Alignments for a candidate for paaJ2 in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaJ2 in Paraburkholderia phymatum STM815

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate WP_012403071.1 BPHY_RS19030 3-oxoadipyl-CoA thiolase

Query= uniprot:B2SYZ2
         (400 letters)



>NCBI__GCF_000020045.1:WP_012403071.1
          Length = 400

 Score =  644 bits (1662), Expect = 0.0
 Identities = 320/400 (80%), Positives = 355/400 (88%)

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

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARMS LLAGLP + PGST+NRLCGSGMDAVG AARAIK+GEA LMIAGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAGLMIAGGVESM 120

Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180
           +RAPFVMGKATSAF+RQADIYDTTIGWRF+NPLMK+ YGVDSMPET ENVA ++++SRAD
Sbjct: 121 SRAPFVMGKATSAFSRQADIYDTTIGWRFVNPLMKQLYGVDSMPETGENVATDYNISRAD 180

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240
           QDAFAL SQQKAARAQQDGTLAQEIV V I QKKGD +    DEHPRETSLE+L KLKGV
Sbjct: 181 QDAFALRSQQKAARAQQDGTLAQEIVSVTIPQKKGDAIVVSRDEHPRETSLEALAKLKGV 240

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

Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360
           ATQKLL +L M + Q DVIELNEAFASQG+AVLR LG+ DDD RVNPNGGAIALGHPLG 
Sbjct: 301 ATQKLLARLNMNINQFDVIELNEAFASQGIAVLRALGVADDDARVNPNGGAIALGHPLGM 360

Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400
           SGARL+TTA+YQL+RT GRFALCTMCIGVGQGIA+ IER+
Sbjct: 361 SGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAIERV 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: 590
Number of extensions: 12
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 WP_012403071.1 BPHY_RS19030 (3-oxoadipyl-CoA thiolase)
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.22095.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-226  736.3  11.9   5.2e-226  736.1  11.9    1.0  1  lcl|NCBI__GCF_000020045.1:WP_012403071.1  BPHY_RS19030 3-oxoadipyl-CoA thi


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012403071.1  BPHY_RS19030 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.1  11.9  5.2e-226  5.2e-226       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 736.1 bits;  conditional E-value: 5.2e-226
                                 TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarma 70 
                                               e+ ++dairtpiGry+Gslssvraddl+avplkal++rn+++d++ iddvi+GcanqaGednrnvarm+
  lcl|NCBI__GCF_000020045.1:WP_012403071.1   3 EALLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKEVDWSVIDDVIYGCANQAGEDNRNVARMS 71 
                                               789****************************************************************** PP

                                 TIGR02430  71 allaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakl 139
                                               +llaGlp++vpg+tvnrlcgsg+da+g+aaraik+Gea l+iaGGvesmsrapfv+Gka safsr+a++
  lcl|NCBI__GCF_000020045.1:WP_012403071.1  72 LLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAGLMIAGGVESMSRAPFVMGKATSAFSRQADI 140
                                               ********************************************************************* PP

                                 TIGR02430 140 edttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpve 208
                                                dttiGwrfvnp +k+lyGvdsmpet enva+++++sr+dqdafalrsqq++a+aq+ G +a+eiv+v+
  lcl|NCBI__GCF_000020045.1:WP_012403071.1 141 YDTTIGWRFVNPLMKQLYGVDSMPETGENVATDYNISRADQDAFALRSQQKAARAQQDGTLAQEIVSVT 209
                                               ********************************************************************* PP

                                 TIGR02430 209 ikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltp 277
                                               i+qkkG++ vv++deh+r et+lealaklk+vvr+dgtvtaGnasGvndGaaallla +e++kr+gltp
  lcl|NCBI__GCF_000020045.1:WP_012403071.1 210 IPQKKGDAIVVSRDEHPR-ETSLEALAKLKGVVRPDGTVTAGNASGVNDGAAALLLANAETAKRFGLTP 277
                                               ******************.************************************************** PP

                                 TIGR02430 278 rarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvn 346
                                               rar+l++a+aGv+prvmG+gp+pa++kllar++++++++dvielneafa+q++avlr+lg+adddarvn
  lcl|NCBI__GCF_000020045.1:WP_012403071.1 278 RARVLGIATAGVAPRVMGIGPAPATQKLLARLNMNINQFDVIELNEAFASQGIAVLRALGVADDDARVN 346
                                               ********************************************************************* PP

                                 TIGR02430 347 pnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400
                                               pnGGaialGhplG+sGarlv+ta++ql++++gr+al+t+ciGvGqGia++ierv
  lcl|NCBI__GCF_000020045.1:WP_012403071.1 347 PNGGAIALGHPLGMSGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAIERV 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.43
//
[ok]

This GapMind analysis is from Sep 24 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