Alignments for a candidate for fadA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas putida KT2440

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate PP_3754 PP_3754 Beta-ketothiolase BktB

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__Putida:PP_3754
          Length = 394

 Score =  497 bits (1280), Expect = e-145
 Identities = 248/391 (63%), Positives = 295/391 (75%), Gaps = 1/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           E+ VVS VR+AIG FGGSLKD+  A+L + V R A+ R+ ++ + VGH+V G VI TEPR
Sbjct: 5   EIYVVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSGLAAEQVGHMVMGTVIPTEPR 64

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D YL RVAA+N G+    PA  VNRLCGSGLQAIVSAAQ +LLGDTDVA+  GAESMSR 
Sbjct: 65  DAYLARVAAMNAGIPKETPAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAESMSRG 124

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
           PYL P ARWGARMGD   +D  +G L DPF   HMG+TAENV+ +Y I+R  QDE AL S
Sbjct: 125 PYLLPQARWGARMGDLQGIDYTVGVLQDPFQHFHMGITAENVSAKYGITREMQDELALTS 184

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
            RRA+ AI  G F  QIV +  K RKG V F  DEHVR D T + +  ++PVF K++GTV
Sbjct: 185 QRRAARAIAEGRFASQIVALELKTRKGSVQFSVDEHVRADVTAEQLAGMKPVF-KKDGTV 243

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASG+ND AA +V+       R GLKPLARLV Y HAGV+P+ MG+GP+PAT+  LE
Sbjct: 244 TAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPIPATRKVLE 303

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           + GL + DLDVIE+NEAFAAQACAV + LG DP KVNPNGSGISLGHP+GATGA+I  KA
Sbjct: 304 KTGLNLQDLDVIESNEAFAAQACAVARELGFDPEKVNPNGSGISLGHPVGATGAIIATKA 363

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           +HEL R+QGRYAL TMCIGGGQGIA +FER+
Sbjct: 364 IHELQRIQGRYALATMCIGGGQGIAVVFERV 394


Lambda     K      H
   0.318    0.134    0.381 

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: 474
Number of extensions: 14
Number of successful extensions: 2
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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_3754 PP_3754 (Beta-ketothiolase BktB)
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.1580.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.1e-138  448.3   4.5   1.3e-138  448.1   4.5    1.0  1  lcl|FitnessBrowser__Putida:PP_3754  PP_3754 Beta-ketothiolase BktB


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3754  PP_3754 Beta-ketothiolase BktB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.1   4.5  1.3e-138  1.3e-138       1     385 []       8     392 ..       8     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.1 bits;  conditional E-value: 1.3e-138
                           TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpesv 74 
                                         +v+avR++ig +ggslk+l+ +dL++av ++++er+gl +e++ ++++G+v+++    a +aR aa++ag+p+++
  lcl|FitnessBrowser__Putida:PP_3754   8 VVSAVRSAIGGFGGSLKDLPLADLASAVTRAAIERSGLAAEQVGHMVMGTVIPTEPRdAYLARVAAMNAGIPKET 82 
                                         79********99*****************************************99988***************** PP

                           TIGR01930  75 paltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl..vkt 147
                                         pa++vnr+C+SglqA+ +aaq +  G+ dv+va+G+EsmSr p+ll+++  r+++++g+ +  d ++  l  + +
  lcl|FitnessBrowser__Putida:PP_3754  83 PAFNVNRLCGSGLQAIVSAAQGLLLGDTDVAVAAGAESMSRGPYLLPQA--RWGARMGDLQGIDYTVGVLqdPFQ 155
                                         ***********************************************98..89*****99999977776699999 PP

                           TIGR01930 148 klsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpnttlekL 220
                                         +++mg+tAen+++kygi+Re+qDe+al S+++aa+Ai+eg+f+++iv +e+k++  ++++s De++r+++t+e+L
  lcl|FitnessBrowser__Putida:PP_3754 156 HFHMGITAENVSAKYGITREMQDELALTSQRRAARAIAEGRFASQIVALELKTRkgSVQFSVDEHVRADVTAEQL 230
                                         ****************************************************99999****************** PP

                           TIGR01930 221 akLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLk 295
                                         a++kp+fk+ +g tvtAgN+s++nDGAa l+l++ +++++lgl+plar+v++a+agv+pe mglgp+pA++k+L+
  lcl|FitnessBrowser__Putida:PP_3754 231 AGMKPVFKK-DG-TVTAGNASGINDGAAGLVLATGDAVRRLGLKPLARLVGYAHAGVEPELMGLGPIPATRKVLE 303
                                         *******95.9*.6************************************************************* PP

                           TIGR01930 296 kaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGla 370
                                         k+gl+++d+d++E nEAFAaq+ av++elg  d+ekvN nG+ i+lGHP+Ga+Ga+i ++ ++eL++ +++y+la
  lcl|FitnessBrowser__Putida:PP_3754 304 KTGLNLQDLDVIESNEAFAAQACAVARELG-FDPEKVNPNGSGISLGHPVGATGAIIATKAIHELQRIQGRYALA 377
                                         ******************************.78****************************************** PP

                           TIGR01930 371 tlCvggGqGaAvile 385
                                         t+C+ggGqG+Av++e
  lcl|FitnessBrowser__Putida:PP_3754 378 TMCIGGGQGIAVVFE 392
                                         *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.04
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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