Alignments for a candidate for fadA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas simiae WCS417

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1490 PS417_07580 3-ketoacyl-CoA thiolase

Query= BRENDA::P28790
         (391 letters)



>FitnessBrowser__WCS417:GFF1490
          Length = 391

 Score =  739 bits (1909), Expect = 0.0
 Identities = 367/391 (93%), Positives = 380/391 (97%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60
           MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERN+KVDP EVEDVIWG
Sbjct: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG
Sbjct: 61  CVNQTLEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+RE QDAF +RSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREAQDAFGLRSHQLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240
           HKAT+EGKFKDEIIPM GYDENGFLK+ DYDETIRPDTTLESLAALKPAFNPKGGTVTAG
Sbjct: 181 HKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSAQRA+DLG++PLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG
Sbjct: 241 TSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L + DIDF ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LTINDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQNGG  G++TMCIGLGQGI+TVFERV
Sbjct: 361 LNVMKQNGGNLGVATMCIGLGQGISTVFERV 391


Lambda     K      H
   0.318    0.133    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: 668
Number of extensions: 14
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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: 50 (23.9 bits)

Align candidate GFF1490 PS417_07580 (3-ketoacyl-CoA thiolase)
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.19212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   6.3e-237  771.7   8.3   7.1e-237  771.5   8.3    1.0  1  lcl|FitnessBrowser__WCS417:GFF1490  PS417_07580 3-ketoacyl-CoA thiol


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1490  PS417_07580 3-ketoacyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  771.5   8.3  7.1e-237  7.1e-237       1     385 []       7     391 .]       7     391 .] 1.00

  Alignments for each domain:
  == domain 1  score: 771.5 bits;  conditional E-value: 7.1e-237
                           TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallae 75 
                                         dvvivd++rtpmgrskgg++rntraed+sahl++k+l+rn+kv++ eved++wgcv+qtleqg+niar+a+l+++
  lcl|FitnessBrowser__WCS417:GFF1490   7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWGCVNQTLEQGWNIARMASLMTQ 81 
                                         79************************************************************************* PP

                           TIGR02445  76 vphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltae 150
                                         +ph+ a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd++p++s  +aka+gmmgltae
  lcl|FitnessBrowser__WCS417:GFF1490  82 IPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAE 156
                                         *************************************************************************** PP

                           TIGR02445 151 mlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafd 225
                                         mlgk+hgi+re qdaf++rsh++ah+atlegkfk+eiip++gyd++g+lk  dyde+irp+tt+e+laal+paf+
  lcl|FitnessBrowser__WCS417:GFF1490 157 MLGKMHGITREAQDAFGLRSHQLAHKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAFN 231
                                         *************************************************************************** PP

                           TIGR02445 226 pkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdi 300
                                         pk+gtvtagtss+++dgas+m+vms++raq+lg++p+a+irsmavagvdp+imgygpvpat+kalkragl+i+di
  lcl|FitnessBrowser__WCS417:GFF1490 232 PKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLTINDI 306
                                         *************************************************************************** PP

                           TIGR02445 301 dvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglg 375
                                         d++elneafaaqalpvlkdl++ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++ g+atmciglg
  lcl|FitnessBrowser__WCS417:GFF1490 307 DFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGNLGVATMCIGLG 381
                                         *************************************************************************** PP

                           TIGR02445 376 qgiatvferv 385
                                         qgi+tvferv
  lcl|FitnessBrowser__WCS417:GFF1490 382 QGISTVFERV 391
                                         *********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 10.88
//
[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