GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Pseudomonas fluorescens FW300-N2E3

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AO353_27945 AO353_27945 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20831
         (393 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 AO353_27945 acetyl-CoA
           acetyltransferase
          Length = 393

 Score =  705 bits (1819), Expect = 0.0
 Identities = 360/393 (91%), Positives = 378/393 (96%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQDVVIVAATRTA+GSFQGSLASIPAPELGAAVIR+LL +TGL   QVDEVILGQVLTAG
Sbjct: 1   MQDVVIVAATRTAIGSFQGSLASIPAPELGAAVIRQLLAKTGLAADQVDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           SGQNPARQASILAGLPHAVP+LTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL
Sbjct: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYVLPAARTGLRMGHAKM+DSMI+DGLWDAFNDYHMGITAENLVDKY ++RE QDAFAA
Sbjct: 121 APYVLPAARTGLRMGHAKMVDSMISDGLWDAFNDYHMGITAENLVDKYHLTREEQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           ASQQKATAAI AGRF DEITPILIPQRKG+P++F VDEQPRA TTAESLAKLKPAFKKDG
Sbjct: 181 ASQQKATAAIAAGRFADEITPILIPQRKGEPLSFTVDEQPRAETTAESLAKLKPAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAVLLMSADKAK LGLPVLA+IA+YANAGVDPAIMGI PVSATRRC
Sbjct: 241 SVTAGNASSLNDGAAAVLLMSADKAKQLGLPVLAKIAAYANAGVDPAIMGIAPVSATRRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGW+L  LDLIEANEAFAAQSLAVGKELEWDA KVNVNGGAIA+GHPIGASGCRVLV
Sbjct: 301 LDKAGWNLDQLDLIEANEAFAAQSLAVGKELEWDASKVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393
           +LLHEMIKRDAKKGLATLCIGGGQGVALA+ER+
Sbjct: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALAIERA 393


Lambda     K      H
   0.317    0.133    0.378 

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: 587
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: 393
Length of database: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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 AO353_27945 AO353_27945 (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.31273.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.5e-151  490.6   7.4   1.7e-151  490.5   7.4    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945  AO353_27945 acetyl-CoA acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945  AO353_27945 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  490.5   7.4  1.7e-151  1.7e-151       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 490.5 bits;  conditional E-value: 1.7e-151
                                     TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaa 65 
                                                   iv+a+Rt+ig+++gsl++++a +L+aavi++ll+++gl ++++devilG+vl+ag+++n+aR+a 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945   6 IVAATRTAIGSFQGSLASIPAPELGAAVIRQLLAKTGLAADQVDEVILGQVLTAGSGQNPARQAS 70 
                                                   8**************************************************************** PP

                                     TIGR01930  66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslk 130
                                                   + aglp+ vpalt+n+vC+Sgl+A++l+aq+i++G+a+v++aGG+E+mS +p++l+a+  r +l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945  71 ILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYVLPAA--RTGLR 133
                                                   ********************************************************98..89*** PP

                                     TIGR01930 131 lgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkde 192
                                                   +g+ak+ d++++d+   + ++++mg+tAenl +ky+++ReeqD++a++S+qka++Ai++g+f+de
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 134 MGHAKMVDSMISDGlwdAFNDYHMGITAENLVDKYHLTREEQDAFAAASQQKATAAIAAGRFADE 198
                                                   *****************99********************************************** PP

                                     TIGR01930 193 ivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllms 254
                                                   i+p+ ++++   + +++ De++r++tt+e+LakLkpafk+ +gs vtAgN+s+lnDGAaa+llms
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 199 ITPILIPQRkgePLSFTVDEQPRAETTAESLAKLKPAFKK-DGS-VTAGNASSLNDGAAAVLLMS 261
                                                   ******999999999***********************95.9*7.******************** PP

                                     TIGR01930 255 eevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvla 319
                                                    ++ak+lgl +la+i ++a+agvdp++mg++pv A++++L+kag++++++dl+E nEAFAaq la
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 262 ADKAKQLGLPVLAKIAAYANAGVDPAIMGIAPVSATRRCLDKAGWNLDQLDLIEANEAFAAQSLA 326
                                                   ***************************************************************** PP

                                     TIGR01930 320 vekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384
                                                   v kel+  d +kvNvnGGAiAlGHP+GasG+r++++ll+e+ +r++k GlatlC+ggGqG+A+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 327 VGKELE-WDASKVNVNGGAIALGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALAI 390
                                                   ******.88*****************************************************988 PP

                                     TIGR01930 385 e 385
                                                   e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_27945 391 E 391
                                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 10.05
//
[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 preprint 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