YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|110804171, gi...
Organism:	Shigella flexneri 5 str. 8401
Length:	183 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|110804171, gi....

Description	E-value	Query Range	Subject Range
gi\|187427588, gi... - gi\|75176541\|ref\|ZP_00696678.1\| COG3023: Negative regulator of beta-lactamase expression [Shigella bo... gi\|218703367, gi... - gi\|218703367\|ref\|YP_002410886.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli UMN026... gi\|26246044, gi\|... - gi\|26246044\|ref\|NP_752083.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli CFT073], g... gi\|74310728, gi\|... - gi\|74310728\|ref\|YP_309147.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Shigella sonnei Ss046], gi\|... gi\|81244124, gi\|... - gi\|82542713\|ref\|YP_406660.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Shigella boydii Sb227], gi\|...	230.0	[0..1]	[183..1]
gi\|110341913, gi... - gi\|110640321\|ref\|YP_668049.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli 536], gi\|... gi\|75236912, gi\|... - gi\|75236912\|ref\|ZP_00720974.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|218363817, gi... - gi\|218557048\|ref\|YP_002389961.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli S88], ... gi\|91070747, gi\|... - gi\|91209173\|ref\|YP_539159.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli UTI89], gi... gi\|218368516, gi... - gi\|218698530\|ref\|YP_002406159.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli IAI39]... gi\|237704258, gi... - gi\|237704258\|ref\|ZP_04534739.1\| anhydro-N-acetylmuramyl-tripeptide amidase [Escherichia sp. 3_2_53FA... gi\|115511517, gi... - gi\|117622393\|ref\|YP_851306.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli APEC O1],... gi\|170683851, gi... - gi\|170683851\|ref\|YP_001742230.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli SMS-3-5], gi\|1...	229.0	[0..1]	[183..1]
gi\|254037525, gi... - gi\|254037525\|ref\|ZP_04871602.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia sp. 1_1_43], gi\|2268... gi\|254791245, gi... - gi\|254791245\|ref\|YP_003076082.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli O157:H... gi\|208818939, gi... - gi\|208818939\|ref\|ZP_03259259.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC... gi\|209157754, gi... - gi\|209396354\|ref\|YP_002268716.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. E... gi\|15829368, gi\|... - gi\|15829368\|ref\|NP_308141.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli O157:H7 st... gi\|217320354, gi... - gi\|217324133\|ref\|ZP_03440217.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. TW... gi\|189376392, gi... - gi\|189376392\|gb\|EDU94808.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC508]... gi\|195938208 - gi\|195938208\|ref\|ZP_03083590.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli O157:H7... gi\|208727313, gi... - gi\|208807512\|ref\|ZP_03249849.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC... gi\|208813142, gi... - gi\|208813142\|ref\|ZP_03254471.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC... gi\|189360662, gi... - gi\|189360662\|gb\|EDU79081.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4486... gi\|168776818, gi... - gi\|187767850\|gb\|EDU31694.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4196... gi\|15829368, gi\|... - gi\|15829368\|ref\|NP_308141.1\| AmpD [Escherichia coli O157:H7], gi\|13359570\|dbj\|BAB33537.1\| AmpD prote... gi\|168781997, gi... - gi\|189000448\|gb\|EDU69434.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4076... gi\|25336732, gi\|... - pir\|\|B85494 regulates ampC [imported] - Escherichia coli (strain O157:H7, substrain EDL933), pir\|\|B... gi\|168789639, gi... - gi\|189370816\|gb\|EDU89232.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC869]... gi\|12512819, gi\|... - gi\|15799794\|ref\|NP_285806.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli O157:H7 ED... gi\|168752494, gi... - gi\|188013666\|gb\|EDU51788.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4113... gi\|189356986, gi... - gi\|189356986\|gb\|EDU75405.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4401... gi\|168764856, gi... - gi\|189365204\|gb\|EDU83620.1\| N-acetylmuramoyl-L-alanine amidase [Escherichia coli O157:H7 str. EC4501...	227.0	[0..1]	[183..1]
gi\|82775516, gi\|... - gi\|82775516\|ref\|YP_401863.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Shigella dysenteriae Sd197]...	227.0	[0..1]	[183..1]
gi\|68304054 - gi\|68304054\|gb\|AAY89685.1\| AmpD [Escherichia coli] gi\|68304054\|gb\|A... - AmpD [Escherichia coli]	225.0	[0..1]	[183..3]
gi\|124530572, gi... - gi\|124530572\|ref\|ZP_01701175.1\| N-acetylmuramyl-L-alanine amidase, negative regulator of AmpC, AmpD ... EG10041 - 1,6-anhydro-N-acetylmuramyl-L-alanine amidase, Zn-dependent; murein amidase / 1,6-anhydro-N-acetylmu... gi\|238861845, gi... - gi\|238899509\|ref\|YP_002925305.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli BW2952... gi\|251783671, gi... - gi\|251783671\|ref\|YP_002997975.1\| hypothetical protein B21_00108 [Escherichia coli BL21], gi\|24237594... gi\|253976340, gi... - gi\|254287033\|ref\|YP_003052781.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli BL21(D... gi\|253972131, gi... - gi\|254160230\|ref\|YP_003043338.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli B str.... EG10041 - 1,6-anhydro-N-acetylmuramyl-L-alanine amidase, Zn-dependent; murein amidase / 1,6-anhydro-N-acetylmu... gi\|194411660, gi... - gi\|75208422\|ref\|ZP_00708754.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|89106991, gi\|... - gi\|89106991\|ref\|AP_000771.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli str. K-12 ... gi\|190903597, gi... - gi\|75230528\|ref\|ZP_00717009.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|193071238, gi... - gi\|75233837\|ref\|ZP_00718307.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|75258897, gi\|... - gi\|75258897\|ref\|ZP_00730287.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|188495103, gi... - gi\|75511985\|ref\|ZP_00734580.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|169756464, gi... - gi\|170021536\|ref\|YP_001726490.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli ATCC 8... AMPD_ECOLI - Protein ampD - Escherichia coli gi\|83569690, gi\|... - gi\|83569690\|ref\|ZP_00921140.1\| COG3023: Negative regulator of beta-lactamase expression [Shigella dy... gi\|209917301, gi... - gi\|209917301\|ref\|YP_002291385.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli SE11],... gi\|194440194, gi... - gi\|83584488\|ref\|ZP_00923169.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|170079747, gi... - gi\|170079747\|ref\|YP_001729067.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli str. K... gi\|75189209, gi\|... - gi\|75189209\|ref\|ZP_00702476.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|218350308, gi... - gi\|218693576\|ref\|YP_002401243.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli 55989]... gi\|157159578, gi... - gi\|75194325\|ref\|ZP_00704395.1\| COG3023: Negative regulator of beta-lactamase expression [Escherichia... gi\|218359458, gi... - gi\|218552690\|ref\|YP_002385603.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Escherichia coli IAI1],...	225.0	[0..1]	[183..1]
gi\|13660767 - gi\|13660767\|gb\|AAK32970.1\| anhydro-N-acetylmuramyl-tripeptide amidase [Enterobacter cloacae]	222.0	[0..1]	[178..1]
gi\|56126677, gi\|... - gi\|56412420\|ref\|YP_149495.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Salmonella enterica subsp. ... gi\|197243164, gi... - gi\|197264909\|ref\|ZP_03164983.1\| N-acetyl-anhydromuramyl-L-alanine amidase [Salmonella enterica subsp... gi\|7688346\|emb\|C... - AmpD protein [Salmonella typhimurium] AMPD_SALTS - 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD OS=Salmonella typhimurium (strain SL1344) GN=ampD... gi\|194402356, gi... - gi\|194443693\|ref\|YP_002039378.1\| N-acetyl-anhydromuramyl-L-alanine amidase [Salmonella enterica subs... gi\|205347466, gi... - gi\|205347466\|gb\|EDZ34097.1\| N-acetyl-anhydromuramyl-L-alanine amidase [Salmonella enterica subsp. en... gi\|167990021, gi... - gi\|205331382\|gb\|EDZ18146.1\| N-acetyl-anhydromuramyl-L-alanine amidase [Salmonella enterica subsp. en... lcl\|NC_016856.1_... - [gene=ampD] [protein=N-acetyl-anhydromuranmyl-L-alanine amidase] [protein_id=YP_005235807.1] [locati... gi\|199604858, gi... - gi\|200387760\|ref\|ZP_03214372.1\| N-acetyl-anhydromuramyl-L-alanine amidase [Salmonella enterica subsp... gi\|7688346 - gi\|7688346\|emb\|CAB89835.1\| AmpD protein [Salmonella typhimurium] gi\|197092831, gi... - gi\|197361356\|ref\|YP_002140991.1\| N-acetyl-anhydromuranmyl-L-alanine amidase [Salmonella enterica sub...	221.0	[0..1]	[179..1]

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Predicted Domain #1

Region A:
Residues: [1-183]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLLEQGWLVG ARRVPSPHYD CRLDDETPTL LVVHNISLPP GEFGGPWIDA LFTGTIDPQA  60
   61 HPFFAEIAHL RVSAHCLIRR DGEIVQYVPF DKRAWHAGVS QYQGRERCND FSIGIELEGT 120
  121 DTLAYTDAQY QQLAAVTRAL IDRYPDIANN MTGHCDIAPD RKTDPGPAFD WARFRALVSK 180
  181 ETT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	57.0
Match:	1j3gA
Description:	AmpD protein
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
N-acetylmuramoyl-L-alanine amidase activity	5.57894011339111	bayes_pls_golite062009
peptidoglycan binding	3.64373264470797	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	3.57069794427757	bayes_pls_golite062009
catalytic activity	0.998996028203371	bayes_pls_golite062009
hydrolase activity	0.83639977289922	bayes_pls_golite062009
pattern binding	0.274968943680442	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0631264776586918	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: