YRC Public Data Repository - Protein Structure Prediction

Protein:	YPDC_ECOLI
Organism:	Escherichia coli
Length:	285 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 YPDC_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|26248763, gi\|... - gi\|26248763\|ref\|NP_754803.1\| putative transcriptional regulator YpdC [Escherichia coli CFT073], gi\|2... gi\|218428089, gi... - gi\|218690525\|ref\|YP_002398737.1\| putative DNA-binding protein [Escherichia coli ED1a], gi\|218428089\|... gi\|227835783, gi... - gi\|227887433\|ref\|ZP_04005238.1\| transcriptional regulator YpdC [Escherichia coli 83972], gi\|22783578...	180.0	[0..1]	[285..1]
gi\|110344164, gi... - gi\|110642572\|ref\|YP_670302.1\| transcriptional regulator YpdC [Escherichia coli 536], gi\|110344164\|gb... gi\|75237948, gi\|... - gi\|75237948\|ref\|ZP_00721955.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi...	179.0	[0..1]	[285..1]
gi\|209764420, gi... - pir\|\|H85880 probable ARAC-type regulatory protein Z3647 [imported] - Escherichia coli (strain O157:H... gi\|15802924, gi\|... - gi\|15802924\|ref\|NP_288952.1\| putative ARAC-type regulatory protein [Escherichia coli O157:H7 EDL933]... gi\|15832516, gi\|... - gi\|15832516\|ref\|NP_311289.1\| putative ARAC-type regulatory protein [Escherichia coli O157:H7], gi\|13... gi\|254794344, gi... - gi\|254794344\|ref\|YP_003079181.1\| predicted DNA-binding protein [Escherichia coli O157:H7 str. TW1435... gi\|217319957, gi... - gi\|217327590\|ref\|ZP_03443673.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str... gi\|195938736 - gi\|195938736\|ref\|ZP_03084118.1\| putative ARAC-type regulatory protein [Escherichia coli O157:H7 str.... gi\|168800723, gi... - gi\|189377010\|gb\|EDU95426.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|189372949, gi... - gi\|189372949\|gb\|EDU91365.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|189002139, gi... - gi\|189002139\|gb\|EDU71125.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|209157546, gi... - gi\|209396146\|ref\|YP_002271868.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 st... gi\|208819613, gi... - gi\|208819613\|ref\|ZP_03259933.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str... gi\|208813446, gi... - gi\|208813446\|ref\|ZP_03254775.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str... gi\|208726705, gi... - gi\|208806904\|ref\|ZP_03249241.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str... gi\|188017323, gi... - gi\|188017323\|gb\|EDU55445.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|15832516, gi\|... - gi\|15832516\|ref\|NP_311289.1\| putative ARAC-type regulatory protein [Escherichia coli O157:H7 str. Sa... gi\|168772779, gi... - gi\|187771015\|gb\|EDU34859.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|189360252, gi... - gi\|189360252\|gb\|EDU78671.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|189366311, gi... - gi\|189366311\|gb\|EDU84727.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC... gi\|189355582, gi... - gi\|189355582\|gb\|EDU74001.1\| transcriptional regulator, AraC family [Escherichia coli O157:H7 str. EC...	179.0	[0..1]	[285..1]
gi\|73856407, gi\|... - gi\|74312930\|ref\|YP_311349.1\| putative ARAC-type regulatory protein [Shigella sonnei Ss046], gi\|73856... gi\|192932061, gi... - gi\|75259824\|ref\|ZP_00731126.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|193069743, gi... - gi\|75235570\|ref\|ZP_00719761.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|191165500, gi... - gi\|75231330\|ref\|ZP_00717718.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|124501999, gi... - gi\|124526528\|ref\|ZP_01698481.1\| transcriptional regulator, AraC family [Escherichia coli B], gi\|1245... gi\|218370837, gi... - gi\|218700851\|ref\|YP_002408480.1\| putative DNA-binding protein [Escherichia coli IAI39], gi\|218370837... gi\|251785726, gi... - gi\|251785726\|ref\|YP_003000030.1\| hypothetical protein B21_02253 [Escherichia coli BL21], gi\|24237799... gi\|253974276, gi... - gi\|254162375\|ref\|YP_003045483.1\| predicted DNA-binding protein [Escherichia coli B str. REL606], gi\|... gi\|254289136, gi... - gi\|254289136\|ref\|YP_003054884.1\| predicted DNA-binding protein [Escherichia coli BL21(DE3)], gi\|2539... gi\|194413334, gi... - gi\|75210172\|ref\|ZP_00710344.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|218361693, gi... - gi\|218554925\|ref\|YP_002387838.1\| putative DNA-binding protein [Escherichia coli IAI1], gi\|218361693\|... gi\|157155013, gi... - gi\|75187147\|ref\|ZP_00700414.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|218696025, gi... - gi\|218696025\|ref\|YP_002403692.1\| putative DNA-binding protein [Escherichia coli 55989], gi\|218352757... gi\|194440140, gi... - gi\|83584534\|ref\|ZP_00923209.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Escherichi... gi\|169754254, gi... - gi\|170019326\|ref\|YP_001724280.1\| AraC family transcriptional regulator [Escherichia coli ATCC 8739],... gi\|209919870, gi... - gi\|209919870\|ref\|YP_002293954.1\| putative transcriptional regulator [Escherichia coli SE11], gi\|2099...	178.0	[0..1]	[285..1]
gi\|83570019, gi\|... - gi\|83570019\|ref\|ZP_00921466.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Shigella d...	178.0	[0..1]	[285..1]
gi\|187730955, gi... - gi\|75177843\|ref\|ZP_00697905.1\| COG2207: AraC-type DNA-binding domain-containing proteins [Shigella b...	178.0	[0..1]	[285..1]
gi\|117624599, gi... - gi\|117624599\|ref\|YP_853512.1\| putative DNA-binding protein [Escherichia coli APEC O1], gi\|115513723\|... gi\|218366106, gi... - gi\|218559337\|ref\|YP_002392250.1\| putative DNA-binding protein [Escherichia coli S88], gi\|218366106\|e... gi\|226901276, gi... - gi\|237704910\|ref\|ZP_04535391.1\| transcriptional regulator YpdC [Escherichia sp. 3_2_53FAA], gi\|22690... gi\|91211725, gi\|... - gi\|91211725\|ref\|YP_541711.1\| transcriptional regulator YpdC [Escherichia coli UTI89], gi\|91073299\|gb...	178.0	[0..1]	[285..1]
gi\|81246261, gi\|... - gi\|82544850\|ref\|YP_408797.1\| putative ARAC-type regulatory protein [Shigella boydii Sb227], gi\|81246...	176.0	[0..1]	[285..1]
gi\|110615882, gi... - gi\|110806334\|ref\|YP_689854.1\| putative ARAC-type regulatory protein [Shigella flexneri 5 str. 8401],...	173.0	[0..1]	[285..1]
gi\|82569002 - gi\|82569002\|emb\|CAJ31227.1\| YpdC protein [Kluyvera ascorbata]	165.0	[0..1]	[285..1]

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Predicted Domain #1

Region A:
Residues: [1-175]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKAPGLPADQ QFFADLFSGL VLNPQLLGRV WFASQPASLP VGSLCIDFPR LDIVLRGEYG  60
   61 NLLEAKQQRL VEGEMLFIPA RAANLPVNNK PVMLLSLVFA PTWLGLSFYD SRTTSLLHPA 120
  121 RQIQLPSLQR GEGEAMLTAL THLSRSPLEQ NIIQPLVLSL LHLCRSVVNM PPGNS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.30103
Match:	2h0vA
Description:	No description for 2h0vA was found.

Predicted Domain #2

Region A:
Residues: [176-285]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QPRGDFLYHS ICNWVQDNYA QPLTRESVAQ FFNITPNHLS KLFAQHGTMR FIEYVRWVRM  60
   61 AKARMILQKY HLSIHEVAQR CGFPDSDYFC RVFRRQFGLT PGEYSARFQG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.30103
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	3.00143272905695	bayes_pls_golite062009
nucleic acid binding	2.89825020286436	bayes_pls_golite062009
transcription factor activity	2.53664874743748	bayes_pls_golite062009
binding	1.68817361068715	bayes_pls_golite062009
sequence-specific DNA binding	0.46503550280898	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.24108783215685	bayes_pls_golite062009
transcription repressor activity	0.20862059645422	bayes_pls_golite062009
protein binding	0.111941607625758	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: