Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Pseudomonas fluorescens FW300-N2E2

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate Pf6N2E2_2539 3-ketoacyl-CoA thiolase (EC 2.3.1.16)

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539
          Length = 394

 Score =  335 bits (859), Expect = 1e-96
 Identities = 185/396 (46%), Positives = 247/396 (62%), Gaps = 10/396 (2%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M+E VIV   RT + K+ +G     RPDD+ A CV   L R      +++D I+G  + E
Sbjct: 1   MREVVIVDSVRTGLAKSFRGKFNMTRPDDMAAHCVDALLARNDINPASVEDCIVGAGSNE 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
             QG N+ RN+  L+ L      +T+NR+CSSGLQ+IA AA +I  G  D  +AGG ES+
Sbjct: 61  GAQGYNIGRNVAVLSRLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESI 120

Query: 121 SQVPMM---GHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           S         H+  P   L E+ P  Y  MG TAE VA++Y VSRE+QD +A++S Q  A
Sbjct: 121 SLTMKSVNTDHLINP--LLKEQVPGIYFPMGQTAEIVARRYQVSREEQDRYALQSQQRTA 178

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQF---VFSQDEGVRPQTTADILSTLRPAF 234
           KA A G F DEI+P+ +      ED      Q    V  +D+  RP TT + L+ L+P F
Sbjct: 179 KAQAAGLFDDEIIPMAIKYRV--EDKNTGAVQILDGVVDRDDCNRPDTTYESLAGLKPVF 236

Query: 235 SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEA 294
           + DG+VTAGNSSQ SDGA+  +++  EKA ALGL P   FR F V G  P+ MGIGPV +
Sbjct: 237 AEDGSVTAGNSSQLSDGASMTLVISLEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFS 296

Query: 295 IPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGT 354
           +P+ LK  GLQ+ DI L+ELNEAFASQ +     L ID  K NVNGG+I++GHP G TG+
Sbjct: 297 VPKLLKAKGLQIADIDLWELNEAFASQCLYSRNRLEIDPGKYNVNGGSISIGHPFGMTGS 356

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
           +    L+ E++RRN ++GVVTMC+GGGMGA G+FE+
Sbjct: 357 RQVGHLVRELQRRNLRYGVVTMCVGGGMGATGLFEM 392


Lambda     K      H
   0.316    0.133    0.377 

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: 425
Number of extensions: 16
Number of successful extensions: 3
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: 391
Length of database: 394
Length adjustment: 31
Effective length of query: 360
Effective length of database: 363
Effective search space:   130680
Effective search space used:   130680
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate Pf6N2E2_2539 (3-ketoacyl-CoA thiolase (EC 2.3.1.16))
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.29051.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.1e-134  433.2   0.1   4.7e-134  433.1   0.1    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539  3-ketoacyl-CoA thiolase (EC 2.3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539  3-ketoacyl-CoA thiolase (EC 2.3.1.16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.1   0.1  4.7e-134  4.7e-134       1     385 []       6     391 ..       6     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 433.1 bits;  conditional E-value: 4.7e-134
                                      TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaR 62 
                                                    ivd vRt  + +++g ++ ++++d++a+ +++ll+r++++p+ +++ i+G+  ++g+q  ni+R
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539   6 IVDSVRTGLAkSFRGKFNMTRPDDMAAHCVDALLARNDINPASVEDCIVGAGSNEGAQgYNIGR 69 
                                                    8*********99**************************************************** PP

                                      TIGR01930  63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrr 126
                                                    ++a+ ++l++ ++++t+nr+C+SglqA+a+aa++i++G  d++vaGGvEs+S +  +++ +   
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539  70 NVAVLSRLGTGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESISLTMKSVNTD--- 130
                                                    ****************************************************998877775... PP

                                      TIGR01930 127 eslklgkakledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfk 190
                                                    + +++  +++        +   ++mg+tAe +a++y++sReeqD+yal+S+q++akA+++g f+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 131 HLINPLLKEQV-------PGIYFPMGQTAEIVARRYQVSREEQDRYALQSQQRTAKAQAAGLFD 187
                                                    67777444444.......5789****************************************** PP

                                      TIGR01930 191 deivpvevkgk............kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssq 242
                                                    dei+p+ +k +            + vv++D++ rp+tt e+La+Lkp+f+e +gs vtAgNssq
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 188 DEIIPMAIKYRvedkntgavqilDGVVDRDDCNRPDTTYESLAGLKPVFAE-DGS-VTAGNSSQ 249
                                                    *******99999999*****9999999**********************96.9*7.******** PP

                                      TIGR01930 243 lnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidl 306
                                                    l+DGA+++l+ s e+a +lgl+p+a +++++vag++p+emg+gpv +++k+Lk  gl+i didl
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 250 LSDGASMTLVISLEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFSVPKLLKAKGLQIADIDL 313
                                                    **************************************************************** PP

                                      TIGR01930 307 vEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGla 370
                                                    +E+nEAFA+q+l++++ l+ +d+ k+NvnGG+i++GHP+G++G+r v +l++eL++r+ +yG++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 314 WELNEAFASQCLYSRNRLE-IDPGKYNVNGGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGVV 376
                                                    *******************.88****************************************** PP

                                      TIGR01930 371 tlCvggGqGaAvile 385
                                                    t+CvggG+Ga+ ++e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2539 377 TMCVGGGMGATGLFE 391
                                                    *********998876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.84
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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