Alignments for a candidate for fadA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Halomonas desiderata SP1

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_086510452.1 BZY95_RS13540 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_002151265.1:WP_086510452.1
          Length = 391

 Score =  580 bits (1496), Expect = e-170
 Identities = 294/392 (75%), Positives = 333/392 (84%), Gaps = 1/392 (0%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQDVVIVAA RTA+G+F GSLA I A +LGA VI+ +L  TG+   Q+DEV+LGQVLTAG
Sbjct: 1   MQDVVIVAARRTAIGAFGGSLAGIAASDLGALVIKDILASTGVAADQIDEVLLGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
            GQNPARQA+I AGLP AVP++T+NKVCGSGLKALHL  QAIRCGDAE+IIAGG ENMS 
Sbjct: 61  VGQNPARQAAIKAGLPAAVPAMTINKVCGSGLKALHLATQAIRCGDAELIIAGGQENMSA 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           +P+VLP +R G RMG  K ID+M+ DGLWDAFNDYHMGITAENL +KYGI+RE  D FAA
Sbjct: 121 SPHVLPNSRNGQRMGDWKAIDTMVHDGLWDAFNDYHMGITAENLAEKYGITREEMDEFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           ASQQKA AAI  GRF  +I P+ IPQRKGDPV F  DE PR   +A+ LA ++PAFKKDG
Sbjct: 181 ASQQKAAAAIREGRFKGQIVPVEIPQRKGDPVVFDTDENPRE-VSADKLAGMRPAFKKDG 239

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           ++TAGNASS+NDGAAAV++ SA KAK LGL  LARIA+Y+NAGVDPAIMGIGP  ATRRC
Sbjct: 240 TITAGNASSINDGAAAVMICSAAKAKELGLEPLARIAAYSNAGVDPAIMGIGPAPATRRC 299

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           L+KAGWSL DLDLIEANEAFAAQ+L+V KEL WD  KVNVNGGAIA+GHPIGASGCRVLV
Sbjct: 300 LEKAGWSLDDLDLIEANEAFAAQALSVNKELGWDTSKVNVNGGAIALGHPIGASGCRVLV 359

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           +LLHEMI RDAKKGLATLCIGGGQGVALA+ER
Sbjct: 360 SLLHEMIARDAKKGLATLCIGGGQGVALAIER 391


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: 508
Number of extensions: 12
Number of successful extensions: 2
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: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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_086510452.1 BZY95_RS13540 (acetyl-CoA C-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.20257.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-150  486.3   7.4   3.5e-150  486.1   7.4    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510452.1  BZY95_RS13540 acetyl-CoA C-acety


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510452.1  BZY95_RS13540 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.1   7.4  3.5e-150  3.5e-150       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 486.1 bits;  conditional E-value: 3.5e-150
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a Rt+ig++ggsl+ + a+dL+a vik +l+ +g+ +++idev lG+vl+ag ++n+aR+aa++ag
  lcl|NCBI__GCF_002151265.1:WP_086510452.1   6 IVAARRTAIGAFGGSLAGIAASDLGALVIKDILASTGVAADQIDEVLLGQVLTAGVGQNPARQAAIKAG 74 
                                               89******************************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp  vpa+t+n+vC+Sgl+A++la q+i++G+a++++aGG E+mS +p++l++s  r++ ++g+ k  d
  lcl|NCBI__GCF_002151265.1:WP_086510452.1  75 LPAAVPAMTINKVCGSGLKALHLATQAIRCGDAELIIAGGQENMSASPHVLPNS--RNGQRMGDWKAID 141
                                               *****************************************************8..89*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201
                                               ++++d+   + ++++mg+tAenla+kygi+Ree+De+a++S+qkaa+Ai+eg+fk +ivpve++++   
  lcl|NCBI__GCF_002151265.1:WP_086510452.1 142 TMVHDGlwdAFNDYHMGITAENLAEKYGITREEMDEFAAASQQKAAAAIREGRFKGQIVPVEIPQRkgd 210
                                               *********99*****************************************************999*9 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               ++v+++De++r +++++kLa+++pafk+ +g t+tAgN+s++nDGAaa+++ s ++akelgl+plari 
  lcl|NCBI__GCF_002151265.1:WP_086510452.1 211 PVVFDTDENPR-EVSADKLAGMRPAFKK-DG-TITAGNASSINDGAAAVMICSAAKAKELGLEPLARIA 276
                                               ***********.89************95.9*.6************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               ++++agvdp++mg+gp+pA++++L+kag+s++d+dl+E nEAFAaq+l v+kelg  d++kvNvnGGAi
  lcl|NCBI__GCF_002151265.1:WP_086510452.1 277 AYSNAGVDPAIMGIGPAPATRRCLEKAGWSLDDLDLIEANEAFAAQALSVNKELG-WDTSKVNVNGGAI 344
                                               *******************************************************.88*********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasG+r++++ll+e+  r++k GlatlC+ggGqG+A+ +e
  lcl|NCBI__GCF_002151265.1:WP_086510452.1 345 ALGHPIGASGCRVLVSLLHEMIARDAKKGLATLCIGGGQGVALAIE 390
                                               ******************************************9886 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.34
//
[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 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