Alignments for a candidate for fadA in Desulfarculus baarsii DSM 2075

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Desulfarculus baarsii DSM 2075

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_013259249.1 DEBA_RS12235 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-13468
         (393 letters)



>NCBI__GCF_000143965.1:WP_013259249.1
          Length = 392

 Score =  384 bits (987), Expect = e-111
 Identities = 204/393 (51%), Positives = 277/393 (70%), Gaps = 7/393 (1%)

Query: 1   MREVVIVSAVRTAIGSFGGTLKDVSAVDLGAIVIKEAVKRAGIKPEQVDEVIFGNVIQAG 60
           M +VVI+ A RTA+G FGG+LK V+   LGA+VIKEA+ RAG+ P+QV+EV+F    + G
Sbjct: 1   MSDVVILGAARTAVGRFGGSLKAVTDRQLGALVIKEAMARAGVSPDQVEEVVFAQQYRTG 60

Query: 61  V-GQSLARQSAVYAGLPVEVPAFTVNKLCGSGLRTVSLAASLISNGDADTIVVGGSENMS 119
           V   ++AR  +V AG+P+ VP F+V K CG  L++V LAA  I  GDA  +V GG E+M+
Sbjct: 61  VLPPNMARPISVDAGIPIPVPNFSVAKACGGSLKSVFLAAQAIKAGDARVLVAGGLEHMT 120

Query: 120 ASPYLIPKARFGYRMGEAKIYDAMLHDGLIDSFNNYHMGITAENIAEKWGITREDQDKFA 179
            + YL+P  R+G R+G  ++ D ++   L D  +   MG TAEN+AEK+ I+REDQD FA
Sbjct: 121 NAAYLLPTMRWGQRLGHGQVMDQLV---LFDPISGNTMGETAENVAEKYAISREDQDAFA 177

Query: 180 LASQQKAEAAIKAGKFKDEIVPVTVKMKKKEV-VFDTDEDPRFGTTIETLAKLKPAFKRD 238
           LASQQKA AA  AG+F ++IV V +  KK E  +F  DE PR  TT+E LAKLKP F++ 
Sbjct: 178 LASQQKAAAAQAAGRFDEQIVAVPIPQKKGEPKLFARDEHPRPETTLEELAKLKPVFRKG 237

Query: 239 GTGTVTAGNSSGINDSSAALILMSADKAKELGVKPMAKYVDFASAGLDPAIMGYGPYYAT 298
           G+  VTAGNSSG+ND +AA ++     A E G+KP+A  V +AS G++P++MG GP  AT
Sbjct: 238 GS--VTAGNSSGMNDGAAATVVAQRQWAAERGLKPLASVVGYASVGVEPSLMGIGPVDAT 295

Query: 299 KKVLAKTNLTIKDFDLIEANEAFAAQSIAVARDLEFDMSKVNVNGGAIALGHPVGCSGAR 358
           K VLAKT L++ D  L+E NEAFA+QS+A  R+L  DM +VNVNGGAIALGHP+  +G  
Sbjct: 296 KAVLAKTGLSVSDIGLVELNEAFASQSLACIRELGLDMERVNVNGGAIALGHPISGTGGV 355

Query: 359 ILVTLLHEMQKRDAKKGLATLCIGGGQGTAVVV 391
           IL  L++EM++   + GLAT+C+GGGQG A++V
Sbjct: 356 ILTKLVYEMKRAGVELGLATMCLGGGQGVALIV 388


Lambda     K      H
   0.316    0.133    0.369 

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: 434
Number of extensions: 13
Number of successful extensions: 5
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: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 WP_013259249.1 DEBA_RS12235 (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.13413.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-136  440.3   3.1   3.4e-136  440.1   3.1    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013259249.1  DEBA_RS12235 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013259249.1  DEBA_RS12235 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.1   3.1  3.4e-136  3.4e-136       1     384 [.       6     388 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 440.1 bits;  conditional E-value: 3.4e-136
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               i++a+Rt++g++ggslk ++  +L+a vike+++rag++p++++ev++++  ++g    n+aR + + a
  lcl|NCBI__GCF_000143965.1:WP_013259249.1   6 ILGAARTAVGRFGGSLKAVTDRQLGALVIKEAMARAGVSPDQVEEVVFAQQYRTGVLpPNMARPISVDA 74 
                                               789****************************************************************** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+p  vp ++v ++C+ +l++v laaq+ikaG+a+v+vaGG+E+m+++ +ll+    r++ +lg+ +++
  lcl|NCBI__GCF_000143965.1:WP_013259249.1  75 GIPIPVPNFSVAKACGGSLKSVFLAAQAIKAGDARVLVAGGLEHMTNAAYLLPTM--RWGQRLGHGQVM 141
                                               *****************************************************96..899999999999 PP

                                 TIGR01930 138 dqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kk 203
                                               dql+   + ++ +mgetAen+a+ky+isRe+qD++al+S+qkaa+A+++g+f+++iv v +++k   +k
  lcl|NCBI__GCF_000143965.1:WP_013259249.1 142 DQLVLFDPISGNTMGETAENVAEKYAISREDQDAFALASQQKAAAAQAAGRFDEQIVAVPIPQKkgePK 210
                                               9666655899***************************************************999999** PP

                                 TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsa 272
                                                +++De++rp+ttle+LakLkp+f++  gs vtAgNss++nDGAaa++++++++a+e gl+pla +v++
  lcl|NCBI__GCF_000143965.1:WP_013259249.1 211 LFARDEHPRPETTLEELAKLKPVFRK-GGS-VTAGNSSGMNDGAAATVVAQRQWAAERGLKPLASVVGY 277
                                               ************************95.797.************************************** PP

                                 TIGR01930 273 avagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAl 341
                                               a +gv+p+ mg+gpv A++++L+k+gls+sdi lvE+nEAFA+q la+++elg ld e+vNvnGGAiAl
  lcl|NCBI__GCF_000143965.1:WP_013259249.1 278 ASVGVEPSLMGIGPVDATKAVLAKTGLSVSDIGLVELNEAFASQSLACIRELG-LDMERVNVNGGAIAL 345
                                               *****************************************************.89************* PP

                                 TIGR01930 342 GHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384
                                               GHP+  +G+ i+++l++e+k+ g+++Glat+C ggGqG+A+i+
  lcl|NCBI__GCF_000143965.1:WP_013259249.1 346 GHPISGTGGVILTKLVYEMKRAGVELGLATMCLGGGQGVALIV 388
                                               *****************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 8.14
//
[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