Alignments for a candidate for ilvE in Escherichia coli BW25113

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Escherichia coli BW25113

Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate 1937119 b3770 branched-chain amino acid aminotransferase (NCBI)

Query= CharProtDB::CH_024500
         (309 letters)



>FitnessBrowser__Keio:1937119
          Length = 309

 Score =  628 bits (1620), Expect = 0.0
 Identities = 309/309 (100%), Positives = 309/309 (100%)

Query: 1   MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60
           MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR
Sbjct: 1   MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60

Query: 61  LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120
           LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV
Sbjct: 61  LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120

Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180
           IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY
Sbjct: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180

Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240
           QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ
Sbjct: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240

Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300
           VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK
Sbjct: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300

Query: 301 WGWLDQVNQ 309
           WGWLDQVNQ
Sbjct: 301 WGWLDQVNQ 309


Lambda     K      H
   0.319    0.136    0.413 

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: 491
Number of extensions: 9
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: 309
Length of database: 309
Length adjustment: 27
Effective length of query: 282
Effective length of database: 282
Effective search space:    79524
Effective search space used:    79524
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 1937119 b3770 (branched-chain amino acid aminotransferase (NCBI))
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.953.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-151  489.8   0.0   1.5e-151  489.6   0.0    1.0  1  lcl|FitnessBrowser__Keio:1937119  b3770 branched-chain amino acid 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:1937119  b3770 branched-chain amino acid aminotransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.6   0.0  1.5e-151  1.5e-151       1     298 []      10     307 ..      10     307 .. 1.00

  Alignments for each domain:
  == domain 1  score: 489.6 bits;  conditional E-value: 1.5e-151
                         TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 
                                       w++Ge+v++edakvhv++halhYGt+vfeGiR+Y+++kg+++fr++eh++Rl+dsaki+r+++++s +el+e++++v
  lcl|FitnessBrowser__Keio:1937119  10 WFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIYRFPVSQSIDELMEACRDV 86 
                                       9**************************************************************************** PP

                         TIGR01122  78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154
                                       +rknnl+saYiRpl++vG+ ++g++p+++++++viiaa++wgaylg+eale+Gi+++vss++raa+n+ipt+aka+g
  lcl|FitnessBrowser__Keio:1937119  87 IRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGG 163
                                       ***************************************************************************** PP

                         TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231
                                       nYl+sll++sea+r+Gy+e+i+Ld +Gy++eG+Gen+f vkdgvl+tPp+++s+L gitrda+iklakelgiev+e+
  lcl|FitnessBrowser__Keio:1937119 164 NYLSSLLVGSEARRHGYQEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240
                                       ***************************************************************************** PP

                         TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298
                                       ++sre+ly+aDevf++Gtaae+tP+r+vDg+++geg++Gpvtk++q+aff l++g+te+k++wl++v
  lcl|FitnessBrowser__Keio:1937119 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307
                                       ****************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (309 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 9.41
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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