Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Cupriavidus basilensis 4G11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate RR42_RS25455 RR42_RS25455 acetyl-CoA acetyltransferase

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Cup4G11:RR42_RS25455
          Length = 394

 Score =  708 bits (1827), Expect = 0.0
 Identities = 358/394 (90%), Positives = 379/394 (96%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVSGVRTAIGTFGGSLKD++P ++GA+VVREALARAQVSGDDVGHVVFGNVIQT
Sbjct: 1   MTREVVVVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALARAQVSGDDVGHVVFGNVIQT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EPRDMYLGRVAAV GGVTI+APALTVNRLCGSGLQAIVSAAQTILLGD DVAIGGGAESM
Sbjct: 61  EPRDMYLGRVAAVEGGVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAESM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAPYLA +ARWGARMGDA ++DMMLGALHDPFH IHMGVTAENVAKEYDISR QQDEAA
Sbjct: 121 SRAPYLAQSARWGARMGDAKMLDMMLGALHDPFHGIHMGVTAENVAKEYDISRVQQDEAA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           LESHRRASAAI+AG+FKDQI+PV  KGRKGDVTFDTDEHVRHDA ++DMTKL+PVFVKEN
Sbjct: 181 LESHRRASAAIRAGHFKDQILPVTLKGRKGDVTFDTDEHVRHDAVMEDMTKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASGLNDAAAAVV+MERAEAE+RGLKP+ARLVSY HAGVDPK MGIGPVPATK 
Sbjct: 241 GTVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVSYAHAGVDPKTMGIGPVPATKK 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           ALERAGL V+DLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALERAGLTVADLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKAL+EL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKALYELQRVQGRYALVTMCIGGGQGIAAIFERV 394


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: 635
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: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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 RR42_RS25455 RR42_RS25455 (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.24039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-144  466.8   7.9   3.1e-144  466.6   7.9    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS25455  RR42_RS25455 acetyl-CoA acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS25455  RR42_RS25455 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.6   7.9  3.1e-144  3.1e-144       1     385 []       7     392 ..       7     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 466.6 bits;  conditional E-value: 3.1e-144
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 
                                               +v++vRt+ig++ggslk+ls+ +++a+v++e+l+ra+++ +++ +v++Gnv+q+    + ++R aa++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455   7 VVSGVRTAIGTFGGSLKDLSPTQMGAMVVREALARAQVSGDDVGHVVFGNVIQTEPRdMYLGRVAAVEG 75 
                                               79***************************************************99999*********** PP

                                 TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137
                                               g+  + paltvnr+C+SglqA+ +aaq i  G+adv++ GG+EsmSr+p+l +++  r+++++g+ak+ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455  76 GVTIDAPALTVNRLCGSGLQAIVSAAQTILLGDADVAIGGGAESMSRAPYLAQSA--RWGARMGDAKML 142
                                               **************************************************99997..9*********** PP

                                 TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               d++l  l  + ++++mg+tAen+ak+y+isR +qDe al+Sh++a++Ai++g+fkd+i+pv++kg+  +
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455 143 DMMLGALhdPFHGIHMGVTAENVAKEYDISRVQQDEAALESHRRASAAIRAGHFKDQILPVTLKGRkgD 211
                                               *9999889999********************************************************** PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               +++++De++r +  +e++ kLkp+f +++g tvtAgN+s+lnD+Aaa++lm+++ a++ gl+p+ar+vs
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455 212 VTFDTDEHVRHDAVMEDMTKLKPVFVKENG-TVTAGNASGLNDAAAAVVLMERAEAEKRGLKPMARLVS 279
                                               ******************************.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gpvpA++kaL++agl++ d+d++E nEAFAaq+ av+k+lg ld++kvN nG+ i+
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455 280 YAHAGVDPKTMGIGPVPATKKALERAGLTVADLDVIEANEAFAAQACAVTKALG-LDPAKVNPNGSGIS 347
                                               ******************************************************.99************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+Ga+Ga i+++ l+eL++ +++y+l+t+C+ggGqG+A+i+e
  lcl|FitnessBrowser__Cup4G11:RR42_RS25455 348 LGHPIGATGALITVKALYELQRVQGRYALVTMCIGGGQGIAAIFE 392
                                               *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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: 12.18
//
[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