YRC Public Data Repository - Protein Structure Prediction

Protein:	YPDA_ECOLI
Organism:	Escherichia coli
Length:	565 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 YPDA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|82777785, gi\|... - gi\|82777785\|ref\|YP_404134.1\| putative sensor protein [Shigella dysenteriae Sd197], gi\|81241933\|gb\|AB...	351.0	[0..1]	[565..1]
gi\|26109167, gi\|... - gi\|26248761\|ref\|NP_754801.1\| hypothetical protein c2919 [Escherichia coli CFT073], gi\|26109167\|gb\|AA... gi\|215265716, gi... - gi\|215487644\|ref\|YP_002330075.1\| predicted sensory kinase in two-component system with YpdB [Escheri... gi\|91211723, gi\|... - gi\|91211723\|ref\|YP_541709.1\| hypothetical protein UTI89_C2712 [Escherichia coli UTI89], gi\|91073297\|... gi\|237704908, gi... - gi\|237704908\|ref\|ZP_04535389.1\| inner membrane protein ypdA [Escherichia sp. 3_2_53FAA], gi\|22690127... gi\|218366104, gi... - gi\|218559335\|ref\|YP_002392248.1\| putative sensory kinase in two-component system with YpdB [Escheric... gi\|218428087, gi... - gi\|218690523\|ref\|YP_002398735.1\| putative sensory kinase in two-component system with YpdB [Escheric...	351.0	[0..1]	[565..1]
gi\|83570022 - gi\|83570022\|ref\|ZP_00921469.1\| COG3275: Putative regulator of cell autolysis [Shigella dysenteriae 1...	341.0	[0..7]	[565..1]
gi\|227835781, gi... - gi\|227887431\|ref\|ZP_04005236.1\| YpdA, sensory kinase in two-component system with YpdB [Escherichia ... gi\|115513721, gi... - gi\|117624597\|ref\|YP_853510.1\| YpdA, sensory kinase in two-component system with YpdB [Escherichia co...	340.0	[0..7]	[565..1]
gi\|75177845, gi\|... - gi\|75177845\|ref\|ZP_00697907.1\| COG3275: Putative regulator of cell autolysis [Shigella boydii BS512]...	340.0	[0..7]	[565..1]
gi\|110642570, gi... - gi\|110642570\|ref\|YP_670300.1\| hypothetical protein ECP_2406 [Escherichia coli 536], gi\|110344162\|gb\|... gi\|75237946, gi\|... - gi\|75237946\|ref\|ZP_00721953.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli F11],...	340.0	[0..7]	[565..1]
gi\|194420926, gi... - gi\|83584536\|ref\|ZP_00923211.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli 101-1... gi\|157077439, gi... - gi\|75187145\|ref\|ZP_00700412.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli E2437... gi\|157161853, gi... - gi\|75196403\|ref\|ZP_00706473.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli HS], ... gi\|194413307, gi... - gi\|75210170\|ref\|ZP_00710342.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli B171]... gi\|191165542, gi... - gi\|75231332\|ref\|ZP_00717720.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli B7A],... gi\|188017264, gi... - gi\|188017264\|gb\|EDU55386.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4113], gi\|16874... gi\|189355599, gi... - gi\|189355599\|gb\|EDU74018.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4401], gi\|16875... gi\|189366306, gi... - gi\|189366306\|gb\|EDU84722.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4501], gi\|16876... gi\|189360232, gi... - gi\|189360232\|gb\|EDU78651.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4486], gi\|16877... gi\|187771142, gi... - gi\|187771142\|gb\|EDU34986.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4196], gi\|16877... gi\|189001991, gi... - gi\|189001991\|gb\|EDU70977.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4076], gi\|16878... gi\|189377057, gi... - gi\|189377057\|gb\|EDU95473.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC508], gi\|168800... gi\|169754256, gi... - gi\|170019328\|ref\|YP_001724282.1\| signal transduction histidine kinase, LytS [Escherichia coli ATCC 8... gi\|124501997, gi... - gi\|124526526\|ref\|ZP_01698479.1\| signal transduction histidine kinase, LytS [Escherichia coli B], gi\|... gi\|170681499, gi... - gi\|170681499\|ref\|YP_001744575.1\| sensor histidine kinase [Escherichia coli SMS-3-5], gi\|170519217\|gb... gi\|195938734 - gi\|195938734\|ref\|ZP_03084116.1\| signal transduction histidine kinase, LytS [Escherichia coli O157:H7... gi\|208807505, gi... - gi\|208807505\|ref\|ZP_03249842.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4206], gi\|2... gi\|208813682, gi... - gi\|208813682\|ref\|ZP_03255011.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4045], gi\|2... gi\|208818950, gi... - gi\|208818950\|ref\|ZP_03259270.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4042], gi\|2... gi\|209161084, gi... - gi\|209399684\|ref\|YP_002271866.1\| sensor histidine kinase [Escherichia coli O157:H7 str. EC4115], gi\|... gi\|217326889, gi... - gi\|217326889\|ref\|ZP_03442972.1\| sensor histidine kinase [Escherichia coli O157:H7 str. TW14588], gi\|... gi\|75235568, gi\|... - gi\|75235568\|ref\|ZP_00719759.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli E1100... gi\|1799791 - dbj\|BAA16250.1\| similar to [SwissProt Accession Number P33357] [Escherichia coli] gi\|75259822, gi\|... - gi\|75259822\|ref\|ZP_00731124.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli E22],... gi\|75515726 - gi\|75515726\|ref\|ZP_00737861.1\| COG3275: Putative regulator of cell autolysis [Escherichia coli 53638...	340.0	[0..7]	[565..1]
gi\|50121360, gi\|... - gi\|50121360\|ref\|YP_050527.1\| two-component sensor kinase [Pectobacterium atrosepticum SCRI1043], gi\|...	336.0	[0..1]	[561..1]
gi\|77958013 - gi\|77958013\|ref\|ZP_00822055.1\| COG3275: Putative regulator of cell autolysis [Yersinia bercovieri AT...	326.0	[0..7]	[563..1]
gi\|238798686, gi... - gi\|77961223\|ref\|ZP_00825066.1\| COG3275: Putative regulator of cell autolysis [Yersinia mollaretii AT...	324.0	[0..7]	[563..1]

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Predicted Domain #1

Region A:
Residues: [1-135]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MHEIFNMLLA VFDRAALMLI CLFFLIRIRL FRELLHKSAH SPKELLAVTA IFSLFALFST  60
   61 WSGVPVEGSL VNVRIIAVMS GGILFGPWVG IITGVIAGIH RYLIDIGGVT AIPCFITSIL 120
  121 AGCISGWINL KIPKA

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	38.568636
Match:	PF07694.3
Description:	No description for PF07694.3 was found.

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [136-308]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QRWRVGILGG MLCETLTMIL VIVWAPTTAL GIDIVSKIGI PMILGSVCIG FIVLLVQSVE  60
   61 GEKEASAARQ AKLALDIANK TLPLFRHVNS ESLRKVCEII RDDIHADAVA ITNTDHVLAY 120
  121 VGVGEHNYQN GDDFISPTTR QAMNYGKIII KNNDEAHRTP EIHSMLVIPL WEK

[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 #3

Region A:
Residues: [309-565]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GVVTGTLKIY YCHAHQITSS LQEMAVGLSQ IISTQLEVSR AEQLREMANK AELRALQSKI  60
   61 NPHFLFNALN AISSSIRLNP DTARQLIFNL SRYLRYNIEL KDDEQIDIKK ELYQIKDYIA 120
  121 IEQARFGDKL TVIYDIDEEV NCCIPSLLIQ PLVENAIVHG IQPCKGKGVV TISVAECGNR 180
  181 VRIAVRDTGH GIDPKVIERV EANEMPGNKI GLLNVHHRVK LLYGEGLHIR RLEPGTEIAF 240
  241 YIPNQRTPVA SQATLLL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	51.221849
Match:	2c2aA
Description:	Structure of the entire cytoplasmic portion of a sensor histidine kinase protein
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