Alignments for a candidate for kbl in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Escherichia coli BW25113

Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate 17678 b3617 2-amino-3-ketobutyrate coenzyme A ligase (NCBI)

Query= BRENDA::P0AB77
         (398 letters)



>FitnessBrowser__Keio:17678
          Length = 398

 Score =  783 bits (2023), Expect = 0.0
 Identities = 398/398 (100%), Positives = 398/398 (100%)

Query: 1   MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD 60
           MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD
Sbjct: 1   MRGEFYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPD 60

Query: 61  LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE 120
           LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE
Sbjct: 61  LIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFE 120

Query: 121 TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT 180
           TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT
Sbjct: 121 TLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIAT 180

Query: 181 DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG 240
           DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG
Sbjct: 181 DGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITG 240

Query: 241 TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRD 300
           TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRD
Sbjct: 241 TLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRD 300

Query: 301 RLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVV 360
           RLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVV
Sbjct: 301 RLWANARQFREQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVV 360

Query: 361 PKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVIA 398
           PKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVIA
Sbjct: 361 PKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVIA 398


Lambda     K      H
   0.320    0.135    0.388 

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: 694
Number of extensions: 16
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: 398
Length of database: 398
Length adjustment: 31
Effective length of query: 367
Effective length of database: 367
Effective search space:   134689
Effective search space used:   134689
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: 50 (23.9 bits)

Align candidate 17678 b3617 (2-amino-3-ketobutyrate coenzyme A ligase (NCBI))
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# 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.carbon/TIGR01822.hmm
# target sequence database:        /tmp/gapView.25258.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.7e-229  746.7   4.2     3e-229  746.5   4.2    1.0  1  lcl|FitnessBrowser__Keio:17678  b3617 2-amino-3-ketobutyrate coe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17678  b3617 2-amino-3-ketobutyrate coenzyme A ligase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.5   4.2    3e-229    3e-229       1     393 []       5     397 ..       5     397 .. 1.00

  Alignments for each domain:
  == domain 1  score: 746.5 bits;  conditional E-value: 3e-229
                       TIGR01822   1 lkailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGfGlssvrfic 79 
                                     ++++l+++le++r++Glfk+eriits+q+adi+vadG++v+nfcannylGl++hp++i+aak+++d+hGfG++svrfic
  lcl|FitnessBrowser__Keio:17678   5 FYQQLTNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPDLIAAAKAGMDSHGFGMASVRFIC 83 
                                     6899*************************************************************************** PP

                       TIGR01822  80 GtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGvrlckakryryenadledle 158
                                     Gtqd+hkele+kla+flg+edaily+scfdangGlfe+llg+edaiisdalnhasiidGvrlckakryry+n+d+++le
  lcl|FitnessBrowser__Keio:17678  84 GTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANNDMQELE 162
                                     ******************************************************************************* PP

                       TIGR01822 159 aklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdechatGflGatGrGsaelldvldkvdiitgt 237
                                     a+lkear+agar++liatdGvfsmdG+ia+l+ +c+la+kydalv+vd++ha+Gf+G++GrGs+e++dv+++vdiitgt
  lcl|FitnessBrowser__Keio:17678 163 ARLKEAREAGARHVLIATDGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGT 241
                                     ******************************************************************************* PP

                       TIGR01822 238 lGkalGGasGGfttakkevvellrqrsrpylfsnslapavvgasikvlelleasnelrdklventryfrekleaaGfdv 316
                                     lGkalGGasGG+t+a+kevve+lrqrsrpylfsnslapa+v+asikvle++ea++elrd+l++n+r+fre+++aaGf++
  lcl|FitnessBrowser__Keio:17678 242 LGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWANARQFREQMSAAGFTL 320
                                     ******************************************************************************* PP

                       TIGR01822 317 kpaehaiipvmlydaklaqklaerlleeGiyviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                     ++a+haiipvml+da +aqk+a++l++eGiyv+GffypvvpkGqarir+q+saah+ eq+++aveaf+++G++lgvi
  lcl|FitnessBrowser__Keio:17678 321 AGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQLGVI 397
                                     ***************************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (398 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: 00:00:00.02
# Mc/sec: 6.69
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources