YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|110807075, gi...
Organism:	Shigella flexneri 5 str. 8401
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|110807075, gi....

Description	E-value	Query Range	Subject Range
gi\|71849372, gi\|... - gi\|71909751\|ref\|YP_287338.1\| PAS/PAC sensor hybrid histidine kinase [Dechloromonas aromatica RCB], g...	463.0	[0..2]	[775..120]
gi\|117609989, gi... - gi\|69256468\|ref\|ZP_00606017.1\| PAS [Magnetococcus sp. MC-1], gi\|68247589\|gb\|EAN29674.1\| PAS [Magneto...	454.0	[0..2]	[777..246]
gi\|108805455, gi... - gi\|108805455\|ref\|YP_645392.1\| multi-sensor hybrid histidine kinase [Rubrobacter xylanophilus DSM 994...	453.0	[0..2]	[776..344]
gi\|74313747, gi\|... - gi\|74313747\|ref\|YP_312166.1\| aerobic respiration control sensor protein ArcB [Shigella sonnei Ss046]...	451.0	[0..1]	[778..1]
gi\|75197159, gi\|... - gi\|75197159\|ref\|ZP_00707229.1\| COG0642: Signal transduction histidine kinase [Escherichia coli HS], ...	451.0	[0..1]	[778..1]
gi\|81242672, gi\|... - gi\|82778524\|ref\|YP_404873.1\| aerobic respiration control sensor protein ArcB [Shigella dysenteriae S...	450.0	[0..1]	[778..1]
gi\|75176098, gi\|... - gi\|75176098\|ref\|ZP_00696266.1\| COG0642: Signal transduction histidine kinase [Shigella boydii BS512]...	449.0	[0..1]	[778..1]
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...	449.0	[0..1]	[778..1]
gi\|82495403, gi\|... - gi\|82495403\|ref\|ZP_00880979.1\| PAS [Shewanella sp. MR-4], gi\|82406587\|gb\|EAP47251.1\| PAS [Shewanella...	449.0	[0..12]	[775..442]
gi\|78688636, gi\|... - gi\|78688636\|ref\|ZP_00853304.1\| PAS [Shewanella sp. MR-7], gi\|78512017\|gb\|EAP25371.1\| PAS [Shewanella...	449.0	[0..12]	[775..442]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKQIRLLAQY YVDLMMKLGL VRFSMLLALA LVVLAIVVQM AVTMVLHGQV ESIDVIRSIF  60
   61 FGLLITPWAV YFLSVVVEQL EESRQRLSRL VQKLEEMRER DLSLNVQLKD NIAQLNQEIA 120
  121 VRE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	11.0
Match:	2gj3A
Description:	No description for 2gj3A was found.

Predicted Domain #2

Region A:
Residues: [124-265]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KAEAELQETF GQLKIEIKER EETQIQLEQQ SSFLRSFLDA SPDLVFYRNE DKEFSGCNRA  60
   61 MELLTGKSEK QLVHLKPADV YSPEAAAKVI ETDEKVFRHN VSLTYEQWLD YPDGRKACFE 120
  121 IRKVPYYDRV GKRHGLMGFG RD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.09691
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
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 #3

Region A:
Residues: [266-517]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ITERKRYQDA LERASRDKTT FISTISHELR TPLNGIVGLS RILLDTELTA EQEKYLKTIH  60
   61 VSAVTLGNIF NDIIDMDKME RRKVQLDNQP VDFTSFLADL ENLSALQAQQ KGLRFNLEPT 120
  121 LPLPHQVITD GTRLRQILWN LISNAVKFTQ QGQVTVRVRY DEGDMLHFEV EDSGIGIPQD 180
  181 ELDKIFAMYY QVKDSHGGKP ATGTGIGLAV SRRLAKNMGG DITVTSEQGK GSTFTLTIHA 240
  241 PSVAEEVDDA FD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	42.221849
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: [518-778]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDDMPLPALN VLLVEDIELN VIVARSVLEK LGNSVDVAMT GKAALEMFKP GEYDLVLLDI  60
   61 QLPDMTGLDI SRELTKRYPR EDLPPLVALT ANVLKDKQEY LNAGMDDVLS KPLSVPALTA 120
  121 MIKKFWDTQD DEESTVTTEE NSKSEALLDI PMLEQYLELV GPKLITDGLA VFEKMMPGYV 180
  181 SVLESNLTAQ DKKGIVEEGH KIKGAAGSVG LRHLQQLGQQ IQSPDLPAWE DNVGEWIEEM 240
  241 KEEWRHDVEV LKAWVAKATK K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.0
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	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: