Alignments for a candidate for fadA in Pseudomonas litoralis 2SM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas litoralis 2SM5

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_090272541.1 BLU11_RS06165 acetyl-CoA C-acyltransferase FadA

Query= BRENDA::P28790
         (391 letters)



>NCBI__GCF_900105005.1:WP_090272541.1
          Length = 391

 Score =  700 bits (1806), Expect = 0.0
 Identities = 346/391 (88%), Positives = 372/391 (95%)

Query: 1   MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60
           MSLNPRDVVIVDFGRTPMGRSKGGM+RN RAE +SA LI+ VLERN K+DP EVEDVIWG
Sbjct: 1   MSLNPRDVVIVDFGRTPMGRSKGGMYRNVRAETLSAKLITGVLERNPKIDPAEVEDVIWG 60

Query: 61  CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120
           CVNQTLEQGWNIARMASLMT IPHT+AAQTVSRLCGSSMSALHTAAQAIMTGNGDVFV+G
Sbjct: 61  CVNQTLEQGWNIARMASLMTPIPHTAAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVIG 120

Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180
           GVEHMGHVSMMHGVDPNP +SLYAAKA+GMMGLTAEMLGKMHGI+REQQD F +RSHQLA
Sbjct: 121 GVEHMGHVSMMHGVDPNPALSLYAAKAAGMMGLTAEMLGKMHGITREQQDQFGLRSHQLA 180

Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240
           HKATVEG FKDEIIPM+G+DENGFL++F  DETIRP+TTLESLAAL+PAFNPKGGTVTAG
Sbjct: 181 HKATVEGNFKDEIIPMEGHDENGFLRVFTEDETIRPETTLESLAALRPAFNPKGGTVTAG 240

Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300
           TSSQITDGASCMIVMSA+RAK LGLEPLAVIRSMAVAG DP+IMGYGPVPAT+KALKRAG
Sbjct: 241 TSSQITDGASCMIVMSAERAKALGLEPLAVIRSMAVAGCDPSIMGYGPVPATRKALKRAG 300

Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360
           L++ DID +ELNEAFAAQALPVLKDLK+LDKM++KVNLHGGAIALGHPFGCSGARISGTL
Sbjct: 301 LSIDDIDHVELNEAFAAQALPVLKDLKLLDKMDQKVNLHGGAIALGHPFGCSGARISGTL 360

Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391
           LNVMKQNGGT G+STMCIGLGQGI TVFERV
Sbjct: 361 LNVMKQNGGTIGMSTMCIGLGQGITTVFERV 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: 640
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: 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 WP_090272541.1 BLU11_RS06165 (acetyl-CoA C-acyltransferase FadA)
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.1643474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.7e-231  753.8   7.2     2e-231  753.6   7.2    1.0  1  NCBI__GCF_900105005.1:WP_090272541.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090272541.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  753.6   7.2    2e-231    2e-231       1     385 []       7     391 .]       7     391 .] 1.00

  Alignments for each domain:
  == domain 1  score: 753.6 bits;  conditional E-value: 2e-231
                             TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaall 73 
                                           dvvivd++rtpmgrskgg++rn+rae lsa+l+ ++l+rnpk+++aeved++wgcv+qtleqg+niar+a+l+
  NCBI__GCF_900105005.1:WP_090272541.1   7 DVVIVDFGRTPMGRSKGGMYRNVRAETLSAKLITGVLERNPKIDPAEVEDVIWGCVNQTLEQGWNIARMASLM 79 
                                           79*********************************************************************** PP

                             TIGR02445  74 aevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmg 146
                                           + +ph+ aa+tv+rlcgssm+alh+aa+aimtg+++v++iggvehmghvsm+hgvd++p ls  +akaagmmg
  NCBI__GCF_900105005.1:WP_090272541.1  80 TPIPHTAAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVIGGVEHMGHVSMMHGVDPNPALSLYAAKAAGMMG 152
                                           ************************************************************************* PP

                             TIGR02445 147 ltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaa 219
                                           ltaemlgk+hgi+reqqd+f++rsh++ah+at+eg+fk+eiip+eg+d++g+l+v+  de+irpett+e+laa
  NCBI__GCF_900105005.1:WP_090272541.1 153 LTAEMLGKMHGITREQQDQFGLRSHQLAHKATVEGNFKDEIIPMEGHDENGFLRVFTEDETIRPETTLESLAA 225
                                           ************************************************************************* PP

                             TIGR02445 220 lrpafdpkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkr 292
                                           lrpaf+pk+gtvtagtss+++dgas+m+vms+era+ lg++p+a+irsmavag+dpsimgygpvpat+kalkr
  NCBI__GCF_900105005.1:WP_090272541.1 226 LRPAFNPKGGTVTAGTSSQITDGASCMIVMSAERAKALGLEPLAVIRSMAVAGCDPSIMGYGPVPATRKALKR 298
                                           ************************************************************************* PP

                             TIGR02445 293 aglsisdidvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakf 365
                                           aglsi+did +elneafaaqalpvlkdl+lldk+d+kvnl+ggaialghp+gcsgaris+tlln+m++++++ 
  NCBI__GCF_900105005.1:WP_090272541.1 299 AGLSIDDIDHVELNEAFAAQALPVLKDLKLLDKMDQKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTI 371
                                           ************************************************************************* PP

                             TIGR02445 366 glatmciglgqgiatvferv 385
                                           g++tmciglgqgi+tvferv
  NCBI__GCF_900105005.1:WP_090272541.1 372 GMSTMCIGLGQGITTVFERV 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: 0.00u 0.04s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 3.32
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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