Alignments for a candidate for fadA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Escherichia coli BW25113

Align 3-ketoacyl-CoA thiolase FadA; Acetyl-CoA acyltransferase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 1937156 b3845 acetyl-CoA acetyltransferase (NCBI)

Query= SwissProt::P21151
         (387 letters)



>FitnessBrowser__Keio:1937156
          Length = 387

 Score =  761 bits (1964), Expect = 0.0
 Identities = 387/387 (100%), Positives = 387/387 (100%)

Query: 1   MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60
           MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ
Sbjct: 1   MEQVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQ 60

Query: 61  TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120
           TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH
Sbjct: 61  TLEQGFNIARNAALLAEVPHSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEH 120

Query: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT 180
           MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT
Sbjct: 121 MGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLARMHGISREMQDAFAARSHARAWAAT 180

Query: 181 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA 240
           QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA
Sbjct: 181 QSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMVTAGTSSA 240

Query: 241 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300
           LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS
Sbjct: 241 LSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSAS 300

Query: 301 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM 360
           DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM
Sbjct: 301 DIGVFEMNEAFAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLM 360

Query: 361 ERKDVQFGLATMCIGLGQGIATVFERV 387
           ERKDVQFGLATMCIGLGQGIATVFERV
Sbjct: 361 ERKDVQFGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.320    0.133    0.387 

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: 651
Number of extensions: 17
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: 387
Length of database: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 1937156 b3845 (acetyl-CoA acetyltransferase (NCBI))
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))

# 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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.28835.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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-247  806.9   8.7   1.5e-247  806.7   8.7    1.0  1  lcl|FitnessBrowser__Keio:1937156  b3845 acetyl-CoA acetyltransfera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:1937156  b3845 acetyl-CoA acetyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  806.7   8.7  1.5e-247  1.5e-247       1     385 []       3     387 .]       3     387 .] 1.00

  Alignments for each domain:
  == domain 1  score: 806.7 bits;  conditional E-value: 1.5e-247
                         TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevp 77 
                                       +vvivda+rtpmgrskggafrn+raedlsahl+++llarnp++eaa+++diywgcvqqtleqgfniarnaallaevp
  lcl|FitnessBrowser__Keio:1937156   3 QVVIVDAIRTPMGRSKGGAFRNVRAEDLSAHLMRSLLARNPALEAAALDDIYWGCVQQTLEQGFNIARNAALLAEVP 79 
                                       79*************************************************************************** PP

                         TIGR02445  78 hevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgk 154
                                       h+v+avtvnrlcgssmqalhdaar+imtgda++cl+ggvehmghv+mshgvdfhpgls++vakaagmmgltaeml++
  lcl|FitnessBrowser__Keio:1937156  80 HSVPAVTVNRLCGSSMQALHDAARMIMTGDAQACLVGGVEHMGHVPMSHGVDFHPGLSRNVAKAAGMMGLTAEMLAR 156
                                       ***************************************************************************** PP

                         TIGR02445 155 lhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtv 231
                                       +hgisre+qdafaarshara+aat++++fkneiipt+g+dadgvlk+++ydevirpettveala+lrpafdp+ng+v
  lcl|FitnessBrowser__Keio:1937156 157 MHGISREMQDAFAARSHARAWAATQSAAFKNEIIPTGGHDADGVLKQFNYDEVIRPETTVEALATLRPAFDPVNGMV 233
                                       ***************************************************************************** PP

                         TIGR02445 232 tagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelnea 308
                                       tagtssalsdga+amlvmse+ra+elg+kprar+rsmav+g+dpsimgygpvpa+k+alk+agls+sdi+v+e+nea
  lcl|FitnessBrowser__Keio:1937156 234 TAGTSSALSDGAAAMLVMSESRAHELGLKPRARVRSMAVVGCDPSIMGYGPVPASKLALKKAGLSASDIGVFEMNEA 310
                                       ***************************************************************************** PP

                         TIGR02445 309 faaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385
                                       faaq+lp++kdlgl++++dek+nlnggaialghplgcsgaristtllnlmerkd++fglatmciglgqgiatvferv
  lcl|FitnessBrowser__Keio:1937156 311 FAAQILPCIKDLGLIEQIDEKINLNGGAIALGHPLGCSGARISTTLLNLMERKDVQFGLATMCIGLGQGIATVFERV 387
                                       ****************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (387 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: 7.66
//
[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