Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N1B4

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate Pf1N1B4_5133 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::Q0KBP1
         (394 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133
          Length = 394

 Score =  488 bits (1257), Expect = e-143
 Identities = 239/391 (61%), Positives = 297/391 (75%), Gaps = 1/391 (0%)

Query: 4   EVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPR 63
           ++ VVS VR+AIG+FGGSLKDV P +L   V R A+ R+ ++ + +GH V G+VI TE R
Sbjct: 5   DIFVVSAVRSAIGSFGGSLKDVPPIQLATDVCRAAIERSGLAPEHIGHAVMGHVIPTEAR 64

Query: 64  DMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRA 123
           D Y+ R  A+N G+T   PA  VNRLCGSGLQAIVSAAQ+++LGD   A+ GG ESMSR 
Sbjct: 65  DAYISRAVAINAGLTKETPAFNVNRLCGSGLQAIVSAAQSLMLGDAGAALAGGVESMSRG 124

Query: 124 PYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALES 183
            YL P ARWGARMGD   +D MLG L DPF   HMG+TAEN+A+ Y I+R  QDE AL S
Sbjct: 125 AYLLPQARWGARMGDMQAIDYMLGVLQDPFAGFHMGITAENIAEHYGITRQAQDELALLS 184

Query: 184 HRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTV 243
            +RA+ AI  G F  QIVP+  + RKG VTF TDEHVR +   + +++++P F K++G+V
Sbjct: 185 QQRAARAIAEGRFAGQIVPIEIETRKGTVTFATDEHVRAEVNAEQLSRMKPAF-KKDGSV 243

Query: 244 TAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALE 303
           TAGNASGLND A A++M      + +GLKP+ARLV Y HAGV+P  MG+GP+PAT++ L+
Sbjct: 244 TAGNASGLNDGAGALIMATGQVVQEQGLKPMARLVGYAHAGVEPSMMGLGPIPATRLVLK 303

Query: 304 RAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKA 363
           RAGL V+DLDVIE+NEAFAAQACAV + LG DP KVNPNGSGISLGHP+GATGA+I  KA
Sbjct: 304 RAGLTVADLDVIESNEAFAAQACAVAQELGFDPQKVNPNGSGISLGHPVGATGAIIATKA 363

Query: 364 LHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           +HEL+R QGRYAL TMCIGGGQGIA +FER+
Sbjct: 364 IHELHRCQGRYALATMCIGGGQGIAVLFERV 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: 489
Number of extensions: 18
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 Pf1N1B4_5133 (3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9))
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.13169.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   7.4e-139  448.9   8.2   8.4e-139  448.7   8.2    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133  3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.7   8.2  8.4e-139  8.4e-139       1     385 []       8     392 ..       8     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 448.7 bits;  conditional E-value: 8.4e-139
                                      TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaRe 63 
                                                    +v+avR++ig++ggslk++++ +L++ v ++++er+gl pe+i ++++G+v+++ +  a i R 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133   8 VVSAVRSAIGSFGGSLKDVPPIQLATDVCRAAIERSGLAPEHIGHAVMGHVIPTEARdAYISRA 71 
                                                    79***************************************************99999****** PP

                                      TIGR01930  64 aalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrre 127
                                                    +a++agl +++pa++vnr+C+SglqA+ +aaq+++ G+a +++aGGvEsmSr  +ll+++  r+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133  72 VAINAGLTKETPAFNVNRLCGSGLQAIVSAAQSLMLGDAGAALAGGVESMSRGAYLLPQA--RW 133
                                                    **********************************************************98..8* PP

                                      TIGR01930 128 slklgkakledqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkf 189
                                                    ++++g+++  d +l  l  + ++++mg+tAen+a++ygi+R+ qDe+al S+q+aa+Ai+eg+f
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 134 GARMGDMQAIDYMLGVLqdPFAGFHMGITAENIAEHYGITRQAQDELALLSQQRAARAIAEGRF 197
                                                    ***********8888889999******************************************* PP

                                      TIGR01930 190 kdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaall 251
                                                    + +ivp+e++++  ++++++De++r+++++e+L+++kpafk+ +gs vtAgN+s+lnDGA+al+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 198 AGQIVPIEIETRkgTVTFATDEHVRAEVNAEQLSRMKPAFKK-DGS-VTAGNASGLNDGAGALI 259
                                                    **********99999*************************95.9*7.***************** PP

                                      TIGR01930 252 lmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAa 315
                                                    +++ +v++e gl+p+ar+v++a+agv+p+ mglgp+pA++ +Lk+agl++ d+d++E nEAFAa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 260 MATGQVVQEQGLKPMARLVGYAHAGVEPSMMGLGPIPATRLVLKRAGLTVADLDVIESNEAFAA 323
                                                    **************************************************************** PP

                                      TIGR01930 316 qvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqG 379
                                                    q+ av++elg  d++kvN nG+ i+lGHP+Ga+Ga+i ++ ++eL++ +++y+lat+C+ggGqG
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 324 QACAVAQELG-FDPQKVNPNGSGISLGHPVGATGAIIATKAIHELHRCQGRYALATMCIGGGQG 386
                                                    **********.78*************************************************** PP

                                      TIGR01930 380 aAvile 385
                                                    +Av++e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133 387 IAVLFE 392
                                                    ***997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.55
//
[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)
Rules (tab-delimited)
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