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-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF5 HP15_5 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20831
         (393 letters)



>FitnessBrowser__Marino:GFF5
          Length = 416

 Score =  555 bits (1430), Expect = e-163
 Identities = 276/392 (70%), Positives = 332/392 (84%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQ VVIVAATRTA+GSFQG+L+   A +LGA VIR LL  T L+P  VD V++GQVL+AG
Sbjct: 24  MQGVVIVAATRTAIGSFQGALSDTSAVDLGATVIRSLLSSTSLNPELVDNVVMGQVLSAG 83

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
            GQNPARQ++I AGLP   P++TLNK+CGSGL++++L AQAI+C +A+V++AGGME+MS 
Sbjct: 84  CGQNPARQSAIKAGLPFTTPAMTLNKLCGSGLESVNLAAQAIQCKEADVVVAGGMESMSQ 143

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           +PY+L  AR+GLRMGH+++ DSM+TDGL DAFN YHMG+TAENL +KY I+RE QDAFA 
Sbjct: 144 SPYLLGKARSGLRMGHSQIEDSMLTDGLIDAFNHYHMGVTAENLAEKYQITREQQDAFAV 203

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
            SQ K + A+ +GRF DEITP+ IPQRKG P+ F  DEQPR   ++  L+KL+PAF K G
Sbjct: 204 ISQLKGSEAVASGRFKDEITPVEIPQRKGSPLKFDTDEQPRGDVSSAGLSKLRPAFAKGG 263

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAVLLMSA+KA  LGL VLARI SYA+A VDP+IMGIGPV ATR+C
Sbjct: 264 SVTAGNASSLNDGAAAVLLMSAEKATELGLTVLARIKSYASAAVDPSIMGIGPVPATRKC 323

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           L K  WS+GDLDLIEANEAFAAQ L+VGKEL W++EKVNVNGGAIA+GHPIGASGCR+LV
Sbjct: 324 LAKVNWSVGDLDLIEANEAFAAQCLSVGKELGWESEKVNVNGGAIALGHPIGASGCRILV 383

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           TLL+EM +RD+KKGLATLCIGGGQGVA+ALER
Sbjct: 384 TLLYEMTRRDSKKGLATLCIGGGQGVAMALER 415


Lambda     K      H
   0.317    0.133    0.378 

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: 465
Number of extensions: 7
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: 393
Length of database: 416
Length adjustment: 31
Effective length of query: 362
Effective length of database: 385
Effective search space:   139370
Effective search space used:   139370
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 GFF5 HP15_5 (acetyl-CoA acetyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.30486.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.5e-153  496.5   4.1   2.9e-153  496.3   4.1    1.0  1  lcl|FitnessBrowser__Marino:GFF5  HP15_5 acetyl-CoA acetyltransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF5  HP15_5 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.3   4.1  2.9e-153  2.9e-153       1     385 []      29     414 ..      29     414 .. 0.99

  Alignments for each domain:
  == domain 1  score: 496.3 bits;  conditional E-value: 2.9e-153
                        TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpalt 78 
                                      iv+a+Rt+ig+++g+l+++sa+dL+a+vi++ll  + l+pe +d+v++G+vl+ag+++n+aR+ a++aglp ++pa+t
  lcl|FitnessBrowser__Marino:GFF5  29 IVAATRTAIGSFQGALSDTSAVDLGATVIRSLLSSTSLNPELVDNVVMGQVLSAGCGQNPARQSAIKAGLPFTTPAMT 106
                                      8***************************************************************************** PP

                        TIGR01930  79 vnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmge 153
                                      +n++C+Sgl++v+laaq+i++ eadvvvaGG+EsmS++p+ll ++  r++l++g+++ ed++l d+   + ++++mg+
  lcl|FitnessBrowser__Marino:GFF5 107 LNKLCGSGLESVNLAAQAIQCKEADVVVAGGMESMSQSPYLLGKA--RSGLRMGHSQIEDSMLTDGlidAFNHYHMGV 182
                                      *******************************************98..89********************99******* PP

                        TIGR01930 154 tAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafk 228
                                      tAenla+ky+i+Re+qD++a+ S+ k ++A+++g+fkdei+pve++++   +  +++De++r +++ + L+kL+paf+
  lcl|FitnessBrowser__Marino:GFF5 183 TAENLAEKYQITREQQDAFAVISQLKGSEAVASGRFKDEITPVEIPQRkgsPLKFDTDEQPRGDVSSAGLSKLRPAFA 260
                                      **********************************************99999999***********************9 PP

                        TIGR01930 229 ekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidl 306
                                      +  gs vtAgN+s+lnDGAaa+llms e+a elglt+lari s+a a+vdp++mg+gpvpA++k+L+k ++s+ d+dl
  lcl|FitnessBrowser__Marino:GFF5 261 K-GGS-VTAGNASSLNDGAAAVLLMSAEKATELGLTVLARIKSYASAAVDPSIMGIGPVPATRKCLAKVNWSVGDLDL 336
                                      6.797.************************************************************************ PP

                        TIGR01930 307 vEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384
                                      +E nEAFAaq+l v kelg  + ekvNvnGGAiAlGHP+GasG+ri++tll+e+ +r+ k GlatlC+ggGqG+A+ l
  lcl|FitnessBrowser__Marino:GFF5 337 IEANEAFAAQCLSVGKELG-WESEKVNVNGGAIALGHPIGASGCRILVTLLYEMTRRDSKKGLATLCIGGGQGVAMAL 413
                                      *******************.88******************************************************98 PP

                        TIGR01930 385 e 385
                                      e
  lcl|FitnessBrowser__Marino:GFF5 414 E 414
                                      7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (416 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.53
//
[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