Alignments for a candidate for fadA in Burkholderia vietnamiensis G4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Burkholderia vietnamiensis G4

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_011879792.1 3-ketoacyl-CoA thiolase

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_000016205.1:WP_011879792.1
          Length = 397

 Score =  592 bits (1527), Expect = e-174
 Identities = 302/392 (77%), Positives = 335/392 (85%)

Query: 3   REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62
           +EVVVVS VRTAIG FGGSLKD +P +LGA VV E LARA V GD VGHVVFG+V+ TEP
Sbjct: 6   KEVVVVSAVRTAIGDFGGSLKDFSPTDLGAKVVGEVLARANVPGDAVGHVVFGHVVNTEP 65

Query: 63  RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122
           +DMYL RVAAVNGGV  + PALTVNRLCGSGLQAIVSAAQTI+LGD +VAI GG+E+MSR
Sbjct: 66  KDMYLARVAAVNGGVAQHTPALTVNRLCGSGLQAIVSAAQTIMLGDAEVAIAGGSENMSR 125

Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182
           APY  P+AR+G RMGDA L+DMMLGALHDPF  IHMGVTAENVA++Y ISR  QD  ALE
Sbjct: 126 APYTVPSARFGQRMGDAKLIDMMLGALHDPFQTIHMGVTAENVARKYGISRDAQDALALE 185

Query: 183 SHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242
           SHRRA+ AI  G FKDQI+P+  + +KG+V FDTDEHVRHDA  DD TKL+PVFVKE GT
Sbjct: 186 SHRRAARAIAEGRFKDQILPISIRTKKGEVAFDTDEHVRHDAGPDDFTKLKPVFVKEEGT 245

Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302
           VTAGNASG+NDAAAAV+MM    A  +G KPLARLV+Y HAGVDP  MGIGPVPAT+  L
Sbjct: 246 VTAGNASGINDAAAAVLMMSADAARAQGAKPLARLVAYAHAGVDPAYMGIGPVPATQKVL 305

Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362
           +RAGL V+DLDVIEANEAFAAQACAVT+ LGLDPAKVNPNGSGISLGHPIGATGALITVK
Sbjct: 306 QRAGLTVADLDVIEANEAFAAQACAVTQELGLDPAKVNPNGSGISLGHPIGATGALITVK 365

Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           AL+EL R+ GRYALVTMCIGGGQGIAAIFE I
Sbjct: 366 ALYELKRIGGRYALVTMCIGGGQGIAAIFENI 397


Lambda     K      H
   0.318    0.134    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: 546
Number of extensions: 8
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: 394
Length of database: 397
Length adjustment: 31
Effective length of query: 363
Effective length of database: 366
Effective search space:   132858
Effective search space used:   132858
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_011879792.1 (3-ketoacyl-CoA thiolase)
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.17625.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-143  462.5   7.0   5.9e-143  462.4   7.0    1.0  1  lcl|NCBI__GCF_000016205.1:WP_011879792.1  3-ketoacyl-CoA thiolase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016205.1:WP_011879792.1  3-ketoacyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.4   7.0  5.9e-143  5.9e-143       1     385 []      10     395 ..      10     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 462.4 bits;  conditional E-value: 5.9e-143
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               +v+avRt+ig +ggslk++s+ dL+a+v+ e+l+ra++  +++ +v++G+v+++  + + +aR aa++ 
  lcl|NCBI__GCF_000016205.1:WP_011879792.1  10 VVSAVRTAIGDFGGSLKDFSPTDLGAKVVGEVLARANVPGDAVGHVVFGHVVNTEPKdMYLARVAAVNG 78 
                                               79***************************************************99999*********** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+ +++paltvnr+C+SglqA+ +aaq i+ G+a+v++aGG E+mSr+p+ ++++  r + ++g+akl 
  lcl|NCBI__GCF_000016205.1:WP_011879792.1  79 GVAQHTPALTVNRLCGSGLQAIVSAAQTIMLGDAEVAIAGGSENMSRAPYTVPSA--RFGQRMGDAKLI 145
                                               *****************************************************98..89********** PP

                                 TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               d++l  l  + + ++mg+tAen+a+kygisR+ qD++al+Sh++aa+Ai+eg+fkd+i+p+++++k  +
  lcl|NCBI__GCF_000016205.1:WP_011879792.1 146 DMMLGALhdPFQTIHMGVTAENVARKYGISRDAQDALALESHRRAARAIAEGRFKDQILPISIRTKkgE 214
                                               *99998899999****************************************************99999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               + +++De++r +   ++  kLkp+f +++g tvtAgN+s++nD+Aaa+l+ms ++a++ g +plar+v+
  lcl|NCBI__GCF_000016205.1:WP_011879792.1 215 VAFDTDEHVRHDAGPDDFTKLKPVFVKEEG-TVTAGNASGINDAAAAVLMMSADAARAQGAKPLARLVA 282
                                               ******************************.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gpvpA++k+L++agl++ d+d++E nEAFAaq+ av++elg ld++kvN nG+ i+
  lcl|NCBI__GCF_000016205.1:WP_011879792.1 283 YAHAGVDPAYMGIGPVPATQKVLQRAGLTVADLDVIEANEAFAAQACAVTQELG-LDPAKVNPNGSGIS 350
                                               ******************************************************.99************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+Ga+Ga i+++ l+eLk+ g++y+l+t+C+ggGqG+A+i+e
  lcl|NCBI__GCF_000016205.1:WP_011879792.1 351 LGHPIGATGALITVKALYELKRIGGRYALVTMCIGGGQGIAAIFE 395
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (397 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.42
//
[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