YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|29138262, gi\|...
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. Ty2
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 gi|29138262, gi|....

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], ...	0.0	[1..403]	[1..403]
gi\|75240786, gi\|... - gi\|75240786\|ref\|ZP_00724693.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli F11], ... gi\|74311168, gi\|... - gi\|74311168\|ref\|YP_309587.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella sonnei Ss046],... gi\|190902607, gi... - gi\|75229484\|ref\|ZP_00716031.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli B7A], ... gi\|75236613 - gi\|75236613\|ref\|ZP_00720701.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli E11001... gi\|82775901, gi\|... - gi\|82775901\|ref\|YP_402248.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella dysenteriae Sd... gi\|168770236, gi... - gi\|189360912\|gb\|EDU79331.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 str. ... gi\|187766838, gi... - gi\|187766838\|gb\|EDU30682.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 str. ... gi\|157159257, gi... - gi\|75189670\|ref\|ZP_00702937.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli E24377... gi\|75194815 - gi\|75194815\|ref\|ZP_00704885.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli HS] DACA_ECOLI - Penicillin-binding protein 5 precursor (D-alanyl-D-alanine carboxypeptidase fraction A) (EC 3.4.16.4... gi\|194437465, gi... - gi\|83586934\|ref\|ZP_00925564.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli 101-1]... gi\|209159918, gi... - gi\|209398518\|ref\|YP_002269267.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 ... gi\|209917890, gi... - gi\|209917890\|ref\|YP_002291974.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli SE... gi\|215485672, gi... - gi\|215485672\|ref\|YP_002328103.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli O1... gi\|217326125, gi... - gi\|217326125\|ref\|ZP_03442209.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 s... gi\|218359942, gi... - gi\|218553174\|ref\|YP_002386087.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli IA... gi\|218364339, gi... - gi\|218557570\|ref\|YP_002390483.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli S8... gi\|254791798, gi... - gi\|254791798\|ref\|YP_003076635.1\| D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) ... gi\|218426019, gi... - gi\|218688455\|ref\|YP_002396667.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli ED... gi\|254160714, gi... - gi\|254160714\|ref\|YP_003043822.1\| D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) ... gi\|218694072, gi... - gi\|218694072\|ref\|YP_002401739.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli 55... gi\|189002783, gi... - gi\|189002783\|gb\|EDU71769.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 str. ... gi\|253774382, gi... - gi\|254287502\|ref\|YP_003053250.1\| D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) ... gi\|189373492, gi... - gi\|189373492\|gb\|EDU91908.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 str. ... gi\|242376408, gi... - gi\|251784135\|ref\|YP_002998439.1\| hypothetical protein B21_00590 [Escherichia coli BL21], gi\|24237640... gi\|169888046, gi... - gi\|170080312\|ref\|YP_001729632.1\| D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) ... gi\|238860729, gi... - gi\|238899909\|ref\|YP_002925705.1\| D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) ... gi\|170521438, gi... - gi\|170683720\|ref\|YP_001742748.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli SMS-3-5]... gi\|237707395, gi... - gi\|237707395\|ref\|ZP_04537876.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia sp. 3_2_53FAA]... gi\|188490615, gi... - gi\|188495416\|ref\|ZP_03002686.1\| penicillin-binding protein 5 [Escherichia coli 53638], gi\|188490615\|... gi\|227838475, gi... - gi\|227884389\|ref\|ZP_04002194.1\| serine family D-Ala-D-Ala carboxypeptidase [Escherichia coli 83972],... gi\|208728050, gi... - gi\|208808249\|ref\|ZP_03250586.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 s... gi\|208815700, gi... - gi\|208815700\|ref\|ZP_03256879.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 s... gi\|208823277, gi... - gi\|208823277\|ref\|ZP_03263595.1\| serine-type D-Ala-D-Ala carboxypeptidase [Escherichia coli O157:H7 s... DACA_ECO57 - D-alanyl-D-alanine carboxypeptidase DacA OS=Escherichia coli O157:H7 GN=dacA PE=3 SV=1 DACA_ECOL6 - D-alanyl-D-alanine carboxypeptidase DacA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UP... gi\|89107501, gi\|... - gi\|89107501\|ref\|AP_001281.1\| D-alanyl-D-alanine carboxypeptidase [Escherichia coli str. K-12 substr.... EG10201 - D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) / D-alanine D-alanine carboxypept... gi\|91209679, gi\|... - gi\|91209679\|ref\|YP_539665.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli UTI89]... gi\|15800346, gi\|... - gi\|15800346\|ref\|NP_286358.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli O157:H... gi\|218368990, gi... - gi\|218699004\|ref\|YP_002406633.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli IA... gi\|218431063, gi... - gi\|218703966\|ref\|YP_002411485.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli UM... gi\|110342453, gi... - gi\|110640861\|ref\|YP_668589.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli 536],... gi\|117622848, gi... - gi\|117622848\|ref\|YP_851761.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Escherichia coli APEC ... DACA_ECOL6 - D-alanyl-D-alanine carboxypeptidase dacA OS=Escherichia coli O6 GN=dacA PE=3 SV=1 EG10201 - D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) / D-alanine D-alanine carboxypept...	0.0	[1..403]	[1..403]
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...	0.0	[1..403]	[25..427]
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...	0.0	[1..403]	[1..403]
gi\|187731390, gi... - gi\|75175902\|ref\|ZP_00696089.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Shigella boydii BS512],...	0.0	[1..403]	[1..403]
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...	0.0	[1..403]	[1..403]
gi\|110614267, gi... - gi\|110804719\|ref\|YP_688239.1\| D-alanyl-D-alanine carboxypeptidase fraction A [Shigella flexneri 5 st...	0.0	[1..403]	[25..427]
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...	0.0	[1..403]	[1..403]
gi\|75514725 - gi\|75514725\|ref\|ZP_00736980.1\| COG1686: D-alanyl-D-alanine carboxypeptidase [Escherichia coli 53638]	0.0	[5..403]	[1..399]
gi\|74095596 - gi\|74095596\|emb\|CAJ27362.1\| strongly similar to penicillin-binding protein 5 precursor [Enterobacter...	0.0	[1..403]	[1..404]

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Predicted Domain #1

Region A:
Residues: [1-403]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKTTFSARFM QRMALTTALC ATFISTAHAD DLNIKTMIPG VPQIDAESYI LIDYNSGKVL  60
   61 AEQNADERRD PASLTKMMTS YVIGQAMKAG KFKETDLVTV GNDAWATGNP VFKGSSLMFL 120
  121 KPGMQVPVSQ LIRGINLQSG NDACVAMADF AAGSQDAFVG LMNSYVNALG LKNTHFQTVH 180
  181 GLDADGQYSS ARDMALIGQA LIRDVPNEYA VYKEKEFTFN GIRQLNRNGL LWDNSLNVDG 240
  241 IKTGHTSKAG YNLVASATEG QMRLISAVMG GRTYKGRETE SKKLLTWGFR FFETVNPLKA 300
  301 GKEFASEPAW FGNTDRASLG VDKDVYLTIP RGRMKDLKAS YVLNTAELHA PLQKNQVVGT 360
  361 INFQLDGKTI EQRPLVVLQE IPEGNFFGKI IDYIKLMFHH WFG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	98.0
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: