YRC Public Data Repository - Protein Structure Prediction

Protein:	YDDV_ECOLI
Organism:	Escherichia coli
Length:	460 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 YDDV_ECOLI.

Description	E-value	Query Range	Subject Range
DOSC_SHISS - Diguanylate cyclase DosC OS=Shigella sonnei (strain Ss046) GN=dosC PE=3 SV=1	297.0	[0..1]	[460..1]
gi\|75195591 - gi\|75195591\|ref\|ZP_00705661.1\| COG2199: FOG: GGDEF domain [Escherichia coli HS]	290.0	[0..8]	[460..1]
gi\|75512558 - gi\|75512558\|ref\|ZP_00735081.1\| COG2199: FOG: GGDEF domain [Escherichia coli 53638]	289.0	[0..8]	[460..1]
gi\|75239891 - gi\|75239891\|ref\|ZP_00723852.1\| COG2199: FOG: GGDEF domain [Escherichia coli E110019] gi\|75190539 - gi\|75190539\|ref\|ZP_00703806.1\| COG2199: FOG: GGDEF domain [Escherichia coli E24377A]	288.0	[0..8]	[460..1]
gi\|83587828 - gi\|83587828\|ref\|ZP_00926454.1\| COG2199: FOG: GGDEF domain [Escherichia coli 101-1]	288.0	[0..8]	[460..1]
gi\|75231751 - gi\|75231751\|ref\|ZP_00718092.1\| COG2199: FOG: GGDEF domain [Escherichia coli B7A]	288.0	[0..8]	[460..1]
gi\|75257756 - gi\|75257756\|ref\|ZP_00729241.1\| COG2199: FOG: GGDEF domain [Escherichia coli E22] gi\|75212861 - gi\|75212861\|ref\|ZP_00712859.1\| COG2199: FOG: GGDEF domain [Escherichia coli B171]	287.0	[0..8]	[460..1]
gi\|78363780, gi\|... - gi\|78485494\|ref\|YP_391419.1\| diguanylate cyclase/phosphodiesterase [Thiomicrospira crunogena XCL-2],...	285.0	[0..21]	[460..779]
gi\|78368063, gi\|... - gi\|78368063\|ref\|ZP_00838317.1\| PAS:GGDEF [Shewanella sp. PV-4], gi\|78359894\|gb\|EAP01742.1\| PAS:GGDEF...	282.0	[0..22]	[460..307]
gi\|71144549, gi\|... - gi\|71278809\|ref\|YP_269948.1\| sensory box protein [Colwellia psychrerythraea 34H], gi\|71144549\|gb\|AAZ...	279.0	[0..13]	[459..492]

Back

Predicted Domain #1

Region A:
Residues: [1-79]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MEMYFKRMKD EWTGLVEQAD PPIRAKAAEI AVAHAHYLSI EFYRIVRIDP HAEEFLSNEQ  60
   61 VERQLKSAME RWIINVLSA

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	2.43
Match:	1or4A
Description:	Crystal Structure of HemAT sensor domain from B.subtilis in the cyano-liganded form
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	0.151597543144863	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [80-460]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QVDDVERLIQ IQHTVAEVHA RIGIPVEIVE MGFRVLKKIL YPVIFSSDYS AAEKLQVYHF  60
   61 SINSIDIAME VMTRAFTFSD SSASKEDENY RIFSLLENAE EEKERQIASI LSWEIDIIYK 120
  121 ILLDSDLGSS LPLSQADFGL WFNHKGRHYF SGIAEVGHIS RLIQDFDGIF NQTMRNTRNL 180
  181 NNRSLRVKFL LQIRNTVSQI ITLLRELFEE VSRHEVGMDV LTKLLNRRFL PTIFKREIAH 240
  241 ANRTGTPLSV LIIDVDKFKE INDTWGHNTG DEILRKVSQA FYDNVRSSDY VFRYGGDEFI 300
  301 IVLTEASENE TLRTAERIRS RVEKTKLKAA NGEDIALSLS IGAAMFNGHP DYERLIQIAD 360
  361 EALYIAKRRG RNRVELWKAS L

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	43.522879
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	0.916519233091696	bayes_pls_golite062009
DNA binding	0.504254929272308	bayes_pls_golite062009
nucleic acid binding	0.317238312592983	bayes_pls_golite062009
signal transducer activity	0.153335668160196	bayes_pls_golite062009
molecular transducer activity	0.153335668160196	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:

Predicted functions: