YRC Public Data Repository - Protein Structure Prediction

Protein:	AMIB_ECOLI
Organism:	Escherichia coli
Length:	445 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 AMIB_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|82546590, gi\|... - gi\|82546590\|ref\|YP_410537.1\| N-acetylmuramoyl-l-alanine amidase II [Shigella boydii Sb227], gi\|81248...	368.0	[0..1]	[445..1]
gi\|75179460, gi\|... - gi\|75179460\|ref\|ZP_00699464.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Shigella boydii BS512], ...	368.0	[0..1]	[445..1]
gi\|56384135, gi\|... - gi\|56480584\|ref\|NP_710034.2\| N-acetylmuramoyl-l-alanine amidase II [Shigella flexneri 2a str. 301], ... gi\|30065541, gi\|... - gi\|30065541\|ref\|NP_839712.1\| N-acetylmuramoyl-l-alanine amidase II [Shigella flexneri 2a str. 2457T]...	368.0	[0..1]	[445..1]
gi\|91213718, gi\|... - gi\|91213718\|ref\|YP_543704.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli UTI89], gi\|9107...	368.0	[0..1]	[445..6]
gi\|218430067, gi... - gi\|218692503\|ref\|YP_002400715.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli ED1a], gi\|2... gi\|26111493, gi\|... - gi\|26251061\|ref\|NP_757101.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli CFT073], gi\|261...	367.0	[0..1]	[445..6]
gi\|110808087, gi... - gi\|110808087\|ref\|YP_691607.1\| N-acetylmuramoyl-l-alanine amidase II [Shigella flexneri 5 str. 8401],...	367.0	[0..1]	[445..1]
gi\|218354650, gi... - gi\|218697918\|ref\|YP_002405585.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli 55989], gi\|... gi\|192926329, gi... - gi\|193066006\|ref\|ZP_03047064.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli E22], gi\|1... gi\|218556721, gi... - gi\|218556721\|ref\|YP_002389635.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli IAI1], gi\|2... gi\|157163632, gi... - gi\|157163632\|ref\|YP_001460950.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli HS], gi\|157... gi\|157157404, gi... - gi\|157157404\|ref\|YP_001465666.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli E24377A], g... gi\|193070885, gi... - gi\|75234282\|ref\|ZP_00718670.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli E110019... gi\|190904335, gi... - gi\|75231239\|ref\|ZP_00717646.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli B7A], g... gi\|75212282 - gi\|75212282\|ref\|ZP_00712322.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli B171]	367.0	[0..1]	[445..1]
gi\|110644526, gi... - gi\|110644526\|ref\|YP_672256.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli 536], gi\|11034... gi\|115515640, gi... - gi\|117626516\|ref\|YP_859839.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli APEC O1], gi\|1... gi\|75236178, gi\|... - gi\|75236178\|ref\|ZP_00720300.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli F11], g... gi\|237703836, gi... - gi\|237703836\|ref\|ZP_04534317.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia sp. 3_2_53FAA], g... gi\|218368097, gi... - gi\|218561328\|ref\|YP_002394241.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli S88], gi\|21...	366.0	[0..1]	[445..1]
gi\|254796188, gi... - gi\|254796188\|ref\|YP_003081025.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli O157:H7 str... gi\|13364622, gi\|... - gi\|15834399\|ref\|NP_313172.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli O157:H7], gi\|13... gi\|209396446, gi... - gi\|209396446\|ref\|YP_002273711.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 s... gi\|25349214, gi\|... - pir\|\|A86113 N-acetylmuramoyl-l-alanine amidase II [imported] - Escherichia coli (strain O157:H7, sub... gi\|217322276, gi... - gi\|217326055\|ref\|ZP_03442139.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 st... gi\|15804758, gi\|... - gi\|15804758\|ref\|NP_290799.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli O157:H7 EDL933]... gi\|195935959 - gi\|195935959\|ref\|ZP_03081341.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli O157:H7 str.... gi\|208809429, gi... - gi\|208809429\|ref\|ZP_03251766.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 st... gi\|208813873, gi... - gi\|208813873\|ref\|ZP_03255202.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 st... gi\|208821878, gi... - gi\|208821878\|ref\|ZP_03262198.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 st... gi\|168766446, gi... - gi\|189364003\|gb\|EDU82422.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|187770197, gi... - gi\|187770197\|gb\|EDU34041.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|189001668, gi... - gi\|189001668\|gb\|EDU70654.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|168784804, gi... - gi\|189375161\|gb\|EDU93577.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|188014496, gi... - gi\|188014496\|gb\|EDU52618.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|168754738, gi... - gi\|189357860\|gb\|EDU76279.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli O157:H7 str. E... gi\|13364622, gi\|... - gi\|15834399\|ref\|NP_313172.1\| N-acetylmuramoyl-l-alanine amidase II [Escherichia coli O157:H7 str. Sa...	366.0	[0..1]	[445..1]
gi\|75255896 - gi\|75255896\|ref\|ZP_00727628.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli E22] gi\|194426704, gi... - gi\|194426704\|ref\|ZP_03059258.1\| N-acetylmuramoyl-L-alanine amidase AmiB [Escherichia coli B171], gi\|... gi\|75198015 - gi\|75198015\|ref\|ZP_00708085.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli HS] gi\|75188880 - gi\|75188880\|ref\|ZP_00702147.1\| COG0860: N-acetylmuramoyl-L-alanine amidase [Escherichia coli E24377A...	364.0	[0..2]	[445..1]

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Predicted Domain #1

Region A:
Residues: [1-186]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MMYRIRNWLV ATLLLLCTPV GAATLSDIQV SNGNQQARIT LSFIGDPDYA FSHQSKRTVA  60
   61 LDIKQTGVIQ GLPLLFSGNN LVKAIRSGTP KDAQTLRLVV DLTENGKTEA VKRQNGSNYT 120
  121 VVFTINADVP PPPPPPPVVA KRVETPAVVA PRVSEPARNP FKTESNRTTG VISSNTVTRP 180
  181 AARATA

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [187-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NTGDKIIIAI DAGHGGQDPG AIGPGGTREK NVTIAIARKL RTLLNDDPMF KGVLTRDGDY  60
   61 FISVMGRSDV ARKQNANFLV SIHADAAPNR SATGASVWVL SNRRANSEMA SWLEQHEKQS 120
  121 ELLGGAGDVL ANSQSDPYLS QAVLDLQFGH SQRVGYDVAT SMISQLQRIG EIHKRRPEHA 180
  181 SLGVLRSPDI PSVLVETGFI SNNSEERLLA SDDYQQQLAE AIYKGLRNYF LAHPMQSAPQ 240
  241 GATAQTASTV TTPDRTLPN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.221849
Match:	1jwqA
Description:	Structure of the catalytic domain of CwlV, N-acetylmuramoyl-L-alanine amidase from Bacillus(Paenibacillus) polymyxa var.colistinus
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
N-acetylmuramoyl-L-alanine amidase activity	3.38642352843344	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	2.43845541073558	bayes_pls_golite062009
carboxypeptidase activity	2.33105751789147	bayes_pls_golite062009
hydrolase activity	1.7824202462173	bayes_pls_golite062009
catalytic activity	1.76936806579991	bayes_pls_golite062009
peptidase activity	1.69812537802871	bayes_pls_golite062009
peptidase activity, acting on L-amino acid peptides	1.41029347724469	bayes_pls_golite062009
exopeptidase activity	0.82896398764377	bayes_pls_golite062009
metallopeptidase activity	0.1586028474273	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: