Alignments for a candidate for fadA in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfobulbus mediterraneus DSM 13871

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_028584037.1 G494_RS0107490 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_000429965.1:WP_028584037.1
          Length = 395

 Score =  337 bits (863), Expect = 5e-97
 Identities = 193/391 (49%), Positives = 246/391 (62%), Gaps = 2/391 (0%)

Query: 2   QDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAGS 61
           QD+ IV A RT  GSF GSLA +PAPEL AAVI  LL ++GL    VDEVI+GQVL  G 
Sbjct: 6   QDIFIVEALRTPFGSFLGSLAEVPAPELAAAVIPELLGRSGLGGTLVDEVIIGQVLQGGC 65

Query: 62  GQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLA 121
           GQ PARQA  LAGLP  V +LT+NKVCGSGL A+ L A  IR G+A ++IAGGMENMSLA
Sbjct: 66  GQAPARQAMRLAGLPDQVHALTINKVCGSGLVAMMLAANTIRAGEASLVIAGGMENMSLA 125

Query: 122 PYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAAA 181
           P+VL  AR G R GH +++D ++ DGL DA +   MG   E  +  + ISR  QDA+A  
Sbjct: 126 PHVLARARKGQRFGHGEILDLLLLDGLEDAASGRSMGEITEEWLRGHRISRREQDAYALR 185

Query: 182 SQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDGS 241
           S   A  A++   F  E+  +     KG  V  A DE+P      E  A L   F++ GS
Sbjct: 186 SYGLAQQALKEQIFAPELVEVRFNSGKGWLVV-AEDEEPWR-CDPEKFASLPTVFREQGS 243

Query: 242 VTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRCL 301
           +TAGNAS++NDGAA  L+      +  GL   AR+ + A A   P +     V A R  +
Sbjct: 244 ITAGNASTINDGAALALVAGGAAVERYGLRPRARLVAAATASTGPQLFPEADVEAIRLAV 303

Query: 302 DKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLVT 361
            +AG SL D+DL E NEAFAA +L   + L  D  +VNVNGGA+AIGHPIGASG R++ T
Sbjct: 304 ARAGLSLEDIDLFEINEAFAAVALLTMELLAIDPARVNVNGGAVAIGHPIGASGGRLVAT 363

Query: 362 LLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           L+ E+ +++ + G+ TLCIGGG+ VA   ER
Sbjct: 364 LIRELERQEKRYGVVTLCIGGGEAVAAVFER 394


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: 382
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: 395
Length adjustment: 31
Effective length of query: 362
Effective length of database: 364
Effective search space:   131768
Effective search space used:   131768
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_028584037.1 G494_RS0107490 (acetyl-CoA C-acyltransferase)
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.4470.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.7e-125  402.6   0.3   9.8e-125  402.4   0.3    1.0  1  lcl|NCBI__GCF_000429965.1:WP_028584037.1  G494_RS0107490 acetyl-CoA C-acyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429965.1:WP_028584037.1  G494_RS0107490 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.4   0.3  9.8e-125  9.8e-125       1     385 []      10     393 ..      10     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.4 bits;  conditional E-value: 9.8e-125
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a+Rtp+g++ gsl+e++a +L+aavi ell r+gl    +devi+G+vlq g+++++aR+a+  ag
  lcl|NCBI__GCF_000429965.1:WP_028584037.1  10 IVEALRTPFGSFLGSLAEVPAPELAAAVIPELLGRSGLGGTLVDEVIIGQVLQGGCGQAPARQAMRLAG 78 
                                               8******************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp++v alt+n+vC+Sgl A++laa+ i+aGea++v+aGG+E+mS +p++l ++  r++ ++g+ +  d
  lcl|NCBI__GCF_000429965.1:WP_028584037.1  79 LPDQVHALTINKVCGSGLVAMMLAANTIRAGEASLVIAGGMENMSLAPHVLARA--RKGQRFGHGEILD 145
                                               ***************************************************998..8999********* PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                                ll d+   + ++ smge +e+  + ++isR+eqD+yalrS+  a++A +e  f+ e+v v+++     
  lcl|NCBI__GCF_000429965.1:WP_028584037.1 146 LLLLDGledAASGRSMGEITEEWLRGHRISRREQDAYALRSYGLAQQALKEQIFAPELVEVRFNSGkgW 214
                                               9999999998899**************************************************987866 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                                vv++De++  +   ek a+L+++f+e +gs +tAgN+s +nDGAa++l++  ++++++gl+p ar+v+
  lcl|NCBI__GCF_000429965.1:WP_028584037.1 215 LVVAEDEEPW-RCDPEKFASLPTVFRE-QGS-ITAGNASTINDGAALALVAGGAAVERYGLRPRARLVA 280
                                               6667777765.89************96.8*7.************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               aa+a+  p+ ++ + v+Ai+ a+++agls++didl+EinEAFAa++l+ ++ l+ +d+++vNvnGGA+A
  lcl|NCBI__GCF_000429965.1:WP_028584037.1 281 AATASTGPQLFPEADVEAIRLAVARAGLSLEDIDLFEINEAFAAVALLTMELLA-IDPARVNVNGGAVA 348
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasG+r+v+tl++eL++++k+yG++tlC+ggG ++A+++e
  lcl|NCBI__GCF_000429965.1:WP_028584037.1 349 IGHPIGASGGRLVATLIRELERQEKRYGVVTLCIGGGEAVAAVFE 393
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (395 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 0.00s 00:00:00.01 Elapsed: 00:00:00.04
# Mc/sec: 3.21
//
[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