Alignments for a candidate for fadA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Marinobacter adhaerens HP15

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1551 HP15_1513 acetyl-CoA acetyltransferase

Query= reanno::Marino:GFF1551
         (374 letters)



>FitnessBrowser__Marino:GFF1551
          Length = 374

 Score =  743 bits (1917), Expect = 0.0
 Identities = 374/374 (100%), Positives = 374/374 (100%)

Query: 1   MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQIS 60
           MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQIS
Sbjct: 1   MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQIS 60

Query: 61  LLTRIPHESAAQTVNRLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVPMTEGFDHN 120
           LLTRIPHESAAQTVNRLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVPMTEGFDHN
Sbjct: 61  LLTRIPHESAAQTVNRLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVPMTEGFDHN 120

Query: 121 PAASKYSAKASNMMGLTAEMLAKMHGITREQQDEFGARSHRLAHEATLEGRFKNEIVPIE 180
           PAASKYSAKASNMMGLTAEMLAKMHGITREQQDEFGARSHRLAHEATLEGRFKNEIVPIE
Sbjct: 121 PAASKYSAKASNMMGLTAEMLAKMHGITREQQDEFGARSHRLAHEATLEGRFKNEIVPIE 180

Query: 181 GHDENGFKVLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTSSQLTDGAAAMVLMSA 240
           GHDENGFKVLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTSSQLTDGAAAMVLMSA
Sbjct: 181 GHDENGFKVLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTSSQLTDGAAAMVLMSA 240

Query: 241 ERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVEDIDFWELNEAFAG 300
           ERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVEDIDFWELNEAFAG
Sbjct: 241 ERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVEDIDFWELNEAFAG 300

Query: 301 QSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQAKGGKLGVSTMC 360
           QSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQAKGGKLGVSTMC
Sbjct: 301 QSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQAKGGKLGVSTMC 360

Query: 361 IGLGQGIATVWERL 374
           IGLGQGIATVWERL
Sbjct: 361 IGLGQGIATVWERL 374


Lambda     K      H
   0.316    0.132    0.381 

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: 632
Number of extensions: 11
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: 374
Length of database: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate GFF1551 HP15_1513 (acetyl-CoA acetyltransferase)
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.14695.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.1e-210  682.5   3.0     9e-210  682.3   3.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1551  HP15_1513 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1551  HP15_1513 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.3   3.0    9e-210    9e-210      12     384 ..       1     373 [.       1     374 [] 1.00

  Alignments for each domain:
  == domain 1  score: 682.3 bits;  conditional E-value: 9e-210
                           TIGR02445  12 mgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevphevaavtvn 86 
                                         mgr+k g frn+rae lsa l+++l++rnpk+++ eved++wgcv+qt eqgfn+ar+ +ll+++phe+aa+tvn
  lcl|FitnessBrowser__Marino:GFF1551   1 MGRAKNGCFRNVRAETLSANLIEALFERNPKLDPKEVEDVIWGCVNQTKEQGFNVARQISLLTRIPHESAAQTVN 75 
                                         9************************************************************************** PP

                           TIGR02445  87 rlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgklhgisre 161
                                         rlcgs+m+a+h+aa+aimtg+++v+++ggvehmghv+m+ g d +p  sk  aka+ mmgltaeml+k+hgi+re
  lcl|FitnessBrowser__Marino:GFF1551  76 RLCGSAMSAIHTAAQAIMTGNGDVFFVGGVEHMGHVPMTEGFDHNPAASKYSAKASNMMGLTAEMLAKMHGITRE 150
                                         *************************************************************************** PP

                           TIGR02445 162 qqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvtagts 236
                                         qqd+f+arsh +ah+atleg+fknei+p+eg+d++g+   ++ de+irpett e+l++l+pafdpkngtvtagts
  lcl|FitnessBrowser__Marino:GFF1551 151 QQDEFGARSHRLAHEATLEGRFKNEIVPIEGHDENGFKVLIEEDETIRPETTAESLSQLKPAFDPKNGTVTAGTS 225
                                         *************************************************************************** PP

                           TIGR02445 237 salsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaa 311
                                         s+l+dga+am++ms+era+ lg+kp a+irsmavag+dp+imgygpvpatkkalkragl ++did+ elneafa 
  lcl|FitnessBrowser__Marino:GFF1551 226 SQLTDGAAAMVLMSAERAEALGLKPIAKIRSMAVAGCDPAIMGYGPVPATKKALKRAGLKVEDIDFWELNEAFAG 300
                                         *************************************************************************** PP

                           TIGR02445 312 qalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvfer 384
                                         q+lpvlkdl+ll +++ekvnlnggaialghplgcsgaristtlln+m++k++k g++tmciglgqgiatv+er
  lcl|FitnessBrowser__Marino:GFF1551 301 QSLPVLKDLKLLGVMEEKVNLNGGAIALGHPLGCSGARISTTLLNVMQAKGGKLGVSTMCIGLGQGIATVWER 373
                                         ************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (374 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: 11.80
//
[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