Alignments for a candidate for paaJ2 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Burkholderia phytofirmans PsJN

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BPHYT_RS29385 BPHYT_RS29385 acetyl-CoA acetyltransferase

Query= uniprot:B2SYZ2
         (400 letters)



>FitnessBrowser__BFirm:BPHYT_RS29385
          Length = 400

 Score =  650 bits (1678), Expect = 0.0
 Identities = 319/400 (79%), Positives = 360/400 (90%)

Query: 1   MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60
           M +AF+CDAIRTPIGRY G+L  VRADDLGAVP+KAL+ERN  VDW  +DDVIYGCANQA
Sbjct: 1   MTEAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKDVDWNAIDDVIYGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARMS LLAGLP   PG+T+NRLCGSGMDAVG AARAIK+GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPQGVPGTTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESM 120

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           +RAPFVMGKA +AF+RQA+IYDTTIGWRF+NPLMK+ YGVDSMPET ENVA ++++SRAD
Sbjct: 121 SRAPFVMGKAPTAFSRQAEIYDTTIGWRFVNPLMKKLYGVDSMPETGENVATDYNISRAD 180

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240
           QDAFA+ SQQKAARAQ+DGTLAQEIVGV IAQKKGDP+  L DEHPRETSLE+L KLKGV
Sbjct: 181 QDAFAVRSQQKAARAQRDGTLAQEIVGVTIAQKKGDPITVLQDEHPRETSLETLAKLKGV 240

Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
           VRPDG+VTAGNASGVNDGA ALLLAN++ A ++GL  RARV+G+ATAGV PR+MGIGPAP
Sbjct: 241 VRPDGTVTAGNASGVNDGAAALLLANEETARRFGLTPRARVLGIATAGVAPRVMGIGPAP 300

Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360
           ATQKLL +L MT++Q DVIELNEAFASQG+AVLR LG+ DDD RVNPNGGAIALGHPLG 
Sbjct: 301 ATQKLLARLNMTIDQFDVIELNEAFASQGIAVLRALGVADDDARVNPNGGAIALGHPLGM 360

Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
           SGARL+TTA+YQL RT GRFALCTMCIGVGQGIA+ IER+
Sbjct: 361 SGARLVTTAMYQLHRTQGRFALCTMCIGVGQGIAIAIERV 400


Lambda     K      H
   0.318    0.135    0.386 

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: 599
Number of extensions: 14
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 BPHYT_RS29385 BPHYT_RS29385 (acetyl-CoA acetyltransferase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

# 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/TIGR02430.hmm
# target sequence database:        /tmp/gapView.16435.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02430  [M=400]
Accession:   TIGR02430
Description: pcaF: 3-oxoadipyl-CoA thiolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     2e-225  734.1  11.1   2.3e-225  734.0  11.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS29385  BPHYT_RS29385 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS29385  BPHYT_RS29385 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  734.0  11.1  2.3e-225  2.3e-225       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 734.0 bits;  conditional E-value: 2.3e-225
                                TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaa 71 
                                              e++++dairtpiGry+Gslssvraddl+avplkal++rn+++d++aiddvi+GcanqaGednrnvarm++
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385   3 EAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKDVDWNAIDDVIYGCANQAGEDNRNVARMSL 72 
                                              89******************************************************************** PP

                                TIGR02430  72 llaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakled 141
                                              llaGlp+ vpgttvnrlcgsg+da+g+aaraik+Gea l++aGGvesmsrapfv+Gka +afsr+a++ d
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385  73 LLAGLPQGVPGTTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESMSRAPFVMGKAPTAFSRQAEIYD 142
                                              ********************************************************************** PP

                                TIGR02430 142 ttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikq 211
                                              ttiGwrfvnp +k+lyGvdsmpet enva+++++sr+dqdafa+rsqq++a+aq  G +a+eiv v+i+q
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385 143 TTIGWRFVNPLMKKLYGVDSMPETGENVATDYNISRADQDAFAVRSQQKAARAQRDGTLAQEIVGVTIAQ 212
                                              ********************************************************************** PP

                                TIGR02430 212 kkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprari 281
                                              kkG++ +v +deh+r et+le+laklk+vvr+dgtvtaGnasGvndGaaallla ee+++r+gltprar+
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385 213 KKGDPITVLQDEHPR-ETSLETLAKLKGVVRPDGTVTAGNASGVNDGAAALLLANEETARRFGLTPRARV 281
                                              ***************.****************************************************** PP

                                TIGR02430 282 laaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGa 351
                                              l++a+aGv+prvmG+gp+pa++kllar++++++++dvielneafa+q++avlr+lg+adddarvnpnGGa
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385 282 LGIATAGVAPRVMGIGPAPATQKLLARLNMTIDQFDVIELNEAFASQGIAVLRALGVADDDARVNPNGGA 351
                                              ********************************************************************** PP

                                TIGR02430 352 ialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                              ialGhplG+sGarlv+ta++ql++++gr+al+t+ciGvGqGia++ierv
  lcl|FitnessBrowser__BFirm:BPHYT_RS29385 352 IALGHPLGMSGARLVTTAMYQLHRTQGRFALCTMCIGVGQGIAIAIERV 400
                                              ************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (400 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: 6.71
//
[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