Alignments for a candidate for paaJ2 in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Paraburkholderia bryophila 376MFSha3.1

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate H281DRAFT_05723 H281DRAFT_05723 acetyl-CoA acyltransferase

Query= uniprot:A0A2Z5MFE9
         (400 letters)



>FitnessBrowser__Burk376:H281DRAFT_05723
          Length = 400

 Score =  774 bits (1999), Expect = 0.0
 Identities = 395/400 (98%), Positives = 398/400 (99%)

Query: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIQRNPGVDWRAVDDVIYGCANQA 60
           MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALI+RNPGVDWRAVDDVIYGCANQA
Sbjct: 1   MNDAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRAVDDVIYGCANQA 60

Query: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120
           GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESM 120

Query: 121 TRAPFVMGKAASAFTRQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180
           TRAPFVMGKAASAF RQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD
Sbjct: 121 TRAPFVMGKAASAFARQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRAD 180

Query: 181 QDAFALASQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLARLKGV 240
           QDAFAL SQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLA+LKGV
Sbjct: 181 QDAFALVSQQKAARAQRDGTLAQEIVGVEIAQKKGDAIRVTLDEHPRETSLESLAKLKGV 240

Query: 241 VRPDGTVTAGNASGVNDGACALLIASQQAAEQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
           VRPDGTVTAGNASGVNDGACALLIASQQAA+QYGLRRRARVVGMATAGVEPRIMGIGPAP
Sbjct: 241 VRPDGTVTAGNASGVNDGACALLIASQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300

Query: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360
           ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA
Sbjct: 301 ATQKLLRQLGMTLDQLDVIELNEAFASQGLAVLRMLGLRDDDPRVNPNGGAIALGHPLGA 360

Query: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400
           SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL
Sbjct: 361 SGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVIERL 400


Lambda     K      H
   0.319    0.134    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: 698
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate H281DRAFT_05723 H281DRAFT_05723 (acetyl-CoA acyltransferase)
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.28771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.6e-224  730.5  12.6   2.9e-224  730.3  12.6    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05723  H281DRAFT_05723 acetyl-CoA acylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05723  H281DRAFT_05723 acetyl-CoA acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.3  12.6  2.9e-224  2.9e-224       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 730.3 bits;  conditional E-value: 2.9e-224
                                    TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnva 67 
                                                  ++yi+dairtpiGrygG+l  vraddl+avp+kal++rnp +d+ a+ddvi+GcanqaGednrnva
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723   3 DAYICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRAVDDVIYGCANQAGEDNRNVA 68 
                                                  79**************************************************************** PP

                                    TIGR02430  68 rmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsaf 133
                                                  rm+allaGlp++ pg+t+nrlcgsg+da+g+aaraikaGea+l+iaGGvesm+rapfv+Gka+saf
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723  69 RMSALLAGLPADAPGATINRLCGSGMDAVGTAARAIKAGEAQLMIAGGVESMTRAPFVMGKAASAF 134
                                                  ****************************************************************** PP

                                    TIGR02430 134 srsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGf 199
                                                  +r+a+++dttiGwrfvnp +k++yGvdsmpetaenvae+fg+sr+dqdafal sqq++a+aq  G 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 135 ARQAEIHDTTIGWRFVNPLMKRQYGVDSMPETAENVAEQFGISRADQDAFALVSQQKAARAQRDGT 200
                                                  ****************************************************************** PP

                                    TIGR02430 200 faeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaallla 265
                                                  +a+eiv vei+qkkG++  v  deh+r et+le+laklk+vvr+dgtvtaGnasGvndGa+all+a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 201 LAQEIVGVEIAQKKGDAIRVTLDEHPR-ETSLESLAKLKGVVRPDGTVTAGNASGVNDGACALLIA 265
                                                  ***************************.************************************** PP

                                    TIGR02430 266 seeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331
                                                  s++a+ ++gl+ rar++++a+aGvepr+mG+gp+pa++kll+++g++l++ldvielneafa+q+la
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 266 SQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAPATQKLLRQLGMTLDQLDVIELNEAFASQGLA 331
                                                  ****************************************************************** PP

                                    TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvi 397
                                                  vlr lgl+ddd rvnpnGGaialGhplGasGarlv+tal+qle+s+gr+al+t+ciGvGqGialvi
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 332 VLRMLGLRDDDPRVNPNGGAIALGHPLGASGARLVTTALHQLERSNGRFALCTMCIGVGQGIALVI 397
                                                  ****************************************************************** PP

                                    TIGR02430 398 erv 400
                                                  er+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05723 398 ERL 400
                                                  *96 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.71
//
[ok]

This GapMind analysis is from Sep 17 2021. 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 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