Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Sphingomonas koreensis DSMZ 15582

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate Ga0059261_0982 Ga0059261_0982 acetyl-CoA acetyltransferases

Query= metacyc::MONOMER-13585
         (391 letters)



>FitnessBrowser__Korea:Ga0059261_0982
          Length = 390

 Score =  556 bits (1432), Expect = e-163
 Identities = 283/390 (72%), Positives = 326/390 (83%)

Query: 1   MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60
           MT VVI +A RT VGSF GAFASTPAH+LG   IEA + +A +   +VSE ILGQVLTA 
Sbjct: 1   MTEVVITAAKRTPVGSFLGAFASTPAHELGRIAIEAALEQAEVKGEEVSEVILGQVLTAA 60

Query: 61  QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120
           QGQNPARQA + AG+P+E  AW +NQVCGSGLRAVALAAQ VQ GDA+IVVAGGQE+MSL
Sbjct: 61  QGQNPARQASMAAGVPKEVPAWGLNQVCGSGLRAVALAAQAVQTGDATIVVAGGQESMSL 120

Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180
           + H   LRAG KMGD+  ID+MIKDGL D FNGYHMG TAEN+A ++Q++R  QDEFAV 
Sbjct: 121 AAHAQSLRAGAKMGDVGLIDTMIKDGLTDVFNGYHMGITAENLAEQYQVTRGEQDEFAVR 180

Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240
           SQN AEAA+  GRF DEI P  IK RKGD  VD DEYIR GATLD++A LRPAF KDGTV
Sbjct: 181 SQNLAEAARSEGRFKDEIAPVTIKGRKGDTVVDQDEYIRAGATLDSVAGLRPAFKKDGTV 240

Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300
           TA NASG+NDGAAA++VMS EEA+KRG + LA I S+ATAG+DPSIMG+GP+ AS+KALE
Sbjct: 241 TAGNASGLNDGAAALVVMSREEADKRGATVLATIKSWATAGVDPSIMGIGPVPASKKALE 300

Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360
           KAGW V DLDL+EANEAFAAQA +V K++G+DP+ VNVNGGAIAIGHPIGASGARVL TL
Sbjct: 301 KAGWTVADLDLIEANEAFAAQALSVGKELGFDPNKVNVNGGAIAIGHPIGASGARVLTTL 360

Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390
           L+EMQRR+AKKGLATLCIGGGMG+AMC+ER
Sbjct: 361 LYEMQRRDAKKGLATLCIGGGMGIAMCVER 390


Lambda     K      H
   0.317    0.130    0.375 

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: 477
Number of extensions: 12
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: 391
Length of database: 390
Length adjustment: 31
Effective length of query: 360
Effective length of database: 359
Effective search space:   129240
Effective search space used:   129240
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 Ga0059261_0982 Ga0059261_0982 (acetyl-CoA acetyltransferases)
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.28448.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-146  472.4  11.9     6e-146  472.2  11.9    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0982  Ga0059261_0982 acetyl-CoA acetyl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0982  Ga0059261_0982 acetyl-CoA acetyltransferases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.2  11.9    6e-146    6e-146       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 472.2 bits;  conditional E-value: 6e-146
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a Rtp+g++ g++++++a++L++ +i+++le+a+++ e++ evilG+vl+a++++n+aR+a +aag
  lcl|FitnessBrowser__Korea:Ga0059261_0982   6 ITAAKRTPVGSFLGAFASTPAHELGRIAIEAALEQAEVKGEEVSEVILGQVLTAAQGQNPARQASMAAG 74 
                                               7799***************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p++vpa+ +n+vC+Sgl+Avalaaq++++G+a++vvaGG EsmS + +  +    r+++k+g+  l d
  lcl|FitnessBrowser__Korea:Ga0059261_0982  75 VPKEVPAWGLNQVCGSGLRAVALAAQAVQTGDATIVVAGGQESMSLAAHAQSL---RAGAKMGDVGLID 140
                                               ***********************************************865544...799********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               +++kd+   v ++++mg+tAenla++y+++R eqDe+a+rS++ a++A +eg+fkdei pv++kg+  +
  lcl|FitnessBrowser__Korea:Ga0059261_0982 141 TMIKDGltdVFNGYHMGITAENLAEQYQVTRGEQDEFAVRSQNLAEAARSEGRFKDEIAPVTIKGRkgD 209
                                               *********99********************************************************99 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               +vv++De ir++ tl+++a+L+pafk+ +g tvtAgN+s+lnDGAaal++ms+e a++ g t+la+i s
  lcl|FitnessBrowser__Korea:Ga0059261_0982 210 TVVDQDEYIRAGATLDSVAGLRPAFKK-DG-TVTAGNASGLNDGAAALVVMSREEADKRGATVLATIKS 276
                                               9************************95.9*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gpvpA++kaL+kag+++ d+dl+E nEAFAaq+l v kelg  d++kvNvnGGAiA
  lcl|FitnessBrowser__Korea:Ga0059261_0982 277 WATAGVDPSIMGIGPVPASKKALEKAGWTVADLDLIEANEAFAAQALSVGKELG-FDPNKVNVNGGAIA 344
                                               ******************************************************.78************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasGar+++tll+e+++r++k GlatlC+ggG+G+A+ +e
  lcl|FitnessBrowser__Korea:Ga0059261_0982 345 IGHPIGASGARVLTTLLYEMQRRDAKKGLATLCIGGGMGIAMCVE 389
                                               ******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (390 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.16
//
[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