVLM 180
  181 ITYAVPFGVQ PDYFGVTTVD LALDRLPEQL GIAPSRLVVL DDQGRLIFHS DKEKVLAASS 240
  241 SGWLDKQNIK NIAFATLLND GQAGQASFVD DKGTVYLASV AEVAKLKWRV VVMV

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	3.71
Match:	2p7jA
Description:	No description for 2p7jA was found.

Predicted functions:

Term	Confidence	Notes
two-component sensor activity	2.88093868237858	bayes_pls_golite062009
protein histidine kinase activity	2.86151216540335	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.80671328721504	bayes_pls_golite062009
protein kinase activity	1.74105675066805	bayes_pls_golite062009
two-component response regulator activity	1.62873572477094	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	1.58981311381645	bayes_pls_golite062009
kinase activity	1.5133458700147	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	1.31628115739307	bayes_pls_golite062009
signal transducer activity	1.10204821596482	bayes_pls_golite062009
molecular transducer activity	1.10204821596482	bayes_pls_golite062009
catalytic activity	0.970922685016416	bayes_pls_golite062009
transferase activity	0.821780694868473	bayes_pls_golite062009
binding	0.704248066961418	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [295-410]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PKHELFASLL DDIASAILNL SLLTLLLLLT CYIAAKRLTR PLEALESGIL AFGQGKAQEL  60
   61 TIPKGAVSEI VTLSETFNQM AALLAEREQA ILDSRGNRFA RLIDGMSDKS FYCSLD

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	3.45
Match:	2f95B
Description:	M intermediate structure of sensory rhodopsin II/transducer complex in combination with the ground state structure
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [411-498]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PDGQLAQVSE GVTKVLGIPP ELLKRKYQRL FSANPLNEKN WEYTDLALKG QNVPPHQIEL  60
   61 VDAKGQARRL DVFMQPLVSD TGELMSVE

[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.

Predicted Domain #4

Region A:
Residues: [499-628]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFTDVTEQF SAAAWSNAVL EAAPEAMLIV DQNGQIVFSN SRCQQLFGYD AKAMLALQIE  60
   61 TLLPEELRHL HTGERLDFLR EGRDRPMASA RHVRALKSDG GEFVAEIALS ILPSDFDGRR 120
  121 QVAASIRDMT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.154902
Match:	1d06A
Description:	Histidine kinase FixL heme domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ion transmembrane transporter activity	1.94020112661684	bayes_pls_golite062009
transcription regulator activity	1.88422125389203	bayes_pls_golite062009
binding	1.79230776794479	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.70629448457771	bayes_pls_golite062009
cation transmembrane transporter activity	1.55042643398568	bayes_pls_golite062009
DNA binding	1.54206275665781	bayes_pls_golite062009
two-component response regulator activity	1.45691562840107	bayes_pls_golite062009
nucleic acid binding	1.41817054839611	bayes_pls_golite062009
metal ion transmembrane transporter activity	1.31850321187865	bayes_pls_golite062009
transcription factor activity	1.12946889905444	bayes_pls_golite062009
protein binding	1.0133195984081	bayes_pls_golite062009
potassium channel activity	0.93265112299626	bayes_pls_golite062009
voltage-gated ion channel activity	0.92661046549451	bayes_pls_golite062009
voltage-gated cation channel activity	0.926512767264521	bayes_pls_golite062009
voltage-gated potassium channel activity	0.92204538811959	bayes_pls_golite062009
voltage-gated channel activity	0.91469735366704	bayes_pls_golite062009
ion channel activity	0.75430461252947	bayes_pls_golite062009
cation channel activity	0.73262554730695	bayes_pls_golite062009
gated channel activity	0.67217953143815	bayes_pls_golite062009
substrate-specific channel activity	0.650205954115699	bayes_pls_golite062009
passive transmembrane transporter activity	0.64202076714636	bayes_pls_golite062009
channel activity	0.64202076714636	bayes_pls_golite062009
two-component sensor activity	0.58151911764083	bayes_pls_golite062009
protein histidine kinase activity	0.56538125817883	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	0.518111391350209	bayes_pls_golite062009
signal transducer activity	0.441034662376355	bayes_pls_golite062009
molecular transducer activity	0.441034662376355	bayes_pls_golite062009
transporter activity	0.360938622392148	bayes_pls_golite062009
catalytic activity	0.285447488878019	bayes_pls_golite062009
transcription factor binding	0.24293756478811	bayes_pls_golite062009
transmembrane transporter activity	0.217804199010847	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [629-771]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QKIMVEQKIR DSELRFRGLV TNIPGAVYRT RIGEVWVIEY VSDNIAEITG YAASQFIENR  60
   61 QRTFTSLILE DDRALCNQHI ERALAQQETF EVEYRIRHRD GSIRWVHEKG KASYSEEGLP 120
  121 LWFDGSIDDV TESKLAIDEI EAS

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	5.51
Match:	2pr5A
Description:	No description for 2pr5A was found.

Predicted Domain #6

Region A:
Residues: [772-900]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RQQLTNITES IPCTVYQLRW VSPTDRSFTF LSGAALAMLG LHREELLRDF NIIAERIFDE  60
   61 ERPEVISALA GKSDDQLRWI REFRYRHPNG GIRWMEAGAS GHYADDGSII WNGYVMDVTE 120
  121 RKSIEEELA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.69897
Match:	2pr5A
Description:	No description for 2pr5A was found.

Predicted Domain #7

Region A:
Residues: [901-1020]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VSEAHFKALF DGATIGIVNV DIKGLILDCN YQFCEDMGLS RDELRSTPIF DVLSAQDKDV  60
   61 AKAQFKELVE GKIDHYRGER SFVRPSGEPL WMTVNVSTLL DSQNQFESAV VSMVDMTELK 120
  121

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.522879
Match:	1dp6A
Description:	Histidine kinase FixL heme domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ion transmembrane transporter activity	1.94020112661684	bayes_pls_golite062009
transcription regulator activity	1.88422125389203	bayes_pls_golite062009
binding	1.79230776794479	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.70629448457771	bayes_pls_golite062009
cation transmembrane transporter activity	1.55042643398568	bayes_pls_golite062009
DNA binding	1.54206275665781	bayes_pls_golite062009
two-component response regulator activity	1.45691562840107	bayes_pls_golite062009
nucleic acid binding	1.41817054839611	bayes_pls_golite062009
metal ion transmembrane transporter activity	1.31850321187865	bayes_pls_golite062009
transcription factor activity	1.12946889905444	bayes_pls_golite062009
protein binding	1.0133195984081	bayes_pls_golite062009
potassium channel activity	0.93265112299626	bayes_pls_golite062009
voltage-gated ion channel activity	0.92661046549451	bayes_pls_golite062009
voltage-gated cation channel activity	0.926512767264521	bayes_pls_golite062009
voltage-gated potassium channel activity	0.92204538811959	bayes_pls_golite062009
voltage-gated channel activity	0.91469735366704	bayes_pls_golite062009
ion channel activity	0.75430461252947	bayes_pls_golite062009
cation channel activity	0.73262554730695	bayes_pls_golite062009
gated channel activity	0.67217953143815	bayes_pls_golite062009
substrate-specific channel activity	0.650205954115699	bayes_pls_golite062009
passive transmembrane transporter activity	0.64202076714636	bayes_pls_golite062009
channel activity	0.64202076714636	bayes_pls_golite062009
two-component sensor activity	0.58151911764083	bayes_pls_golite062009
protein histidine kinase activity	0.56538125817883	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	0.518111391350209	bayes_pls_golite062009
signal transducer activity	0.441034662376355	bayes_pls_golite062009
molecular transducer activity	0.441034662376355	bayes_pls_golite062009
transporter activity	0.360938622392148	bayes_pls_golite062009
catalytic activity	0.285447488878019	bayes_pls_golite062009
transcription factor binding	0.24293756478811	bayes_pls_golite062009
transmembrane transporter activity	0.217804199010847	bayes_pls_golite062009

Predicted Domain #8

Region A:
Residues: [1021-1145]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLSDELLVAK DEADAASKAK GDFLANMSHE IRTPMNAIIG MSQLCLQTQL DKKQKNYLEK  60
   61 IERASQSLLS IINDILDFSK IEAGKLDIEN VSFQLDTMLE DLSDMFSERA AQKQIELLFA 120
  121 VAPNV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.39794
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #9

Region A:
Residues: [1146-1273]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PRHLLGDPLR LGQVLINLMN NAIKFTERGE VLLSLSLVEQ QNDDVVLRFS VRDSGIGLTQ  60
   61 EQQSKLFKSF TQADTSTTRK YGGTGLGLAI SKQLVELMGG SIGVESQLGH GSTFFFTVKL 120
  121 CISSGQKL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.69897
Match:	2q2eB
Description:	No description for 2q2eB was found.

Predicted Domain #10

Region A:
Residues: [1274-1639]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FVGQELDGMS ILVADDNATA RDIMRTTLES MGFNVDTVRS GDEAIMRCSQ QEYAVALIDW  60
   61 KMPNLDGIET AKQIKQQTKN APRILMVSAH ANQDFLTQIE QLGLAGYISK PISASRLLDG 120
  121 IMNALGRSGI LPVRRHQDNI APELLLPLKG KRILLVEDNE MNLEVATEFL EQVGIILSIA 180
  181 TNGQIALDKL AQQSFDLVLM DCQMPVMDGY QATKAIRQRP ELAQLPVIAM TANAMAGDKE 240
  241 MCLRAGMNDH IAKPIEVNLL YQTLLKYLGA PVPSLENAEF VVNESLNPLN LDVESVVKWP 300
  301 EHPELDIDRG LQLVQNSKRL YQRIFDRFAT SQRNVVDQIN KALASNKRED AVRMAHTLKG 360
  361 LAGNLS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	30.0
Match:	1w25A
Description:	Response regulator PleD in complex with c-diGMP
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
two-component response regulator activity	7.02872640261738	bayes_pls_golite062009
signal transducer activity	4.51666042720644	bayes_pls_golite062009
molecular transducer activity	4.51666042720644	bayes_pls_golite062009
transcription regulator activity	4.19396540145756	bayes_pls_golite062009
protein histidine kinase activity	2.35011582062573	bayes_pls_golite062009
two-component sensor activity	2.32303301074957	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	2.28838869071567	bayes_pls_golite062009
DNA binding	1.9200042031022	bayes_pls_golite062009
nucleic acid binding	1.7951051076633	bayes_pls_golite062009
transcription factor activity	1.39074763877806	bayes_pls_golite062009
binding	1.22427537074115	bayes_pls_golite062009
protein kinase activity	1.00737355751913	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.811771244977462	bayes_pls_golite062009
kinase activity	0.725824770559857	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.476057209677045	bayes_pls_golite062009

Predicted Domain #11

Region A:
Residues: [1640-1765]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SSKLAELARQ LELHLSENAD YQVELDQIQI LVASICEAIE KAKPQFEETS TSTAEHLPKD  60
   61 ALIAALKQLR QSLEDADSDA VTQMDALKPQ MSALLWQQLS PALTMINQYQ FDEAVDLIDE 120
  121 VLAKLT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	67.69897
Match:	1ny5A
Description:	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleoside-triphosphatase activity	1.95073642969863	bayes_pls_golite062009
pyrophosphatase activity	1.91141407779641	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.9017593265179	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.90014393273511	bayes_pls_golite062009
anion transmembrane transporter activity	1.84572377553607	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.608578860823	bayes_pls_golite062009
transporter activity	1.55572428045529	bayes_pls_golite062009
anion transmembrane-transporting ATPase activity	1.49339466967388	bayes_pls_golite062009
ATPase activity	1.48474288797022	bayes_pls_golite062009
two-component response regulator activity	1.45919623810582	bayes_pls_golite062009
transmembrane transporter activity	1.38483976298883	bayes_pls_golite062009
ATPase activity, coupled	1.37457738689583	bayes_pls_golite062009
catalytic activity	1.37148167194523	bayes_pls_golite062009
inorganic anion transmembrane transporter activity	1.3654237778347	bayes_pls_golite062009
ion transmembrane transporter activity	1.32358677895008	bayes_pls_golite062009
binding	1.30574971150356	bayes_pls_golite062009
active transmembrane transporter activity	1.24278046928678	bayes_pls_golite062009
phosphate transmembrane transporter activity	1.22440281711103	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	1.2014318795788	bayes_pls_golite062009
primary active transmembrane transporter activity	1.19670408144267	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	1.17063957238561	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	1.16918853509059	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	1.16885789920943	bayes_pls_golite062009
hydrolase activity	1.09839981963412	bayes_pls_golite062009
phosphate transmembrane-transporting ATPase activity	1.05293225786874	bayes_pls_golite062009
ribonucleotide binding	0.92950870381166	bayes_pls_golite062009
purine ribonucleotide binding	0.9275205656455	bayes_pls_golite062009
purine nucleotide binding	0.91280662021456	bayes_pls_golite062009
nucleotide binding	0.90809801369052	bayes_pls_golite062009
ATP binding	0.59269193555886	bayes_pls_golite062009
cation transmembrane transporter activity	0.575892074401446	bayes_pls_golite062009
adenyl ribonucleotide binding	0.57504013359401	bayes_pls_golite062009
adenyl nucleotide binding	0.54853610492983	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	0.139527952740579	bayes_pls_golite062009
substrate-specific transporter activity	0.0838665746103899	bayes_pls_golite062009
nucleic acid binding	0.0251017125544788	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:

Predicted functions:

Predicted functions:

Predicted functions: