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 FadI; ACSs; Acetyl-CoA acyltransferase; Acyl-CoA ligase; Beta-ketothiolase; Fatty acid oxidation complex subunit beta; EC 2.3.1.16 (characterized)
to candidate 16448 b2342 acetyl-CoA acetyltransferase (NCBI)

Query= SwissProt::P76503
         (436 letters)



>FitnessBrowser__Keio:16448
          Length = 436

 Score =  845 bits (2183), Expect = 0.0
 Identities = 436/436 (100%), Positives = 436/436 (100%)

Query: 1   MGQVLPLVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIE 60
           MGQVLPLVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIE
Sbjct: 1   MGQVLPLVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIE 60

Query: 61  QLVFGQVVQMPEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRA 120
           QLVFGQVVQMPEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRA
Sbjct: 61  QLVFGQVVQMPEAPNIAREIVLGTGMNVHTDAYSVSRACATSFQAVANVAESLMAGTIRA 120

Query: 121 GIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYST 180
           GIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYST
Sbjct: 121 GIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLRLRDLMPVPPAVAEYST 180

Query: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVE 240
           GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVE
Sbjct: 181 GLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVE 240

Query: 241 DNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY 300
           DNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY
Sbjct: 241 DNNIRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGY 300

Query: 301 LRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSE 360
           LRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSE
Sbjct: 301 LRSYAFTAIDVWQDMLLGPAWSTPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSE 360

Query: 361 RFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT 420
           RFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT
Sbjct: 361 RFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARMITQTLHELRRRGGGFGLVT 420

Query: 421 ACAAGGLGAAMVLEAE 436
           ACAAGGLGAAMVLEAE
Sbjct: 421 ACAAGGLGAAMVLEAE 436


Lambda     K      H
   0.319    0.133    0.377 

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: 764
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: 436
Length of database: 436
Length adjustment: 32
Effective length of query: 404
Effective length of database: 404
Effective search space:   163216
Effective search space used:   163216
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: 51 (24.3 bits)

Align candidate 16448 b2342 (acetyl-CoA acetyltransferase (NCBI))
to HMM TIGR02446 (fadI: acetyl-CoA C-acyltransferase FadI (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/TIGR02446.hmm
# target sequence database:        /tmp/gapView.1990190.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02446  [M=430]
Accession:   TIGR02446
Description: FadI: acetyl-CoA C-acyltransferase FadI
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   5.1e-278  907.9   4.6   5.7e-278  907.8   4.6    1.0  1  lcl|FitnessBrowser__Keio:16448  b2342 acetyl-CoA acetyltransfera


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:16448  b2342 acetyl-CoA acetyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  907.8   4.6  5.7e-278  5.7e-278       1     430 []       7     436 .]       7     436 .] 1.00

  Alignments for each domain:
  == domain 1  score: 907.8 bits;  conditional E-value: 5.7e-278
                       TIGR02446   1 vktrqgeriaivaglrtpfarqatafhgipavdlgkmvvsellarseidaklieqlvfgqvvqmpeapniareivlgtg 79 
                                     ++trqg+riaiv+glrtpfarqatafhgipavdlgkmvv+ellarsei+a++ieqlvfgqvvqmpeapniareivlgtg
  lcl|FitnessBrowser__Keio:16448   7 LVTRQGDRIAIVSGLRTPFARQATAFHGIPAVDLGKMVVGELLARSEIPAEVIEQLVFGQVVQMPEAPNIAREIVLGTG 85 
                                     589**************************************************************************** PP

                       TIGR02446  80 mnvhtdaysvtracatsfqsavnvaesimagaieigiaggadsssvlpigvskklaralvdlnkartlgqklkvlsrlg 158
                                     mnvhtdaysv+racatsfq+++nvaes+mag+i++giaggadsssvlpigvskklar+lvd+nkart++q+lk++srl+
  lcl|FitnessBrowser__Keio:16448  86 MNVHTDAYSVSRACATSFQAVANVAESLMAGTIRAGIAGGADSSSVLPIGVSKKLARVLVDVNKARTMSQRLKLFSRLR 164
                                     ******************************************************************************* PP

                       TIGR02446 159 lkdllpvppavaeystglsmgqtaeqmaktygitraeqdalahrshtlaaqawadgklkeevmtafvepykkfiaednn 237
                                     l+dl+pvppavaeystgl+mg+taeqmaktygitr++qdalahrsh++aaqaw+dgklkeevmtaf++pyk++++ednn
  lcl|FitnessBrowser__Keio:16448 165 LRDLMPVPPAVAEYSTGLRMGDTAEQMAKTYGITREQQDALAHRSHQRAAQAWSDGKLKEEVMTAFIPPYKQPLVEDNN 243
                                     ******************************************************************************* PP

                       TIGR02446 238 irenssladyaklrpafdrkygsvtaanstpltdgaaavilmsegrakelgleilgyirsyaftaidveqdmllgpsya 316
                                     ir+nssladyaklrpafdrk+g+vtaanstpltdgaaavilm+e+rakelgl++lgy+rsyaftaidv+qdmllgp+++
  lcl|FitnessBrowser__Keio:16448 244 IRGNSSLADYAKLRPAFDRKHGTVTAANSTPLTDGAAAVILMTESRAKELGLVPLGYLRSYAFTAIDVWQDMLLGPAWS 322
                                     ******************************************************************************* PP

                       TIGR02446 317 tplalkraglelsdltlidmheafaaqtlanvkllasekfaeeklgrakaigeidmskfnvlggsiayghpfaatgarl 395
                                     tplal+ragl++sdltlidmheafaaqtlan++ll+se+fa+e+lgra+a+ge+d+skfnvlggsiayghpfaatgar+
  lcl|FitnessBrowser__Keio:16448 323 TPLALERAGLTMSDLTLIDMHEAFAAQTLANIQLLGSERFAREALGRAHATGEVDDSKFNVLGGSIAYGHPFAATGARM 401
                                     ******************************************************************************* PP

                       TIGR02446 396 itqtlrelkrrggglglatacaagglgaamileve 430
                                     itqtl+el+rrggg+gl+tacaagglgaam+le+e
  lcl|FitnessBrowser__Keio:16448 402 ITQTLHELRRRGGGFGLVTACAAGGLGAAMVLEAE 436
                                     *********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (430 nodes)
Target sequences:                          1  (436 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: 25.87
//
[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