GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Pseudomonas putida KT2440

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate PP_4636 PP_4636 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Putida:PP_4636
          Length = 392

 Score =  660 bits (1704), Expect = 0.0
 Identities = 332/392 (84%), Positives = 366/392 (93%)

Query: 1   MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60
           M DVVIVAATRTA+GSFQG+LA++PA +LGAAVI++LL+QTGLDPAQVDEVILGQVLTAG
Sbjct: 1   MNDVVIVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQA+I AGLP +VP+LTLNKVCGSGLKALHL AQAIRCGDAEV+IAGG ENMSL
Sbjct: 61  AGQNPARQAAIKAGLPFSVPALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180
           APYV+P+ARTG RMGH ++IDSMITDGLWDAFNDYHMGITAENLVDKYG+SRE QDAFAA
Sbjct: 121 APYVMPSARTGQRMGHGQLIDSMITDGLWDAFNDYHMGITAENLVDKYGLSREQQDAFAA 180

Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240
            SQ+KA AAIEAGRF  EITPI++PQ+KG+P  FA DEQPR  TTAESLAKL+PAFKKDG
Sbjct: 181 ESQRKAVAAIEAGRFDAEITPIVLPQKKGEPKVFARDEQPRPDTTAESLAKLRPAFKKDG 240

Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAVLLMSA KA+ALGLPVLA+IA+YA+AGVDPAIMGIGPVSAT+RC
Sbjct: 241 SVTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRC 300

Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360
           LDKAGW L +LDLIEANEAFAAQ+LAVG  L WDA +VNVNGGAIA+GHPIGASGCRVLV
Sbjct: 301 LDKAGWQLAELDLIEANEAFAAQALAVGNALAWDAARVNVNGGAIALGHPIGASGCRVLV 360

Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           TLLHEMIKRD KKGLATLCIGGGQGVALA+ER
Sbjct: 361 TLLHEMIKRDVKKGLATLCIGGGQGVALAIER 392


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: 556
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: 393
Length of database: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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 PP_4636 PP_4636 (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.7899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.6e-152  492.1   8.1   6.3e-152  491.9   8.1    1.0  1  lcl|FitnessBrowser__Putida:PP_4636  PP_4636 acetyl-CoA acetyltransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4636  PP_4636 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.9   8.1  6.3e-152  6.3e-152       1     385 []       6     391 ..       6     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 491.9 bits;  conditional E-value: 6.3e-152
                           TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvp 75 
                                         iv+a+Rt+ig+++g+l++++a+dL+aavik+ll+++gldp+++devilG+vl+ag+++n+aR+aa++aglp svp
  lcl|FitnessBrowser__Putida:PP_4636   6 IVAATRTAIGSFQGALATVPAVDLGAAVIKQLLKQTGLDPAQVDEVILGQVLTAGAGQNPARQAAIKAGLPFSVP 80 
                                         8************************************************************************** PP

                           TIGR01930  76 altvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vkt 147
                                         alt+n+vC+Sgl+A++laaq+i++G+a+vv+aGG E+mS +p++++++  r + ++g+ +l d+++ d+   + +
  lcl|FitnessBrowser__Putida:PP_4636  81 ALTLNKVCGSGLKALHLAAQAIRCGDAEVVIAGGQENMSLAPYVMPSA--RTGQRMGHGQLIDSMITDGlwdAFN 153
                                         **********************************************97..89999*****************99* PP

                           TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlek 219
                                         +++mg+tAenl +kyg+sRe+qD++a++S++ka +Aie+g+f++ei+p+++++k   +kv+++De++rp+tt+e+
  lcl|FitnessBrowser__Putida:PP_4636 154 DYHMGITAENLVDKYGLSREQQDAFAAESQRKAVAAIEAGRFDAEITPIVLPQKkgePKVFARDEQPRPDTTAES 228
                                         ***************************************************9999******************** PP

                           TIGR01930 220 LakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaL 294
                                         LakL+pafk+ +gs vtAgN+s+lnDGAaa+llms ++a++lgl +la+i ++a agvdp++mg+gpv A++++L
  lcl|FitnessBrowser__Putida:PP_4636 229 LAKLRPAFKK-DGS-VTAGNASSLNDGAAAVLLMSAAKAEALGLPVLAKIAAYASAGVDPAIMGIGPVSATQRCL 301
                                         ********95.9*7.************************************************************ PP

                           TIGR01930 295 kkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGl 369
                                         +kag+++ ++dl+E nEAFAaq+lav ++l+  d ++vNvnGGAiAlGHP+GasG+r+++tll+e+ +r++k Gl
  lcl|FitnessBrowser__Putida:PP_4636 302 DKAGWQLAELDLIEANEAFAAQALAVGNALA-WDAARVNVNGGAIALGHPIGASGCRVLVTLLHEMIKRDVKKGL 375
                                         *******************************.88***************************************** PP

                           TIGR01930 370 atlCvggGqGaAvile 385
                                         atlC+ggGqG+A+ +e
  lcl|FitnessBrowser__Putida:PP_4636 376 ATLCIGGGQGVALAIE 391
                                         ************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.17
//
[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