YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24346606, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	321 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 gi|24346606, gi|....

Description	E-value	Query Range	Subject Range
gi\|67154144, gi\|... - gi\|67154144\|ref\|ZP_00415889.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Azotobacter vinelandii AvOP... gi\|67154144 - gi\|67154144\|ref\|ZP_00415889.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Azotobacter vinelandii AvOP...	266.0	[0..1]	[320..1]
gi\|91796763, gi\|... - gi\|92113673\|ref\|YP_573601.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Chromohalobacter salexigens D...	260.0	[0..47]	[320..3]
gi\|148549880, gi... - gi\|82738224\|ref\|ZP_00901061.1\| D-alanyl-D-alanine carboxypeptidase [Pseudomonas putida F1], gi\|82714...	259.0	[0..1]	[320..18]
gi\|254848079, gi... - gi\|75830691\|ref\|ZP_00759964.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae MO10], ... gi\|229344714, gi... - gi\|229517999\|ref\|ZP_04407443.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae RC9], gi\|229344... gi\|229350843, gi... - gi\|229510878\|ref\|ZP_04400357.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae B33], gi\|229350... gi\|124115667, gi... - gi\|153213833\|ref\|ZP_01949039.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae 1587], gi\|12411... gi\|229608471, gi... - gi\|229608471\|ref\|YP_002879119.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae MJ-1236], gi\|2... tr\|C6YF70\|C6YF70... - D-alanyl-D-alanine carboxypeptidase OS=Vibrio cholerae MO10 GN=VchoM_00225 PE=3 SV=1	259.0	[0..1]	[321..1]
gi\|197753055, gi... - gi\|254285618\|ref\|ZP_04960582.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae AM-19226], gi\|1... tr\|A0A085SB94\|A0... - D-alanyl-D-alanine carboxypeptidase family protein OS=Vibrio cholerae GN=DN30_2542 PE=4 SV=1 gi\|229512959, gi... - gi\|229512959\|ref\|ZP_04402425.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae TMA 21], gi\|229... gi\|229333730, gi... - gi\|229529956\|ref\|ZP_04419346.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae 12129(1)], gi\|2... gi\|229339623, gi... - gi\|229523260\|ref\|ZP_04412667.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae TM 11079-80], g... gi\|146317546, gi... - gi\|75826260\|ref\|ZP_00755695.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae O395], ... gi\|75816441, gi\|... - gi\|75816441\|ref\|ZP_00746911.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae V52], g... gi\|254225715, gi... - gi\|75818354\|ref\|ZP_00748529.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae V51], g...	258.0	[0..1]	[321..1]
gi\|15640963, gi\|... - gi\|9655406\|gb\|AAF94109.1\| D-alanyl-D-alanine carboxypeptidase [Vibrio cholerae O1 biovar El Tor str.... gi\|11277410 - pir\|\|F82259 D-alanyl-D-alanine carboxypeptidase VC0947 [imported] - Vibrio cholerae (strain N16961 s...	258.0	[0..1]	[321..1]
gi\|24986562, gi\|... - gi\|26991483\|ref\|NP_746908.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Pseudomonas putida KT2440], g...	258.0	[0..1]	[320..1]
gi\|53802656, gi\|... - gi\|53802656\|ref\|YP_112644.1\| D-alanyl-D-alanine carboxypeptidase [Methylococcus capsulatus str. Bath...	257.0	[0..16]	[320..5]
gi\|104783763, gi... - gi\|95112750\|emb\|CAK17478.1\| D-ala-D-ala-carboxypeptidase; penicillin-binding protein 5 (precursor) [... gi\|95112750 - gi\|95112750\|emb\|CAK17478.1\| D-ala-D-ala-carboxypeptidase; penicillin-binding protein 5 (precursor) [...	256.0	[0..1]	[320..1]
gi\|68347052, gi\|... - gi\|70732753\|ref\|YP_262516.1\| D-alanyl-D-alanine carboxypeptidase [Pseudomonas fluorescens Pf-5], gi\|...	256.0	[0..1]	[320..1]

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Predicted Domain #1

Region A:
Residues: [1-321]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKISYLLGSF ILVCSSLTVA ATAHSADSAS VTTKSTATKA TTPKKAHTKQ EVAANSALVV  60
   61 DLKTNEILYS SNPDAVRPIA SVTKLMTAMV TLDAKLPMDE KLTINIKDTK EMRGVYSRVR 120
  121 IGSEISRKEM LLLTLMSSEN RAAASLAHHY PGGHKAFIKA MNAKAKALGM KNSRFVEPTG 180
  181 LSAKNVSSAR DLVVLLKASQ GYPMLGQLSS TEKKTVTFGK PKYSLDFRNT NRLVYKDNWD 240
  241 IHLTKTGFTN AAGHCLVMRT EMAKRKVAFV VLDAKGKYTH MADANRLRNW LETGKVTPIP 300
  301 ADAKQYKKQR SQQQLAKVSE T

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	61.30103
Match:	1nzoA
Description:	The crystal structure of wild type penicillin-binding protein 5 from E. coli
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
serine-type D-Ala-D-Ala carboxypeptidase activity	3.37745387761459	bayes_pls_golite062009
penicillin binding	3.16077730467133	bayes_pls_golite062009
serine-type carboxypeptidase activity	3.02516915958448	bayes_pls_golite062009
serine-type exopeptidase activity	2.98959517344587	bayes_pls_golite062009
carboxypeptidase activity	2.34154596924818	bayes_pls_golite062009
catalytic activity	2.2253600206851	bayes_pls_golite062009
drug binding	2.00354593744547	bayes_pls_golite062009
exopeptidase activity	1.66768404710194	bayes_pls_golite062009
peptidase activity	0.0621279448114327	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: