YRC Public Data Repository - Protein Structure Prediction

Protein:	GADX_SHIFL
Organism:	Shigella flexneri
Length:	274 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 GADX_SHIFL.

Description	E-value	Query Range	Subject Range
gi\|11992160 - gi\|11992160\|gb\|AAG42472.1\|AF311305_1 transcriptional regulator GadY [Escherichia coli] GADX_ECO27 - HTH-type transcriptional regulator gadX OS=Escherichia coli O127:H6 GN=gadX PE=2 SV=1 GADX_ECO27 - HTH-type transcriptional regulator GadX OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=gadX...	176.0	[0..1]	[274..1]
GADX_ECOL6 - HTH-type transcriptional regulator gadX OS=Escherichia coli O6 GN=gadX PE=2 SV=1 gi\|91074596, gi\|... - gi\|91213022\|ref\|YP_543008.1\| DNA-binding transcriptional regulator GadX [Escherichia coli UTI89], gi... gi\|226902547, gi... - gi\|237703283\|ref\|ZP_04533764.1\| transcriptional regulator gadX [Escherichia sp. 3_2_53FAA], gi\|22690... GADX_ECOL6 - HTH-type transcriptional regulator GadX OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPE... gi\|227839554, gi... - gi\|227883675\|ref\|ZP_04001480.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 83972],... gi\|117625799, gi... - gi\|117625799\|ref\|YP_859122.1\| DNA-binding transcriptional regulator GadX [Escherichia coli APEC O1],...	175.0	[0..1]	[274..1]
gi\|191170413, gi... - gi\|191170413\|ref\|ZP_03031966.1\| transcriptional regulator GadX [Escherichia coli F11], gi\|190909221\|... gi\|110345354, gi... - gi\|110643762\|ref\|YP_671492.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 536], gi\|...	175.0	[0..1]	[274..1]
gi\|110617326, gi... - gi\|110807778\|ref\|YP_691298.1\| DNA-binding transcriptional regulator GadX [Shigella flexneri 5 str. 8...	168.0	[0..1]	[274..1]
gi\|82545880, gi\|... - gi\|82545880\|ref\|YP_409827.1\| DNA-binding transcriptional regulator GadX [Shigella boydii Sb227], gi\|... gi\|218697225, gi... - gi\|218697225\|ref\|YP_002404892.1\| DNA-binding transcriptional regulator GadX [Escherichia coli 55989]... gi\|218556066, gi... - gi\|218556066\|ref\|YP_002388979.1\| DNA-binding transcriptional regulator GadX [Escherichia coli IAI1],... gi\|209914235, gi... - gi\|209920976\|ref\|YP_002295060.1\| DNA-binding transcriptional regulator GadX [Escherichia coli SE11],... gi\|194428671, gi... - gi\|194428671\|ref\|ZP_03061208.1\| transcriptional regulator GadX [Escherichia coli B171], gi\|194413254... gi\|192958151, gi... - gi\|193068500\|ref\|ZP_03049462.1\| transcriptional regulator GadX [Escherichia coli E110019], gi\|192958... gi\|193061658, gi... - gi\|193061658\|ref\|ZP_03042755.1\| transcriptional regulator GadX [Escherichia coli E22], gi\|192932448\|... gi\|191165288, gi... - gi\|191165288\|ref\|ZP_03027131.1\| transcriptional regulator GadX [Escherichia coli B7A], gi\|190904690\|... gi\|187730117, gi... - gi\|187730117\|ref\|YP_001882202.1\| transcriptional regulator GadX [Shigella boydii CDC 3083-94], gi\|18... gi\|157157443, gi... - gi\|157157443\|ref\|YP_001464986.1\| DNA-binding transcriptional regulator GadX [Escherichia coli E24377... gi\|74313938, gi\|... - gi\|74313938\|ref\|YP_312357.1\| DNA-binding transcriptional regulator GadX [Shigella sonnei Ss046], gi\|...	168.0	[0..1]	[274..1]
gi\|85676528, gi\|... - gi\|89110497\|ref\|AP_004277.1\| DNA-binding transcriptional dual regulator [Escherichia coli str. K-12 ... gi\|157162995, gi... - gi\|157162995\|ref\|YP_001460313.1\| DNA-binding transcriptional regulator GadX [Escherichia coli HS], g... gi\|251786762, gi... - gi\|251786762\|ref\|YP_003001066.1\| hypothetical protein B21_03317 [Escherichia coli BL21], gi\|24237903... gi\|238860922, gi... - gi\|238902605\|ref\|YP_002928401.1\| DNA-binding transcriptional dual regulator [Escherichia coli BW2952... gi\|254163438, gi... - gi\|254163438\|ref\|YP_003046546.1\| DNA-binding transcriptional dual regulator [Escherichia coli B str.... EG12243 - acid resistance regulon transcriptional activator; autoactivator / Transcriptional activator for gad... gi\|253979495, gi... - gi\|254290188\|ref\|YP_003055936.1\| DNA-binding transcriptional dual regulator [Escherichia coli BL21(D... gi\|124528567, gi... - gi\|124528567\|ref\|ZP_01699845.1\| transcriptional regulator, AraC family [Escherichia coli B], gi\|1245... gi\|194425245, gi... - gi\|194435702\|ref\|ZP_03067805.1\| transcriptional regulator GadX [Escherichia coli 101-1], gi\|19442524... gi\|188489351, gi... - gi\|188494152\|ref\|ZP_03001422.1\| transcriptional regulator GadX [Escherichia coli 53638], gi\|18848935... gi\|169890862, gi... - gi\|170083027\|ref\|YP_001732347.1\| DNA-binding transcriptional dual regulator [Escherichia coli str. K... gi\|169753183, gi... - gi\|170018255\|ref\|YP_001723209.1\| DNA-binding transcriptional regulator GadX [Escherichia coli ATCC 8... GADX_ECOLI - HTH-type transcriptional regulator gadX - Escherichia coli EG12243 - acid resistance regulon transcriptional activator; autoactivator / Transcriptional activator for gad...	168.0	[0..1]	[274..1]
gi\|189369501, gi... - gi\|189369501\|gb\|EDU87917.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4501], g... gi\|168765923, gi... - gi\|189364822\|gb\|EDU83241.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4486], g... gi\|209755556, gi... - pir\|\|E86024 probable ARAC-type regulatory protein yhiX [imported] - Escherichia coli (strain O157:H7... gi\|168772530, gi... - gi\|187771509\|gb\|EDU35353.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4196], g... gi\|168779659, gi... - gi\|189002276\|gb\|EDU71262.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4076], g... gi\|12518228, gi\|... - gi\|15804060\|ref\|NP_290096.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7 ED... gi\|188018486, gi... - gi\|188018486\|gb\|EDU56608.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4113], g... gi\|168753328, gi... - gi\|189359386\|gb\|EDU77805.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4401], g... GADX_ECO57 - HTH-type transcriptional regulator GadX OS=Escherichia coli O157:H7 GN=gadX PE=3 SV=1 gi\|254594869, gi... - gi\|254795469\|ref\|YP_003080306.1\| DNA-binding transcriptional dual regulator [Escherichia coli O157:H... gi\|208735755, gi... - gi\|208814478\|ref\|ZP_03255807.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4045... gi\|208819839, gi... - gi\|208819839\|ref\|ZP_03260159.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4042... gi\|209159511, gi... - gi\|209398111\|ref\|YP_002272993.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC411... gi\|217324900, gi... - gi\|217324900\|ref\|ZP_03440984.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. TW1458... gi\|168785381, gi... - gi\|189374307\|gb\|EDU92723.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC869], gi... gi\|189379897, gi... - gi\|189379897\|gb\|EDU98313.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC508], gi... gi\|195935044 - gi\|195935044\|ref\|ZP_03080426.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7... gi\|15833650, gi\|... - gi\|15833650\|ref\|NP_312423.1\| DNA-binding transcriptional regulator GadX [Escherichia coli O157:H7 st... gi\|208726265, gi... - gi\|208806464\|ref\|ZP_03248801.1\| transcriptional regulator GadX [Escherichia coli O157:H7 str. EC4206...	168.0	[0..1]	[274..1]
gi\|82778652, gi\|... - gi\|82778652\|ref\|YP_405001.1\| DNA-binding transcriptional regulator GadX [Shigella dysenteriae Sd197]...	163.0	[0..1]	[274..1]
gi\|15901726, gi\|... - gi\|66877103\|ref\|ZP_00402748.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Streptococ... gi\|25389448 - pir\|\|A95222 msm operon regulatory protein [imported] - Streptococcus pneumoniae (strain TIGR4) gi\|225725782, gi... - gi\|225857488\|ref\|YP_002738999.1\| Msm operon regulatory protein [Streptococcus pneumoniae P1031], gi\|... gi\|149013558, gi... - gi\|149013558\|ref\|ZP_01834165.1\| msm operon regulatory protein [Streptococcus pneumoniae SP19-BS75], ... gi\|220675097, gi... - gi\|221232635\|ref\|YP_002511789.1\| AraC family regulatory protein [Streptococcus pneumoniae ATCC 70066...	150.0	[0..6]	[245..36]
gi\|25509235 - pir\|\|H98085 hypothetical protein msmR [imported] - Streptococcus pneumoniae (strain R6) gi\|116077109, gi... - gi\|116516533\|ref\|YP_817128.1\| msm operon regulatory protein MsmR [Streptococcus pneumoniae D39], gi\|... gi\|15903756, gi\|... - gi\|15903756\|ref\|NP_359306.1\| MSM (multiple sugar metabolism) operon regulatory protein [Streptococcu... gi\|182630177, gi... - gi\|182684843\|ref\|YP_001836590.1\| msm operon regulatory protein [Streptococcus pneumoniae CGSP14], gi...	148.0	[0..6]	[245..36]

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Predicted Domain #1

Region A:
Residues: [1-138]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQSLHGNCLI AYARHKYILT MVNGEYRYFN GGDLVFADAS QIRVDKCVEN FVLVSRDTLS  60
   61 LFLPMLKEEA LNLHAHKKIS SLLVHHCSRD IPVFQEVAQL SQNKNLRYAE MLRKRALIFA 120
  121 LLSVFLEDEH FIPLLLNV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.0
Match:	1xjaA
Description:	Apo form of the Y31V mutant dimerization domain fragment of Escherichia coli regulatory protein AraC
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [139-274]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LQPNMRTRVC TVINNNIAHE WTLARIASEL LMSPSLLKKK LREEETSYSQ LLTECRMQRA  60
   61 LQLIVIHGFS IKRVAVSCGY HSVSYFIYVF RNYYGMTPTE YQERSAQGLP NRDSAASIVA 120
  121 QGNFYGTNRS AEGIRL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	20.39794
Match:	1bl0A
Description:	MarA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.57523737355937	bayes_pls_golite062009
DNA binding	2.7565055095762	bayes_pls_golite062009
nucleic acid binding	2.48097584527739	bayes_pls_golite062009
transcription factor activity	2.33198016659192	bayes_pls_golite062009
binding	2.21133851845856	bayes_pls_golite062009
sequence-specific DNA binding	0.37638337609693	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.24108783215685	bayes_pls_golite062009
transcription repressor activity	0.20862059645422	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: