YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|24346818, gi\|...
Organism:	Shewanella oneidensis MR-1
Length:	390 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|24346818, gi|....

Description	E-value	Query Range	Subject Range
gi\|78504616, gi\|... - gi\|78687616\|ref\|ZP_00852359.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Shewanella sp. ANA-3], gi\|7...	403.0	[0..1]	[390..35]
gi\|117919440, gi... - gi\|117919440\|ref\|YP_868632.1\| penicillin-binding protein 6 [Shewanella sp. ANA-3], gi\|117611772\|gb\|A... gi\|113969331, gi... - gi\|113969331\|ref\|YP_733124.1\| penicillin-binding protein 6 [Shewanella sp. MR-4], gi\|113884015\|gb\|AB...	402.0	[0..1]	[390..2]
gi\|113888000, gi... - gi\|114046558\|ref\|YP_737108.1\| penicillin-binding protein 6 [Shewanella sp. MR-7], gi\|113888000\|gb\|AB...	402.0	[0..1]	[390..2]
gi\|113949380, gi... - gi\|113949380\|ref\|ZP_01435029.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Shewanella baltica OS195],...	399.0	[0..1]	[390..36]
gi\|116052037, gi... - gi\|116052037\|ref\|YP_789120.1\| D-ala-D-ala-carboxypeptidase [Pseudomonas aeruginosa UCBPP-PA14], gi\|1... gi\|126196061, gi... - gi\|254242683\|ref\|ZP_04936005.1\| D-ala-D-ala-carboxypeptidase [Pseudomonas aeruginosa 2192], gi\|19455... gi\|194547876, gi... - gi\|254236891\|ref\|ZP_04930214.1\| D-ala-D-ala-carboxypeptidase [Pseudomonas aeruginosa C3719], gi\|1945... gi\|11348401, gi\|... - gi\|4887207\|gb\|AAD32234.1\|AF147448_5 penicillin-binding protein 5 [Pseudomonas aeruginosa], pir\|\|C831... gi\|9950191, gi\|1... - gi\|9950191\|gb\|AAG07386.1\|AE004817_10 D-ala-D-ala-carboxypeptidase [Pseudomonas aeruginosa PAO1], gi\|... gi\|218769943, gi... - gi\|218889720\|ref\|YP_002438584.1\| D-ala-D-ala-carboxypeptidase [Pseudomonas aeruginosa LESB58], gi\|21...	399.0	[0..1]	[390..1]
gi\|148549880, gi... - gi\|82738224\|ref\|ZP_00901061.1\| D-alanyl-D-alanine carboxypeptidase [Pseudomonas putida F1], gi\|82714...	397.0	[0..1]	[390..18]
gi\|24986562, gi\|... - gi\|26991483\|ref\|NP_746908.1\| Serine-type D-Ala-D-Ala carboxypeptidase [Pseudomonas putida KT2440], g...	395.0	[0..1]	[390..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...	393.0	[0..1]	[389..1]
gi\|46914457, gi\|... - gi\|54310018\|ref\|YP_131038.1\| putative D-alanyl-D-alanine carboxypeptidase [Photobacterium profundum ...	392.0	[0..1]	[390..1]
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	392.0	[0..1]	[389..1]

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Predicted Domain #1

Region A:
Residues: [1-390]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNFVKSPIKT LLLISSVSLP VYAAQPIVTP DAPTVAAKAY VLMDYYSGQI IAEENAYESL  60
   61 NPASLTKMMT SYVIGQEIKA GNVSPDDDVT ISKNAWSKNF SDSSKMFIEV GKTVKVSDLN 120
  121 RGIIIQSGND ACVAMAEHIA GTEGAFVDMM NSWSKQLGMR DSYFENSHGL DSENHKTTAY 180
  181 DMALLGAALI RDVPEEYRIY SEKYYTFNGI KQYNRNGLLW DNSMNVDGIK TGHTSGAGYN 240
  241 LVASATKDGM RLISVVMGTQ SEAARKAESK KLLTYGFRFF ETVTPYKAGD SFVTQQIWYG 300
  301 DKSTVDLGVA TDTPITVSRG RAKDLKANFE LTKPLDAPLK KGETVGRLYF QLDGKDIAQF 360
  361 PLVTLQEVNE GSWFSKLVDY FKQLFSGWFS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	93.09691
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
drug binding	3.43867028493374	bayes_pls_golite062009
peptidase activity	3.14503902416546	bayes_pls_golite062009
serine-type D-Ala-D-Ala carboxypeptidase activity	3.12650314537616	bayes_pls_golite062009
penicillin binding	2.89507018520983	bayes_pls_golite062009
hydrolase activity	2.80171403488139	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	2.78480589579188	bayes_pls_golite062009
serine-type carboxypeptidase activity	2.70174066798582	bayes_pls_golite062009
serine-type exopeptidase activity	2.69091897402517	bayes_pls_golite062009
carboxypeptidase activity	1.96547160092829	bayes_pls_golite062009
catalytic activity	1.85492008367309	bayes_pls_golite062009
serine hydrolase activity	1.69122379434116	bayes_pls_golite062009
serine-type peptidase activity	1.6885532900392	bayes_pls_golite062009
exopeptidase activity	1.24775184094433	bayes_pls_golite062009
binding	1.11566650386305	bayes_pls_golite062009
protein binding	0.0666688846338231	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: