YRC Public Data Repository - Protein Structure Prediction

Protein:	DACA_ECOLI
Organism:	Escherichia coli
Length:	403 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 DACA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|75258632, gi\|... - gi\|75258632\|ref\|ZP_00730039.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli E22], ...	425.0	[0..1]	[403..1]
gi\|13360128, gi\|... - gi\|15829924\|ref\|NP_308697.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli O157:H... gi\|25297760 - pir\|\|F90712 D-alanyl-D-alanine carboxypeptidase fraction A [imported] - Escherichia coli (strain O15... gi\|13360128, gi\|... - gi\|15829924\|ref\|NP_308697.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli O157:H...	425.0	[0..1]	[403..1]
gi\|192957584, gi... - gi\|193069040\|ref\|ZP_03049998.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli E110019],... gi\|169755939, gi... - gi\|170021011\|ref\|YP_001725965.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli AT... gi\|1778549 - gi\|1778549\|gb\|AAB40832.1\| penicillin-binding protein 5 [Escherichia coli] tr\|A0A0G3HL29\|A0... - D-alanyl-D-alanine carboxypeptidase (Penicillin-binding protein 5) protein OS=Escherichia coli (stra...	425.0	[0..1]	[403..25]
gi\|81244489, gi\|... - gi\|82543078\|ref\|YP_407025.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella boydii Sb227],... gi\|30062179, gi\|... - gi\|30062179\|ref\|NP_836350.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella flexneri 2a st... gi\|24112068, gi\|... - gi\|24112068\|ref\|NP_706578.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella flexneri 2a st...	423.0	[0..1]	[403..1]
gi\|49610765, gi\|... - gi\|50120239\|ref\|YP_049406.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Pectobacterium atrosept...	423.0	[0..1]	[403..1]
gi\|187731390, gi... - gi\|75175902\|ref\|ZP_00696089.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Shigella boydii BS512],...	422.0	[0..1]	[403..1]
gi\|110614267, gi... - gi\|110804719\|ref\|YP_688239.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella flexneri 5 st...	422.0	[0..1]	[403..25]
gi\|75514725 - gi\|75514725\|ref\|ZP_00736980.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli 53638]	421.0	[0..5]	[403..1]
gi\|205347141, gi... - gi\|205347141\|gb\|EDZ33772.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|168465811, gi... - gi\|195631937\|gb\|EDX50457.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|168236628, gi... - gi\|197290404\|gb\|EDY29760.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|168240484, gi... - gi\|205339760\|gb\|EDZ26524.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|205331044, gi... - gi\|205331044\|gb\|EDZ17808.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|168231649, gi... - gi\|205334030\|gb\|EDZ20794.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|161615147, gi... - gi\|161615147\|ref\|YP_001589112.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica... gi\|205324158, gi... - gi\|205324158\|gb\|EDZ11997.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... lcl\|NC_016856.1_... - [gene=dacA] [protein=D-alanyl-D-alanine carboxypeptidase] [protein_id=YP_005236352.1] [location=comp... gi\|62179236, gi\|... - gi\|62179236\|ref\|YP_215653.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica sub... gi\|238911587 - gi\|238911587\|ref\|ZP_04655424.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica ... gi\|207856103, gi... - gi\|207856103\|ref\|YP_002242754.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica... gi\|224467000, gi... - gi\|224582473\|ref\|YP_002636271.1\| D-alanine carboxypeptidase [Salmonella enterica subsp. enterica ser... gi\|204320533, gi... - gi\|204930599\|ref\|ZP_03221529.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp.... gi\|205271706, gi... - gi\|205351925\|ref\|YP_002225726.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica... gi\|197939763, gi... - gi\|198245247\|ref\|YP_002214626.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp... gi\|200389790, gi... - gi\|200389790\|ref\|ZP_03216401.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp.... gi\|194712224, gi... - gi\|194736722\|ref\|YP_002113755.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp... gi\|197250303, gi... - gi\|197250303\|ref\|YP_002145612.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp... gi\|16764014, gi\|... - gi\|16764014\|ref\|NP_459629.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella typhimurium ... gi\|194448720, gi... - gi\|194448720\|ref\|YP_002044671.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica... gi\|194471751, gi... - gi\|194471751\|ref\|ZP_03077735.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp.... gi\|168823261, gi... - gi\|205340474\|gb\|EDZ27238.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp. ent... gi\|194442745, gi... - gi\|194442745\|ref\|YP_002039879.1\| serine-type D-Ala-D-Ala carboxypeptidase [Salmonella enterica subsp...	420.0	[0..1]	[403..1]
gi\|29138262, gi\|... - gi\|29142631\|ref\|NP_805973.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica sub... gi\|16759596 - gi\|16759596\|ref\|NP_455213.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica sub... gi\|197363151, gi... - gi\|197363151\|ref\|YP_002142788.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica... gi\|25297769, gi\|... - gi\|25297769\|pir\|\|AH0580 D-alanine carboxypeptidase [imported] - Salmonella enterica subsp. enterica ... gi\|56414228, gi\|... - gi\|56414228\|ref\|YP_151303.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Salmonella enterica sub...	420.0	[0..1]	[403..1]

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Predicted Domain #1

Region A:
Residues: [1-403]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNTIFSARIM KRLALTTALC TAFISAAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL  60
   61 AEQNADVRRD PASLTKMMTS YVIGQAMKAG KFKETDLVTI GNDAWATGNP VFKGSSLMFL 120
  121 KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH 180
  181 GLDADGQYSS ARDMALIGQA LIRDVPNEYS IYKEKEFTFN GIRQLNRNGL LWDNSLNVDG 240
  241 IKTGHTDKAG YNLVASATEG QMRLISAVMG GRTFKGREAE SKKLLTWGFR FFETVNPLKV 300
  301 GKEFASEPVW FGDSDRASLG VDKDVYLTIP RGRMKDLKAS YVLNSSELHA PLQKNQVVGT 360
  361 INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	104.0
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: