GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2C3

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AO356_21640 AO356_21640 acetyl-CoA acetyltransferase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_21640
          Length = 393

 Score =  716 bits (1847), Expect = 0.0
 Identities = 365/393 (92%), Positives = 380/393 (96%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           MQ+VVIVAATRTA+GSFQGSLA+IPAPELGAAVIRRLLEQTGL   QVDEVILGQVLTAG
Sbjct: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60

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

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISRE QDAFAA
Sbjct: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
           ASQQKA AAIE GRF DEITPILIPQRKGDPVAFA DEQPRAGTTAESL KLKPAFKKDG
Sbjct: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAV+LMSA+KAKALGLPVLA+I++YANAGVDPAIMGIGPVSATRRC
Sbjct: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGWSL  LDLIEANEAFAAQSLAV +EL+WD +KVNVNGGAIA+GHPIGASGCRVLV
Sbjct: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALERS 393
           +LLHEMIKRDAKKGLATLCIGGGQGVALALER+
Sbjct: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALERA 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: 606
Number of extensions: 13
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 AO356_21640 AO356_21640 (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.14868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   1.2e-152  494.2   5.9   1.4e-152  494.1   5.9    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640  AO356_21640 acetyl-CoA acetyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640  AO356_21640 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  494.1   5.9  1.4e-152  1.4e-152       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 494.1 bits;  conditional E-value: 1.4e-152
                                       TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaRe 63 
                                                     iv+a+Rt+ig+++gsl+ ++a +L+aavi++lle++gl+ e++devilG+vl+ag+++n+aR+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640   6 IVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAGSGQNPARQ 68 
                                                     8************************************************************** PP

                                       TIGR01930  64 aalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrr 126
                                                     a + aglp+ vpalt+n+vC+Sgl+A++l+aq+i++G+a+v++aGG+E+mS +p++l+a+  r
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640  69 ASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSLAPYVLPAA--R 129
                                                     **********************************************************98..8 PP

                                       TIGR01930 127 eslklgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAiee 186
                                                      +l++g+ak+ d+++ d+   + ++++mg+tAenl +kygisReeqD++a++S+qka +Aie 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640 130 TGLRMGHAKMIDSMITDGlwdAFNDYHMGITAENLVDKYGISREEQDAFAAASQQKAVAAIEG 192
                                                     9********************99**************************************** PP

                                       TIGR01930 187 gkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDG 246
                                                     g+f+dei+p+ ++++   ++ +++De++r++tt+e+L+kLkpafk+ +gs vtAgN+s+lnDG
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640 193 GRFADEITPILIPQRkgdPVAFATDEQPRAGTTAESLGKLKPAFKK-DGS-VTAGNASSLNDG 253
                                                     ************9999999*************************95.9*7.************ PP

                                       TIGR01930 247 AaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEi 309
                                                     Aaa++lms e+ak+lgl +la+i ++a+agvdp++mg+gpv A++++L+kag+s++++dl+E 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640 254 AAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRCLDKAGWSLEQLDLIEA 316
                                                     *************************************************************** PP

                                       TIGR01930 310 nEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatl 372
                                                     nEAFAaq lav++el+  d +kvNvnGGAiAlGHP+GasG+r++++ll+e+ +r++k Glatl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640 317 NEAFAAQSLAVARELK-WDMDKVNVNGGAIALGHPIGASGCRVLVSLLHEMIKRDAKKGLATL 378
                                                     ****************.88******************************************** PP

                                       TIGR01930 373 CvggGqGaAvile 385
                                                     C+ggGqG+A+ le
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_21640 379 CIGGGQGVALALE 391
                                                     *********9886 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: 12.54
//
[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:

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