YRC Public Data Repository - Protein Structure Prediction

Protein:	YHDA_ECOLI
Organism:	Escherichia coli
Length:	646 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 YHDA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|48859207, gi\|... - gi\|67875521\|ref\|ZP_00504817.1\| PAS:GGDEF [Clostridium thermocellum ATCC 27405], gi\|67850552\|gb\|EAM46...	517.0	[0..94]	[643..288]
gi\|89519310 - gi\|89519310\|gb\|ABD75787.1\| sensory box/GGDEF family protein [uncultured bacterium]	509.0	[0..81]	[645..289]
gi\|78363780, gi\|... - gi\|78485494\|ref\|YP_391419.1\| diguanylate cyclase/phosphodiesterase [Thiomicrospira crunogena XCL-2],...	508.0	[0..81]	[643..891]
gi\|71906314, gi\|... - gi\|71906314\|ref\|YP_283901.1\| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) [Dechlorom...	507.0	[0..87]	[646..331]
gi\|83310313, gi\|... - gi\|83310313\|ref\|YP_420577.1\| signal transduction protein [Magnetospirillum magneticum AMB-1], gi\|829...	506.0	[0..11]	[643..222]
gi\|114332895, gi... - gi\|69949915\|ref\|ZP_00637879.1\| PAS:GGDEF [Shewanella frigidimarina NCIMB 400], gi\|69166539\|gb\|EAN755...	501.0	[0..66]	[645..892]
gi\|221563411, gi... - gi\|222054122\|ref\|YP_002536484.1\| response regulator receiver modulated diguanylate cyclase/phosphodi...	501.0	[0..86]	[641..128]
gi\|24371939, gi\|... - gi\|24371939\|ref\|NP_715981.1\| sensory box protein [Shewanella oneidensis MR-1], gi\|24345777\|gb\|AAN534... SO0341 - sensory box protein	500.0	[0..68]	[643..921]
gi\|84318885, gi\|... - gi\|84318885\|ref\|ZP_00967302.1\| COG2202: FOG: PAS/PAC domain [Pseudomonas aeruginosa C3719], gi\|25423...	499.0	[0..53]	[646..632]
gi\|9946445, gi\|1... - gi\|9946445\|gb\|AAG03964.1\|AE004493_9 conserved hypothetical protein [Pseudomonas aeruginosa PAO1], gi... gi\|11347679 - pir\|\|H83574 conserved hypothetical protein PA0575 [imported] - Pseudomonas aeruginosa (strain PAO1)	499.0	[0..53]	[646..632]

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Predicted Domain #1

Region A:
Residues: [1-385]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV  60
   61 LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR 120
  121 LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER 180
  181 GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN 240
  241 QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL 300
  301 LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT 360
  361 EQVMEHAESA TRNAGLQGGN SWAIY

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	29.39794
Match:	1w25A
Description:	Response regulator PleD in complex with c-diGMP
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
nucleic acid binding	0.0928619295989472	bayes_pls_golite062009
DNA binding	0.0743796794876224	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [386-646]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDSLPEKGRG NVRWRTLIEQ MLSRGGPRLY QKPAVTREGQ VHHRELMCRI FDGNEEVSSA  60
   61 EYMPMVLQFG LSEEYDRLQI SRLIPLLRYW PEENLAIQVT VESLIRPRFQ RWLRDTLMQC 120
  121 EKSQRKRIII ELAEADVGQH ISRLQPVIRL VNALGVRVAV NQAGLTLVST SWIKELNVEL 180
  181 LKLHPGLVRN IEKRTENQLL VQSLVEACSG TSTQVYATGV RSRSEWQTLI QRGVTGGQGD 240
  241 FFASSQPLDT NVKKYSQRYS V

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	69.0
Match:	2r6oA
Description:	No description for 2r6oA was found.

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: