Alignments for a candidate for ilvA in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvA in Escherichia coli BW25113

Align threonine ammonia-lyase; EC 4.3.1.19 (characterized)
to candidate 17191 b3117 threonine dehydratase (NCBI)

Query= CharProtDB::CH_024588
         (329 letters)



>FitnessBrowser__Keio:17191
          Length = 329

 Score =  645 bits (1665), Expect = 0.0
 Identities = 329/329 (100%), Positives = 329/329 (100%)

Query: 1   MHITYDLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIR 60
           MHITYDLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIR
Sbjct: 1   MHITYDLPVAIDDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIR 60

Query: 61  GAFNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDY 120
           GAFNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDY
Sbjct: 61  GAFNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDY 120

Query: 121 SAEVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVI 180
           SAEVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVI
Sbjct: 121 SAEVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVI 180

Query: 181 VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDV 240
           VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDV
Sbjct: 181 VPIGGGGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDV 240

Query: 241 SRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQY 300
           SRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQY
Sbjct: 241 SRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQY 300

Query: 301 IQNRKTVSIISGGNIDLSRVSQITGFVDA 329
           IQNRKTVSIISGGNIDLSRVSQITGFVDA
Sbjct: 301 IQNRKTVSIISGGNIDLSRVSQITGFVDA 329


Lambda     K      H
   0.318    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 472
Number of extensions: 3
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 329
Length of database: 329
Length adjustment: 28
Effective length of query: 301
Effective length of database: 301
Effective search space:    90601
Effective search space used:    90601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 17191 b3117 (threonine dehydratase (NCBI))
to HMM TIGR01127 (ilvA: threonine ammonia-lyase (EC 4.3.1.19))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01127.hmm
# target sequence database:        /tmp/gapView.19296.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01127  [M=380]
Accession:   TIGR01127
Description: ilvA_1Cterm: threonine ammonia-lyase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.3e-119  385.6   3.0   1.6e-119  385.3   3.0    1.0  1  lcl|FitnessBrowser__Keio:17191  b3117 threonine dehydratase (NCB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17191  b3117 threonine dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.3   3.0  1.6e-119  1.6e-119       1     294 [.      28     323 ..      28     326 .. 0.98

  Alignments for each domain:
  == domain 1  score: 385.3 bits;  conditional E-value: 1.6e-119
                       TIGR01127   1 tpleksstlsditgaevylklenlqktGsfkirGalnkiaklseeekkrGvvaasaGnhaqGvalaakvfgikakivmP 79 
                                     t + +s+ +s+ +++e++lk en+q+tGsfkirGa+nk++ l++ ek++Gvva saGnhaqGv+l+  + gi+ k+vmP
  lcl|FitnessBrowser__Keio:17191  28 TGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTDAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMP 106
                                     567789************************************************************************* PP

                       TIGR01127  80 esaplskvkatksyGaeviLhGadfDeayklaeelaeeegrvfvhafdDefviaGqGtlgleiledlpdvdtvivPvGG 158
                                     + ap skv at  y aev+LhG++f++  +  +e+ e egr+f+ ++dD+ viaGqGt+glei+edl dvd vivP+GG
  lcl|FitnessBrowser__Keio:17191 107 KGAPKSKVAATCDYSAEVVLHGDNFNDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGG 185
                                     ******************************************************************************* PP

                       TIGR01127 159 GGLisGvasavkklnpevkviGveaeaapslveslkegkikavesvktiaDGiavkkpgdltfeivkelvDevvavdee 237
                                     GGLi+G+a+a+k++np ++viGv++e+   +++s++ g i+++ ++ t+aDG  v +pg+lt+eiv+elvD++v v+e+
  lcl|FitnessBrowser__Keio:17191 186 GGLIAGIAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYEIVRELVDDIVLVSED 264
                                     ******************************************************************************* PP

                       TIGR01127 238 eiakaillLlerakivaegaGavgvaavleekvd..vkgkkvavvvsGGnidlnlleki 294
                                     ei ++++ L++r+k+v egaGa + aa+l+ k+d   +++k++ ++sGGnidl  +++i
  lcl|FitnessBrowser__Keio:17191 265 EIRNSMIALIQRNKVVTEGAGALACAALLSGKLDqyIQNRKTVSIISGGNIDLSRVSQI 323
                                     **********************************777999*************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (380 nodes)
Target sequences:                          1  (329 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.96
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis