Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Acidovorax sp. GW101-3H11

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Ac3H11_178 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_178
          Length = 394

 Score =  608 bits (1567), Expect = e-178
 Identities = 305/394 (77%), Positives = 338/394 (85%)

Query: 1   MTREVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQT 60
           MTREVVVVS VRTAIGTFGGSLKD+AP +LGALVV+E+LARA V G DVGHVVFG+V+ T
Sbjct: 1   MTREVVVVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNT 60

Query: 61  EPRDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESM 120
           EP+DMYL RVAA+NGG     PA  VNRLCGSGLQAIVSAAQ I LGD DV IG GAE M
Sbjct: 61  EPKDMYLSRVAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVM 120

Query: 121 SRAPYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAA 180
           SRAP+ +   RWGARMGD  +VDMM+GALHDPFH IHMGVTAEN+A ++ ISR  QD+ A
Sbjct: 121 SRAPFASLNMRWGARMGDTKMVDMMIGALHDPFHTIHMGVTAENIAAKWGISREDQDKLA 180

Query: 181 LESHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKEN 240
           +ESH RA  A  AGYFKDQIVPV  K +KGDV + TDEH R  AT+DD  KL+PVFVKEN
Sbjct: 181 VESHNRAERATAAGYFKDQIVPVTLKSKKGDVQYATDEHFRPGATLDDFAKLKPVFVKEN 240

Query: 241 GTVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKI 300
           GTVTAGNASG+NDAAAAVV+M+ A A+ RG KPLARLV+Y HAGVDPK MGIGPVPAT++
Sbjct: 241 GTVTAGNASGINDAAAAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGPVPATQL 300

Query: 301 ALERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALIT 360
           AL++AGL V+DLDVIEANEAFAAQACAVTK LGLDPAKVNPNGSGISLGHPIGATGALIT
Sbjct: 301 ALKKAGLTVADLDVIEANEAFAAQACAVTKDLGLDPAKVNPNGSGISLGHPIGATGALIT 360

Query: 361 VKALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           VKA+HEL RVQGRYALVTMCIGGGQGIAAIFER+
Sbjct: 361 VKAIHELQRVQGRYALVTMCIGGGQGIAAIFERL 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: 569
Number of extensions: 7
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 Ac3H11_178 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.1776162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     9e-141  455.2   8.5     1e-140  455.0   8.5    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase 
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.0   8.5    1e-140    1e-140       1     385 []       7     392 ..       7     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 455.0 bits;  conditional E-value: 1e-140
                                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaR 62 
                                                     +v+avRt+ig++ggslk++ + dL+a v+ke l+ra ++ +++ +v++G+v+++  + + + R
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178   7 VVSAVRTAIGTFGGSLKDIAPTDLGALVVKESLARASVEGKDVGHVVFGHVVNTEPKdMYLSR 69 
                                                     79***************************************************99998***** PP

                                       TIGR01930  63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslr 125
                                                      aa++ g+ e +pa++vnr+C+SglqA+ +aaq+i+ G+adv + +G+E mSr+p+ + +   
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178  70 VAAINGGCAEGTPAFNVNRLCGSGLQAIVSAAQAIQLGDADVTIGAGAEVMSRAPFASLNM-- 130
                                                     *******************************************************998886.. PP

                                       TIGR01930 126 reslklgkakledqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAiee 186
                                                     r+++++g++k+ d+++  l  + + ++mg+tAen+a+k+gisRe+qD++a++Sh++a++A+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 131 RWGARMGDTKMVDMMIGALhdPFHTIHMGVTAENIAAKWGISREDQDKLAVESHNRAERATAA 193
                                                     8************9999989999**************************************** PP

                                       TIGR01930 187 gkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGA 247
                                                     g+fkd+ivpv++k k  ++++++De+ rp+ tl++ akLkp+f +++g tvtAgN+s++nD+A
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 194 GYFKDQIVPVTLKSKkgDVQYATDEHFRPGATLDDFAKLKPVFVKENG-TVTAGNASGINDAA 255
                                                     *************99999999***************************.6************* PP

                                       TIGR01930 248 aalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEin 310
                                                     aa++lm  ++ak+ g +plar+v++a+agvdp++mg+gpvpA++ aLkkagl++ d+d++E n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 256 AAVVLMDAAAAKARGAKPLARLVAYAHAGVDPKYMGIGPVPATQLALKKAGLTVADLDVIEAN 318
                                                     *************************************************************** PP

                                       TIGR01930 311 EAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlC 373
                                                     EAFAaq+ av+k+lg ld++kvN nG+ i+lGHP+Ga+Ga i+++ ++eL++ +++y+l+t+C
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 319 EAFAAQACAVTKDLG-LDPAKVNPNGSGISLGHPIGATGALITVKAIHELQRVQGRYALVTMC 380
                                                     ***************.99********************************************* PP

                                       TIGR01930 374 vggGqGaAvile 385
                                                     +ggGqG+A+i+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_178 381 IGGGQGIAAIFE 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: 00:00:00.00
# Mc/sec: 27.13
//
[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