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

GapMind for catabolism of small carbon sources

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

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate AO356_03560 AO356_03560 acetyl-CoA acetyltransferase

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_03560
          Length = 394

 Score =  338 bits (867), Expect = 2e-97
 Identities = 188/395 (47%), Positives = 247/395 (62%), Gaps = 10/395 (2%)

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

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

Query: 121 SQVPMMGHVTRPNLA---LAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           S    M  V   NL    L E+ P  Y  MG TAE VA++Y VSRE+QD +A++S Q  A
Sbjct: 121 SLT--MKSVNTDNLINPLLKEQVPGIYFPMGQTAEIVARRYQVSREEQDRYALQSQQRTA 178

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

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

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

Query: 355 KLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389
           +    L+ E++RRN ++G+VTMC+GGGMGA G+FE
Sbjct: 357 RQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFE 391


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: 424
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 AO356_03560 AO356_03560 (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.284626.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                   -----------
   7.9e-136  438.9   0.1     9e-136  438.7   0.1    1.0  1  FitnessBrowser__pseudo5_N2C3_1:AO356_03560  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo5_N2C3_1:AO356_03560  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.7   0.1    9e-136    9e-136       1     385 []       6     391 ..       6     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 438.7 bits;  conditional E-value: 9e-136
                                   TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaa 65 
                                                 ivd vRt  + +++g ++ ++++d++a+ +++ll+r++++p+ +++ i+G+  ++g+q  ni+R++a
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560   6 IVDSVRTGLAkSFRGKFNMTRPDDMAAHCVNALLARNDINPASVEDCIVGAGSNEGAQgYNIGRNVA 72 
                                                 8*********99******************************************************* PP

                                   TIGR01930  66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklg 132
                                                 + ++l+  ++++t+nr+C+SglqA+a+aa++i++G  d++vaGGvEs+S +  +++ +   + +++ 
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560  73 VLSQLGIGTAGMTLNRFCSSGLQAIAIAANQIASGCSDIIVAGGVESISLTMKSVNTD---NLINPL 136
                                                 *************************************************998888775...788885 PP

                                   TIGR01930 133 kakledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevk 199
                                                  +++        +   ++mg+tAe +a++y++sReeqD+yal+S+q++akA+++g f+dei+p+ vk
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560 137 LKEQV-------PGIYFPMGQTAEIVARRYQVSREEQDRYALQSQQRTAKAQAAGLFDDEIIPMAVK 196
                                                 55544.......5789**************************************************9 PP

                                   TIGR01930 200 gk............kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllms 254
                                                  +            + vv++D++ rp+tt e+La+Lkp+f+e +gs vtAgNssql+DGA+++l+ms
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560 197 YRvedkntgvvqilDGVVDHDDCNRPDTTYESLAGLKPVFAE-DGS-VTAGNSSQLSDGASMTLVMS 261
                                                 999999*****9999999**********************96.9*7.******************** PP

                                   TIGR01930 255 eevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlave 321
                                                  e+a +lgl+p+a +++++vag++p+emg+gpv +++k+Lk  gl+i didl+E+nEAFA+q+l+++
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560 262 LEKALALGLKPKAFFRGFTVAGCEPDEMGIGPVFSVPKLLKAKGLQIADIDLWELNEAFASQCLYSR 328
                                                 ******************************************************************* PP

                                   TIGR01930 322 kelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                 + l+ +d++k+NvnGG+i++GHP+G++G+r v +l++eL++r+ +yG++t+CvggG+Ga+ ++e
  FitnessBrowser__pseudo5_N2C3_1:AO356_03560 329 DRLE-IDPQKYNVNGGSISIGHPFGMTGSRQVGHLVRELQRRNLRYGIVTMCVGGGMGATGLFE 391
                                                 ****.88***************************************************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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 28.21
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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