YRC Public Data Repository - Protein Structure Prediction

Protein:	SO4002
Organism:	Shewanella oneidensis
Length:	1689 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 SO4002.

Description	E-value	Query Range	Subject Range
gi\|78688544, gi\|... - gi\|78688544\|ref\|ZP_00853212.1\| PAS [Shewanella sp. MR-7], gi\|78511925\|gb\|EAP25279.1\| PAS [Shewanella...	652.0	[0..81]	[1679..87]
gi\|82496864, gi\|... - gi\|82496864\|ref\|ZP_00882427.1\| PAS [Shewanella sp. MR-4], gi\|82405138\|gb\|EAP45815.1\| PAS [Shewanella...	652.0	[0..81]	[1679..87]
gi\|78684236, gi\|... - gi\|78684236\|ref\|ZP_00849021.1\| PAS [Shewanella sp. ANA-3], gi\|78507988\|gb\|EAP21496.1\| PAS [Shewanell...	652.0	[0..81]	[1687..88]
gi\|106882912, gi... - gi\|119944738\|ref\|YP_942418.1\| sensor histidine kinase [Psychromonas ingrahamii 37], gi\|119863342\|gb\|...	635.0	[0..155]	[1678..52]
gi\|91685732, gi\|... - gi\|91781778\|ref\|YP_556984.1\| PAS/PAC sensor hybrid histidine kinase [Burkholderia xenovorans LB400],...	593.0	[0..173]	[1594..56]
gi\|7470855 - pir\|\|S75130 sensory transduction histidine kinase slr2098 - Synechocystis sp. (strain PCC 6803) gi\|1653075, gi\|1... - gi\|1653075\|dbj\|BAA17992.1\| hybrid sensory kinase [Synechocystis sp. PCC 6803], gi\|16330584\|ref\|NP_44...	571.0	[0..636]	[1684..204]
gi\|93357033, gi\|... - gi\|94313181\|ref\|YP_586390.1\| PAS/PAC sensor hybrid histidine kinase [Ralstonia metallidurans CH34], ...	570.0	[0..160]	[1593..5]
gi\|68516760, gi\|... - gi\|68545731\|ref\|ZP_00585281.1\| PAS [Shewanella amazonensis SB2B], gi\|68516760\|gb\|EAN40471.1\| PAS [Sh...	564.0	[0..434]	[1680..519]
gi\|24372448, gi\|... - gi\|24372448\|ref\|NP_716490.1\| sensory box histidine kinase/response regulator [Shewanella oneidensis ... SO0859 - sensory box histidine kinase/response regulator	549.0	[0..539]	[1678..610]

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Predicted Domain #1

Region A:
Residues: [1-408]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAGYGLISLA ILMILSAFKL VNMRTRYLAQ LPLQSNVLWR LFPILFAFLF SSLSVLASPG  60
   61 GQIPLTTAVI DRVSAPTPVL RVSMILSVDT PFNRQIGARA QAAAVDLNIQ LQVLYADGTH 120
  121 DGLMTLGREV MNQGIDGLIF SPVDDFGEAL IREAQKLKIP VVTLRAKLDM LSSAALAELP 180
  181 NFIANVNIND QKSGQLLMHY LLSVDQLNRD VPAVLLIAGP QGYPNVERGV EDVQRFMNSL 240
  241 STRGTLKIAY TDWSVEQALA QFDSAIAAQP ALTTVVTMNA SAAVAVAAKA HQQLGANAPA 300
  301 IGSMIWSESL VQDIKQGKIQ AAITGSEFSG AIALSILFDH LSARGGPSRK GSFVAPLVVI 360
  361 TPNNYQDYES ILDFDPLRLN FRQISQHFNP DLSINELRLA DLLTSEAR

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.43
Match:	1lbgA
Description:	Lac repressor (LacR), N-terminal domain; Lac-repressor (lacR) core (C-terminal domain)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	1.78165889081782	bayes_pls_golite062009
binding	1.48949372339203	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.32274201928316	bayes_pls_golite062009
transcription factor activity	1.13498203900589	bayes_pls_golite062009
DNA binding	1.12854649645915	bayes_pls_golite062009
nucleic acid binding	1.03560994231664	bayes_pls_golite062009
signal transducer activity	0.810070503533362	bayes_pls_golite062009
molecular transducer activity	0.810070503533362	bayes_pls_golite062009
ion transmembrane transporter activity	0.617592178828761	bayes_pls_golite062009
transporter activity	0.34326281633424	bayes_pls_golite062009
transmembrane transporter activity	0.197683590925448	bayes_pls_golite062009
receptor activity	0.1130872982653	bayes_pls_golite062009
cation transmembrane transporter activity	0.0834296454830339	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [409-648]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VNFLKTLTEP ELNFLRQHPS IRVGIEPDGA PIDYVDQAGK HTGLIASYLS EIAKLIPVRF  60
   61 EVQPTQSWGQ TLKDFAADKL DMISLISASE DRKQRILFTD AIGHFPAVIV MRKDAELVDG 120
  121 IEGLFGKTVA VTRGDITEEL LRKKYPEINI IAFDRLEDVL STTLASQVDA AVMLLPKAGQ 180
  181 SLLSPANKEL TIVAPLDDEF EHSIGVRRDW PELQSILNKA LAQIPSSTRA ELDSRWFTVK 240
  241

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.0
Match:	1gggA
Description:	Glutamine-binding protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
anion transmembrane transporter activity	3.60119288506724	bayes_pls_golite062009
inorganic anion transmembrane transporter activity	3.53292741410046	bayes_pls_golite062009
anion transmembrane-transporting ATPase activity	3.51205087813611	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	2.80786841862036	bayes_pls_golite062009
transporter activity	2.37767937786605	bayes_pls_golite062009
phosphate transmembrane transporter activity	2.35121899350011	bayes_pls_golite062009
ion transmembrane transporter activity	2.19564149972908	bayes_pls_golite062009
transmembrane transporter activity	2.14027396604232	bayes_pls_golite062009
molybdate ion transmembrane transporter activity	2.02302864315938	bayes_pls_golite062009
molybdate transmembrane-transporting ATPase activity	2.02302864315938	bayes_pls_golite062009
active transmembrane transporter activity	1.98824826924235	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	1.92247368464925	bayes_pls_golite062009
primary active transmembrane transporter activity	1.91778402126342	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	1.91458600392598	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	1.91458600392598	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	1.91424996753266	bayes_pls_golite062009
phosphate transmembrane-transporting ATPase activity	1.66644014680767	bayes_pls_golite062009
ATPase activity, coupled	1.59154512845516	bayes_pls_golite062009
substrate-specific transporter activity	1.51716707550629	bayes_pls_golite062009
ATPase activity	1.44327228942016	bayes_pls_golite062009
nucleoside-triphosphatase activity	1.36989838880058	bayes_pls_golite062009
pyrophosphatase activity	1.33033652028872	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	1.31993399326424	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	1.31926578892427	bayes_pls_golite062009
binding	1.29220115989941	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of ions	1.06410714245	bayes_pls_golite062009
catalytic activity	1.04475291968158	bayes_pls_golite062009
transcription regulator activity	1.03226687100951	bayes_pls_golite062009
sulfate transmembrane transporter activity	0.9729713541995	bayes_pls_golite062009
transcription factor activity	0.81271953199554	bayes_pls_golite062009
DNA binding	0.7051372893863	bayes_pls_golite062009
sulfate transmembrane-transporting ATPase activity	0.605937181552931	bayes_pls_golite062009
nucleic acid binding	0.579254737490365	bayes_pls_golite062009
hydrolase activity	0.52200036125335	bayes_pls_golite062009
cation transmembrane transporter activity	0.361480611994095	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [649-813]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YDFGMDPQQI KRWAISSAMV ILGLFACFIL WNYGLKRELL RRSRMAAQLE SSMNKFHALF  60
   61 DSVMDACVII DKRGVIKECN AALQTLLGVE DKTALVGTSL TQFHLADTFM GSAVQIAQSV 120
  121 EDVLKQGLLK FEADITDSQG QSIPAEVTLK SIELNTERFV LATYH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.39794
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 #4

Region A:
Residues: [814-934]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NLAERRLVDR LIRHERNLLK NVLGMSPIGV WVCVNGTCRY VNAQMTLMTG LEVEHAVADI  60
   61 FLQPKDYWHY IRELAPEQEC ITFESKLKGY HGQILDVLFT AYPTFYDGQH ANLCWALDIT 120
  121 Q

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	4.522879
Match:	1v9yA
Description:	Crystal Structure of the heme PAS sensor domain of Ec DOS (ferric form)
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: [935-1189]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EKAIQAELAS AKLQADAANR AKSDFLANMS HEIRTPMNAI IGMSYLALQT DLAEKRKDYI  60
   61 AKVHQAAGSL LNIINDILDF SKIEANKLTV EHIEFDLDEV LTQLNNVIGF KVEENSMRLI 120
  121 YDIATDCPRY FIGDPQRLGQ ILLNYCNNAV KFSPKGSDIL LSCQAELDKQ GATLTFCVAD 180
  181 DGIGIPLDKQ ARLFHSFEQG DTSTSRKYGG TGLGLAICKR LSELMQGEVW CESELGQGSR 240
  241 FYLRLHLPLV KPYDL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	48.522879
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [1190-1563]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STQFAALQGE SLSIVGFMPD LSAIYSRFAA RVGMQARTLE MHMALAELSA CTSQHLIMCE  60
   61 TNAFEPELLS VVLANDKLGL LLIGNGSEPV AIQSLVDKHP QIIAKQHPIL LRTLGESLLL 120
  121 LLNRDRAPFG QHLEHQSITT LKNQLAGVEL LLVEDNYLNQ ELAVELLRQA GARVTVAQHG 180
  181 QEALTLLAQQ SFDCVLMDGQ MPVMDGYEAT RLIRAQPQFA DLPIIAMTAN AMDSDRERAL 240
  241 AAGMNAQINK PFQVQQLYST IAQHVSVHSV QSLPESPEAH DLDKAQLKQG LPLVEELDID 300
  301 AGLALCNYNA DLYRHLLTLF VQTGAKLLQN QQNEFSQDNL SALRLSLHTL KGVAGNIGAV 360
  361 SLKEDSGRLE ASLT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	28.30103
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 #7

Region A:
Residues: [1564-1689]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DISSLQQLDA NIQETVSQEI HLLHAKLQQL LTLLAEWQTV NQPDEASQSI SMTELMRLFA  60
   61 QLTQNLKEYN TDALSLVERL SQLTVLQPQR QLIAELKQAT GQFDFSQGLE LAIQLQEWAQ 120
  121 QQLAKE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	57.0
Match:	1ny5A
Description:	Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state
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:

Predicted functions:

Predicted functions:

Predicted functions:

Predicted functions: