YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24346071, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	1188 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|24346071, gi|....

Description	E-value	Query Range	Subject Range
gi\|78688636, gi\|... - gi\|78688636\|ref\|ZP_00853304.1\| PAS [Shewanella sp. MR-7], gi\|78512017\|gb\|EAP25371.1\| PAS [Shewanella...	723.0	[0..1]	[1187..49]
gi\|78508081, gi\|... - gi\|78684329\|ref\|ZP_00849114.1\| PAS [Shewanella sp. ANA-3], gi\|78508081\|gb\|EAP21589.1\| PAS [Shewanell...	723.0	[0..1]	[1187..49]
gi\|82495403, gi\|... - gi\|82495403\|ref\|ZP_00880979.1\| PAS [Shewanella sp. MR-4], gi\|82406587\|gb\|EAP47251.1\| PAS [Shewanella...	722.0	[0..1]	[1187..49]
gi\|160862540, gi... - gi\|160877018\|ref\|YP_001556334.1\| multi-sensor hybrid histidine kinase [Shewanella baltica OS195], gi...	717.0	[0..1]	[1188..49]
gi\|82741440, gi\|... - gi\|82741440\|ref\|ZP_00904161.1\| PAS [Shewanella sp. W3-18-1], gi\|82721184\|gb\|EAP56029.1\| PAS [Shewane... gi\|146294387, gi... - gi\|77815912\|ref\|ZP_00815127.1\| PAS [Shewanella putrefaciens CN-32], gi\|77809127\|gb\|EAO93534.1\| PAS [... gi\|124544859, gi... - gi\|124544859\|ref\|ZP_01704107.1\| multi-sensor hybrid histidine kinase [Shewanella putrefaciens 200], ...	715.0	[0..1]	[1187..49]
gi\|68541595, gi\|... - gi\|68541595\|ref\|ZP_00581337.1\| PAS [Shewanella baltica OS155], gi\|68520654\|gb\|EAN44156.1\| PAS [Shewa...	714.0	[0..1]	[1188..49]
gi\|126636688, gi... - gi\|78365375\|ref\|ZP_00835661.1\| PAS [Shewanella sp. PV-4], gi\|78362382\|gb\|EAP04200.1\| PAS [Shewanella...	697.0	[0..1]	[1184..49]
gi\|68546403, gi\|... - gi\|68546403\|ref\|ZP_00585950.1\| PAS [Shewanella amazonensis SB2B], gi\|68515817\|gb\|EAN39531.1\| PAS [Sh...	691.0	[0..1]	[1188..49]
gi\|69164849, gi\|... - gi\|69951700\|ref\|ZP_00639374.1\| PAS [Shewanella frigidimarina NCIMB 400], gi\|69164849\|gb\|EAN73894.1\| ...	686.0	[0..8]	[1188..56]
gi\|91713904, gi\|... - gi\|91791902\|ref\|YP_561553.1\| ATP-binding region, ATPase-like protein [Shewanella denitrificans OS217...	657.0	[0..1]	[1186..49]

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Predicted Domain #1

Region A:
Residues: [1-347]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEQREEQVER HVLQIDLLLE SSIRAVKSLR DVAVDHLRLG ELVRKERLPQ YGKFNESGQY  60
   61 FTLEPNYAKG GKPFTNMGRI TGAGSLDGRS DKFYQELEML FELSLSFPVA KEAAPKASAI 120
  121 YYLSRQRMMS YFPWTNDDER FRDELLNKKQ FQYATPAMNP QRSVFWSEAY VDSTGKGLLT 180
  181 TLGVPVYLDD EFMGSINLDM TLASLARQIR VYFKMPGTVI LLDQQNNILS HSDFDGSDIN 240
  241 RVYHISQRIP SELHSLPESE LFDAHEGIIR NGYYIHSVAL HNAPWRLLYL QNEDDLFQDS 300
  301 VEKLQLTFIL VVIALSVLVT IVHWQTRRSF VSPASRLLSH LEGCSQE

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	3.96
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	0.839270468560673	bayes_pls_golite062009
binding	0.704248066961418	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [348-513]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PRKPPEKITP GWEPWFLLVS RIFEENKQYT HHLAEQNKRL DKLVARRTER LKDATERRER  60
   61 EYALLRSLLD SIPEAIVFKD KEGNYLGCNK AAERMLGYTE SEMIGLSSED LTSPEMGIRI 120
  121 RAEDAQILKD RTPLRYQEKV ELAGKPVLLD TLKLPFYNRR GELQGL

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.54
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	1.81312487233411	bayes_pls_golite062009
binding	1.67984576110273	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	1.60314341650446	bayes_pls_golite062009
two-component response regulator activity	1.41577088905201	bayes_pls_golite062009
cation transmembrane transporter activity	1.40823491489039	bayes_pls_golite062009
metal ion transmembrane transporter activity	1.10325694432704	bayes_pls_golite062009
transcription regulator activity	0.931375605669218	bayes_pls_golite062009
protein binding	0.888256242702267	bayes_pls_golite062009
voltage-gated ion channel activity	0.563198063703829	bayes_pls_golite062009
potassium channel activity	0.563028071397075	bayes_pls_golite062009
voltage-gated channel activity	0.552480950289765	bayes_pls_golite062009
voltage-gated cation channel activity	0.551619757281389	bayes_pls_golite062009
DNA binding	0.533187513797767	bayes_pls_golite062009
voltage-gated potassium channel activity	0.532581714382914	bayes_pls_golite062009
ion channel activity	0.483348490364346	bayes_pls_golite062009
two-component sensor activity	0.466388018187262	bayes_pls_golite062009
protein histidine kinase activity	0.452475261443277	bayes_pls_golite062009
cation channel activity	0.445728116294453	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	0.409938237891918	bayes_pls_golite062009
substrate-specific channel activity	0.391671932145714	bayes_pls_golite062009
passive transmembrane transporter activity	0.388177774524707	bayes_pls_golite062009
channel activity	0.388177774524707	bayes_pls_golite062009
nucleic acid binding	0.387046112137798	bayes_pls_golite062009
gated channel activity	0.383085563903689	bayes_pls_golite062009
signal transducer activity	0.341738261779128	bayes_pls_golite062009
molecular transducer activity	0.341738261779128	bayes_pls_golite062009
catalytic activity	0.335650048048265	bayes_pls_golite062009
transporter activity	0.308330515689802	bayes_pls_golite062009
transcription factor activity	0.15709070306709	bayes_pls_golite062009
transmembrane transporter activity	0.154730712374367	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [514-649]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IAVWRDVTRE YESAEQLRLS EERYHLAMDA VEDGLWDWYL DSEHIICNPS YYSMLGYKPN  60
   61 EFPALVSAID QLTHPDDRIR VEEYRNQYLE NPVDAYEIEF RILGKNSSYH WVLSRGRVVE 120
  121 FTTDGQPKRM VGTHKD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.09691
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
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
two-component response regulator activity	1.45691562840107	bayes_pls_golite062009
metal ion transmembrane transporter activity	1.31850321187865	bayes_pls_golite062009
transcription regulator activity	1.13913685347546	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
DNA binding	0.73243452463464	bayes_pls_golite062009
gated channel activity	0.67217953143815	bayes_pls_golite062009
substrate-specific channel activity	0.650205954115699	bayes_pls_golite062009
channel activity	0.64202076714636	bayes_pls_golite062009
passive transmembrane transporter activity	0.64202076714636	bayes_pls_golite062009
two-component sensor activity	0.58151911764083	bayes_pls_golite062009
protein histidine kinase activity	0.56538125817883	bayes_pls_golite062009
nucleic acid binding	0.5545839402512	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
transcription factor activity	0.36759096137141	bayes_pls_golite062009
transporter activity	0.360938622392148	bayes_pls_golite062009
catalytic activity	0.285447488878019	bayes_pls_golite062009
transmembrane transporter activity	0.217804199010847	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [650-902]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ITRHKSNEVA LLEAKQDAEL ANLYKSEFLA NMSHEIRTPM NAIIGMLQLA QRTSLTAQQK  60
   61 DYLEKAGFSA QSLLRIINDI LDFSKIEAGK LELERVPFPL DKVLDHALDL NALKAQEQGV 120
  121 ELLLYAPVTA GLILKGDPLR LGQVLINLLS NAVKFTQSGE IELGCEDVGE RDHRITLKFW 180
  181 VRDTGIGISK DQQEKLFDAF AQADGSTTRK YGGTGLGLSI SKHLVSMMGG KMQVQSELGV 240
  241 GSTFSFTISF EIA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.0
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [903-1188]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EEAKIEPLVV PEKLNNLRTL VVDDNPTALQ IYSALMRDFH FEVDTAASGA EALYKLSRDP  60
   61 IDLLLLDWMM PEMDGSDVIS AIDTMVAEGR IAKRPIIIMM TAYAAEPLLH EVDSANVFAV 120
  121 LQKPFKASSL FDEIIAAFAD EPRLNVVQPI AEVAVEEGEH TGLVLLVEDN FINQQVATEL 180
  181 LKSAGYEVVV AGNGQIALDI VDSRPFDAVL MDIQMPVMDG LTAARALRER YSADVLPIIA 240
  241 MTAHAMSGDR EKSLAAGMNA HITKPIVLTE LFETLTHWIK HKHNHR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.30103
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	3.44888100104099	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
binding	1.22427537074115	bayes_pls_golite062009
DNA binding	1.11037597107903	bayes_pls_golite062009
protein kinase activity	1.00737355751913	bayes_pls_golite062009
nucleic acid binding	0.93151849951839	bayes_pls_golite062009
phosphotransferase activity, alcohol group as acceptor	0.811771244977462	bayes_pls_golite062009
kinase activity	0.725824770559857	bayes_pls_golite062009
transcription factor activity	0.62886970109503	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.476057209677045	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: