YRC Public Data Repository - Protein Structure Prediction

Protein:	YCIR_ECOLI
Organism:	Escherichia coli
Length:	661 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 YCIR_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|78195532, gi\|... - gi\|78224277\|ref\|YP_386024.1\| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) [Geobacter...	494.0	[0..4]	[656..225]
gi\|113890838, gi... - gi\|78689926\|ref\|ZP_00854581.1\| PAS:GGDEF [Shewanella sp. MR-7], gi\|78510708\|gb\|EAP24075.1\| PAS:GGDEF...	471.0	[0..8]	[657..556]
gi\|113886832, gi... - gi\|82496212\|ref\|ZP_00881782.1\| PAS:GGDEF [Shewanella sp. MR-4], gi\|82405786\|gb\|EAP46456.1\| PAS:GGDEF...	470.0	[0..8]	[657..556]
gi\|89519310 - gi\|89519310\|gb\|ABD75787.1\| sensory box/GGDEF family protein [uncultured bacterium]	469.0	[0..5]	[657..208]
gi\|56476956, gi\|... - gi\|56476956\|ref\|YP_158545.1\| hypothetical protein ebA2702 [Aromatoleum aromaticum EbN1], gi\|56312999...	468.0	[0..4]	[661..374]
gi\|117614792, gi... - gi\|78684482\|ref\|ZP_00849266.1\| PAS:GGDEF [Shewanella sp. ANA-3], gi\|78507814\|gb\|EAP21323.1\| PAS:GGDE...	467.0	[0..8]	[657..575]
gi\|113949218, gi... - gi\|160877450\|ref\|YP_001556766.1\| diguanylate cyclase/phosphodiesterase with PAS/PAC and Chase sensor...	465.0	[0..9]	[657..563]
gi\|71906314, gi\|... - gi\|71906314\|ref\|YP_283901.1\| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) [Dechlorom...	460.0	[0..8]	[659..242]
gi\|89902813, gi\|... - gi\|89902813\|ref\|YP_525284.1\| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) [Rhodofera...	459.0	[0..7]	[656..391]

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Predicted Domain #1

Region A:
Residues: [1-97]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKTVRESTTL YNFLGSHNPY WRLTESSDVL RFSTTETTEP DRTLQLSAEQ AARIREMTVI  60
   61 TSSLMMSLTV DESDLSVHLV GRKINKREWA GNASAWH

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.0
Match:	2gj3A
Description:	No description for 2gj3A was found.

Predicted Domain #2

Region A:
Residues: [98-237]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DTPAVARDLS HGLSFAEQVV SEAHSAIVIL DSRGNIQRFN RLCEDYTGLK EHDVIGQSVF  60
   61 KLFMSRREAA ASRRNNRVFF RSGNAYEVEL WIPTCKGQRL FLFRNKFVHS GSGKNEIFLI 120
  121 CSGTDITEER RAQERLRILA

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	5.92
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
binding	2.11810529315597	bayes_pls_golite062009
protein binding	1.35116033536319	bayes_pls_golite062009
transcription regulator activity	0.972708865275432	bayes_pls_golite062009
two-component response regulator activity	0.798874220332901	bayes_pls_golite062009
DNA binding	0.737759263759466	bayes_pls_golite062009
nucleic acid binding	0.626552612035066	bayes_pls_golite062009
signal transducer activity	0.386333593205398	bayes_pls_golite062009
molecular transducer activity	0.386333593205398	bayes_pls_golite062009
transcription factor activity	0.233622464289646	bayes_pls_golite062009
protein dimerization activity	0.00745761267362077	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [238-403]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NTDSITGLPN RNAMQDLIDH AINHADNNKV GVVYLDLDNF KKVNDAYGHL FGDQLLRDVS  60
   61 LAILSCLEHD QVLARPGGDE FLVLASNTSQ SALEAMASRI LTRLRLPFRI GLIEVYTSCS 120
  121 VGIALSPEHG SDSTAIIRHA DTAMYTAKEG GRGQFCVFTP EMNQRV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	15.0
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	1.88327307771701	bayes_pls_golite062009
signal transducer activity	1.7438872646629	bayes_pls_golite062009
molecular transducer activity	1.7438872646629	bayes_pls_golite062009
two-component sensor activity	0.300567386918242	bayes_pls_golite062009
protein histidine kinase activity	0.276515698624029	bayes_pls_golite062009
binding	0.145546551776301	bayes_pls_golite062009
cyclase activity	0.135549728707442	bayes_pls_golite062009
phosphotransferase activity, nitrogenous group as acceptor	0.132981161220456	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [404-661]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FEYLWLDTNL RKALENDQLV IHYQPKITWR GEVRSLEALV RWQSPERGLI PPLDFISYAE  60
   61 ESGLIVPLGR WVILDVVRQV AKWRDKGINL RVAVNISARQ LADQTIFTAL KQVLQELNFE 120
  121 YCPIDVELTE SCLIENDELA LSVIQQFSQL GAQVHLDDFG TGYSSLSQLA RFPIDAIKLD 180
  181 QVFVRDIHKQ PVSQSLVRAI VAVAQALNLQ VIAEGVESAK EDAFLTKNGI NERQGFLFAK 240
  241 PMPAVAFERW YKRYLKRA

[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:

Predicted functions: