GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Azospirillum brasilense Sp245

Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase

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



>lcl|FitnessBrowser__azobra:AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA
           acetyltransferase
          Length = 391

 Score =  544 bits (1402), Expect = e-159
 Identities = 269/390 (68%), Positives = 321/390 (82%)

Query: 1   MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60
           MT VVI SAART +GSFNGA +S PAH LG   I   ++RA  D A+V+E ILGQ+LTAG
Sbjct: 1   MTEVVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAG 60

Query: 61  QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120
           QGQNPARQA + AG+P  + A+ INQ+CGSGLR+VAL  Q ++ GDA ++V GGQE+MS 
Sbjct: 61  QGQNPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQ 120

Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180
           +PHV HLR G KMG    +D+M+KDGL DAF GYHMG TAENVA KWQ++R+ QD FA A
Sbjct: 121 APHVMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFAAA 180

Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240
           SQ KAEAAQK+GRF DEI+P  IK RKGD+ V  DEY +HG T +++AKLRPAF K+GTV
Sbjct: 181 SQQKAEAAQKSGRFKDEIIPVTIKGRKGDIIVADDEYPKHGTTAESLAKLRPAFSKEGTV 240

Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300
           TA NASGINDGAAA+++M+AE A +RGL+PLARI S+ATAG+DP+IMG GPI ASR ALE
Sbjct: 241 TAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPIPASRLALE 300

Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360
           KAGWK  DLDL+EANEAFAAQA AVNKD+GWD S VNVNGGAIA+GHP+GASGARVL TL
Sbjct: 301 KAGWKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHPVGASGARVLTTL 360

Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390
           L+EMQ+R+AKKGLATLCIGGGMG+A+ +ER
Sbjct: 361 LYEMQKRDAKKGLATLCIGGGMGIALTVER 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: 461
Number of extensions: 11
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: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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 AZOBR_RS30610 AZOBR_RS30610 (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.6150.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.4e-148  479.2  10.3   5.1e-148  479.0  10.3    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS30610  AZOBR_RS30610 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS30610  AZOBR_RS30610 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.0  10.3  5.1e-148  5.1e-148       1     385 []       6     389 ..       6     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.0 bits;  conditional E-value: 5.1e-148
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a+Rtpig+++g+l++++a+ L++ +i+e+l ra+ d++++ evilG+ l+ag+++n+aR+aa++ag
  lcl|FitnessBrowser__azobra:AZOBR_RS30610   6 IASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAGQGQNPARQAAVNAG 74 
                                               789****************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               +p s  a+ +n++C+Sgl++val++q+i+ G+a+v+v+GG EsmS++p++++    r+++k+g+a++ d
  lcl|FitnessBrowser__azobra:AZOBR_RS30610  75 IPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQAPHVMHL---RNGVKMGAAEMLD 140
                                               ************************************************98886...59*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               ++lkd+   + ++++mg+tAen+a+k++++ReeqD +a++S+qka++A+++g+fkdei+pv++kg+  +
  lcl|FitnessBrowser__azobra:AZOBR_RS30610 141 TMLKDGlmdAFKGYHMGTTAENVAQKWQLTREEQDVFAAASQQKAEAAQKSGRFKDEIIPVTIKGRkgD 209
                                               *********999******************************************************999 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                                +v++De ++ +tt+e+LakL+paf + +g tvtAgN+s++nDGAaal+lm+ e a++ gltplarivs
  lcl|FitnessBrowser__azobra:AZOBR_RS30610 210 IIVADDEYPKHGTTAESLAKLRPAFSK-EG-TVTAGNASGINDGAAALVLMTAENAARRGLTPLARIVS 276
                                               999**********************95.8*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gp+pA++ aL+kag++ +d+dl+E nEAFAaq+lav+k+lg  d++kvNvnGGAiA
  lcl|FitnessBrowser__azobra:AZOBR_RS30610 277 WATAGVDPAIMGTGPIPASRLALEKAGWKHDDLDLIEANEAFAAQALAVNKDLG-WDTSKVNVNGGAIA 344
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               lGHP+GasGar+++tll+e+++r++k GlatlC+ggG+G+A+ +e
  lcl|FitnessBrowser__azobra:AZOBR_RS30610 345 LGHPVGASGARVLTTLLYEMQKRDAKKGLATLCIGGGMGIALTVE 389
                                               *****************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.71
//
[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:

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:

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:

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, or view the source code.

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