YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|165989688, gi...
Organism:	Yersinia pestis biovar Antiqua str. E1979001
Length:	778 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|165989688, gi....

Description	E-value	Query Range	Subject Range
gi\|162351706, gi... - gi\|77635698\|ref\|ZP_00797779.1\| COG0642: Signal transduction histidine kinase [Yersinia pestis Angola...	0.0	[1..778]	[1..778]
gi\|75197159, gi\|... - gi\|75197159\|ref\|ZP_00707229.1\| COG0642: Signal transduction histidine kinase [Escherichia coli HS], ...	0.0	[1..778]	[1..778]
gi\|81242672, gi\|... - gi\|82778524\|ref\|YP_404873.1\| aerobic respiration control sensor protein ArcB [Shigella dysenteriae S...	0.0	[1..778]	[1..778]
gi\|157159325, gi... - gi\|75188016\|ref\|ZP_00701283.1\| COG0642: Signal transduction histidine kinase [Escherichia coli E2437... gi\|254038375, gi... - gi\|254038375\|ref\|ZP_04872433.1\| multi-sensor hybrid histidine kinase [Escherichia sp. 1_1_43], gi\|22... gi\|218701979, gi... - gi\|218701979\|ref\|YP_002409608.1\| aerobic respiration control sensor protein ArcB [Escherichia coli I... gi\|75209653, gi\|... - gi\|75209653\|ref\|ZP_00709865.1\| COG0642: Signal transduction histidine kinase [Escherichia coli B171]... gi\|218353647, gi... - gi\|218696915\|ref\|YP_002404582.1\| aerobic respiration control sensor protein ArcB [Escherichia coli 5... gi\|30042806, gi\|... - gi\|30064547\|ref\|NP_838718.1\| aerobic respiration control sensor protein ArcB [Shigella flexneri 2a s... gi\|191168636, gi... - gi\|75228171\|ref\|ZP_00714836.1\| COG0642: Signal transduction histidine kinase [Escherichia coli B7A],... gi\|110807075, gi... - gi\|110807075\|ref\|YP_690595.1\| aerobic respiration control sensor protein ArcB [Shigella flexneri 5 s... EG10062 - aerobic respiration control sensor histidine protein kinase, cognate to two-component response regul... gi\|75234876, gi\|... - gi\|75234876\|ref\|ZP_00719167.1\| COG0642: Signal transduction histidine kinase [Escherichia coli E1100... gi\|218706830, gi... - gi\|218706830\|ref\|YP_002414349.1\| aerobic respiration control sensor protein ArcB [Escherichia coli U... gi\|75256586, gi\|... - gi\|75256586\|ref\|ZP_00728216.1\| COG0642: Signal transduction histidine kinase [Escherichia coli E22],... gi\|75511887, gi\|... - gi\|75511887\|ref\|ZP_00734499.1\| COG0642: Signal transduction histidine kinase [Escherichia coli 53638... gi\|81246964, gi\|... - gi\|82545553\|ref\|YP_409500.1\| aerobic respiration control sensor protein ArcB [Shigella boydii Sb227]... gi\|89109973, gi\|... - gi\|89109973\|ref\|AP_003753.1\| hybrid sensory histidine kinase in two-component regulatory system with... gi\|124528490, gi... - gi\|124528490\|ref\|ZP_01699779.1\| multi-sensor hybrid histidine kinase [Escherichia coli B], gi\|124500... gi\|169753468, gi... - gi\|170018540\|ref\|YP_001723494.1\| aerobic respiration control sensor protein ArcB [Escherichia coli A... gi\|170683438, gi... - gi\|170683438\|ref\|YP_001745482.1\| aerobic respiration control sensor protein ArcB [Escherichia coli S... gi\|169890579, gi... - gi\|170082744\|ref\|YP_001732064.1\| hybrid sensory histidine kinase in two-component regulatory system ... gi\|218555780, gi... - gi\|218555780\|ref\|YP_002388693.1\| aerobic respiration control sensor protein ArcB [Escherichia coli I... gi\|194439214, gi... - gi\|83585412\|ref\|ZP_00924058.1\| COG0642: Signal transduction histidine kinase [Escherichia coli 101-1... gi\|209920685, gi... - gi\|209920685\|ref\|YP_002294769.1\| aerobic respiration control sensor protein ArcB [Escherichia coli S... ARCB_SHIFL - Aerobic respiration control sensor protein ArcB OS=Shigella flexneri GN=arcB PE=3 SV=1 gi\|24053684, gi\|... - gi\|24114498\|ref\|NP_709008.1\| aerobic respiration control sensor protein ArcB [Shigella flexneri 2a s... EG10062 - aerobic respiration control sensor histidine protein kinase, cognate to two-component response regul... ARCB_ECOLI - Aerobic respiration control sensor protein arcB (EC 2.7.13.3) - Escherichia coli gi\|238902312, gi... - gi\|238902312\|ref\|YP_002928108.1\| hybrid sensory histidine kinase in two-component regulatory system ... gi\|242378753, gi... - gi\|251786480\|ref\|YP_003000784.1\| hypothetical protein B21_03026 [Escherichia coli BL21], gi\|24237875... gi\|253323000, gi... - gi\|254289902\|ref\|YP_003055650.1\| hybrid sensory histidine kinase in two-component regulatory system ...	0.0	[1..778]	[1..778]
gi\|77973384 - gi\|77973384\|ref\|ZP_00828932.1\| COG0642: Signal transduction histidine kinase [Yersinia frederiksenii...	0.0	[15..778]	[1..764]
gi\|62129469, gi\|... - gi\|62181836\|ref\|YP_218253.1\| aerobic respiration control sensor protein ArcB [Salmonella enterica su...	0.0	[1..778]	[1..778]
gi\|74313747, gi\|... - gi\|74313747\|ref\|YP_312166.1\| aerobic respiration control sensor protein ArcB [Shigella sonnei Ss046]...	0.0	[1..778]	[1..778]
gi\|189366120, gi... - gi\|189366120\|gb\|EDU84536.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|168754192, gi... - gi\|189358652\|gb\|EDU77071.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|188014362, gi... - gi\|188014362\|gb\|EDU52484.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... ARCB_ECO57 - Aerobic respiration control sensor protein ArcB OS=Escherichia coli O157:H7 GN=arcB PE=3 SV=1 gi\|25301090, gi\|... - pir\|\|D85985 aerobic respiration sensor-response protein [imported] - Escherichia coli (strain O157:H... gi\|12517831, gi\|... - gi\|15803750\|ref\|NP_289784.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:... gi\|254594559, gi... - gi\|254795159\|ref\|YP_003079996.1\| hybrid sensory histidine kinase in two-component regulatory system ... gi\|13363562, gi\|... - gi\|15833343\|ref\|NP_312116.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:... gi\|217327107, gi... - gi\|217327107\|ref\|ZP_03443190.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O1... gi\|209159326, gi... - gi\|209397926\|ref\|YP_002272680.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O... gi\|189373850, gi... - gi\|189373850\|gb\|EDU92266.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|189001033, gi... - gi\|189001033\|gb\|EDU70019.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|187767463, gi... - gi\|187767463\|gb\|EDU31307.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|168769066, gi... - gi\|189361737\|gb\|EDU80156.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H... gi\|208820710, gi... - gi\|208820710\|ref\|ZP_03261030.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O1... gi\|208813912, gi... - gi\|208813912\|ref\|ZP_03255241.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O1... gi\|208808181, gi... - gi\|208808181\|ref\|ZP_03250518.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O1... gi\|189376853, gi... - gi\|189376853\|gb\|EDU95269.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O157:H...	0.0	[1..778]	[1..778]
gi\|75176098, gi\|... - gi\|75176098\|ref\|ZP_00696266.1\| COG0642: Signal transduction histidine kinase [Shigella boydii BS512]...	0.0	[1..778]	[1..778]
gi\|117625502, gi... - gi\|117625502\|ref\|YP_858825.1\| aerobic respiration control sensor protein ArcB [Escherichia coli APEC... gi\|215266598, gi... - gi\|215488526\|ref\|YP_002330957.1\| aerobic respiration control sensor protein ArcB [Escherichia coli O... gi\|91074209, gi\|... - gi\|91212635\|ref\|YP_542621.1\| aerobic respiration control sensor protein ArcB [Escherichia coli UTI89... gi\|218560280, gi... - gi\|218560280\|ref\|YP_002393193.1\| aerobic respiration control sensor protein ArcB [Escherichia coli S...	0.0	[1..778]	[1..778]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKQIRVLAQY YVDLMVKLGL VRFSLLLASA LVLLAMVVQM AVTFVLRGSV ETLDLVRSIF  60
   61 FGLLITPWAV YFLSVVVEQL EESRQRLSRL VDKLEVMRHR DLELNKQLTE NITQLNQEIV 120
  121 ERE

[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 #2

Region A:
Residues: [124-255]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KAEKAHLQVV DKLKEEMGHR EQAQIELGQQ SALLRSFLDA SPDLVYYRNE DNEFSGCNRA  60
   61 MELLTGKSEK QLVGLTPKDV YAPDIAEKVM ETDEKVFRHN VSLTYEQWLV YPDGRKACFE 120
  121 LRKVPFYDRV GK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.69897
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 #3

Region A:
Residues: [256-514]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RHGLMGFGRD ITERKRYQDA LENASRDKTT FISTISHELR TPLNGIVGLS RILLDTELDA  60
   61 EQLKYLKTIH VSAITLGNIF NDIIEMDKLE RRKVQLDNQP VDFTGFMADL ENLSGLLVQP 120
  121 KGLKFIMEPQ LPLPEKVIAD GTRLRQILWN LIGNAVKFTQ QGKIVVRVRR EGNDRLIFEV 180
  181 EDSGMGIPED EQDKIFAMYY QVKDRNGGRP ATGTGIGLAV SKRLAQSMGG DITVKSTQGV 240
  241 GSCFTLTIKA PAVQEASNA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.39794
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [515-778]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PSGDDMPLPA LHVLLVEDIE LNVIVARSVL EKLGNSVDVA MNGHDALAMF NPEDFDLVLL  60
   61 DIQLPDMSGL DIARQIRAEY GKQSLPPLVA LTANVLKDKK EYLDAGMDDV LSKPLSVPAL 120
  121 TAMIKQFWDS KPSSAVQKQE HKVMQTHESL LDTTMLEQYI DLVGPQLIHQ SLEMFEQMMP 180
  181 GYLAVLDSNM TARDQKGITE EAHKIKGAAG SVGLRHIQQL AQQIQTPTLP AWWDNVQDWV 240
  241 DELKLEWRND VQVLREWAAE VEKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.0
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

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: