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_01504 H281DRAFT_01504 3-oxoadipyl-CoA thiolase

Query= uniprot:B2SYZ2
         (400 letters)



>FitnessBrowser__Burk376:H281DRAFT_01504
          Length = 400

 Score =  657 bits (1695), Expect = 0.0
 Identities = 322/400 (80%), Positives = 362/400 (90%)

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

Query: 61  GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120
           GEDNRNVARMS LLAGLP + PGST+NRLCGSGMDAVG AARAIK+GEA LM+AGGVESM
Sbjct: 61  GEDNRNVARMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESM 120

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

Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240
           QDAFAL SQQKAARAQ+DGTLAQEIVGV IAQKKGDP+    DEHPRETSLE+L KLKGV
Sbjct: 181 QDAFALRSQQKAARAQKDGTLAQEIVGVTIAQKKGDPITVSQDEHPRETSLETLAKLKGV 240

Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300
           VRPDG+VTAGNASGVNDGA ALLLAN++ A ++GL  RARV+G+ATAGV PRIMG+GPAP
Sbjct: 241 VRPDGTVTAGNASGVNDGAAALLLANEETAKRFGLTPRARVLGIATAGVAPRIMGMGPAP 300

Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360
           A QKL+ +L MT++Q DVIELNEAFASQG+AVLRTLG+ DDD RVNPNGGAIALGHPLG 
Sbjct: 301 AAQKLMARLNMTIDQFDVIELNEAFASQGIAVLRTLGVADDDARVNPNGGAIALGHPLGM 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: 604
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 H281DRAFT_01504 H281DRAFT_01504 (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.7959.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.9e-226  736.5  11.7   4.4e-226  736.3  11.7    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01504  H281DRAFT_01504 3-oxoadipyl-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01504  H281DRAFT_01504 3-oxoadipyl-CoA thiolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.3  11.7  4.4e-226  4.4e-226       2     400 .]       3     400 .]       2     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 736.3 bits;  conditional E-value: 4.4e-226
                                    TIGR02430   2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnva 67 
                                                  e++++dairtpiGry+Gslssvraddl+avplkal++rn+++d++ iddvi+GcanqaGednrnva
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504   3 EAFLCDAIRTPIGRYAGSLSSVRADDLGAVPLKALMERNKNVDWSVIDDVIYGCANQAGEDNRNVA 68 
                                                  89**************************************************************** PP

                                    TIGR02430  68 rmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsaf 133
                                                  rm++llaGlp++vpg+tvnrlcgsg+da+g+aaraik+Gea l++aGGvesmsrapfv+Gka saf
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504  69 RMSLLLAGLPKDVPGSTVNRLCGSGMDAVGIAARAIKSGEAALMVAGGVESMSRAPFVMGKATSAF 134
                                                  ****************************************************************** PP

                                    TIGR02430 134 srsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGf 199
                                                  sr+a++ dttiGwrfvnp +k++yGvdsmpet enva+++++sr+dqdafalrsqq++a+aq+ G 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504 135 SRQADIYDTTIGWRFVNPLMKQMYGVDSMPETGENVATDYNISRADQDAFALRSQQKAARAQKDGT 200
                                                  ****************************************************************** PP

                                    TIGR02430 200 faeeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaallla 265
                                                  +a+eiv v+i+qkkG++ +v++deh+r et+le+laklk+vvr+dgtvtaGnasGvndGaaallla
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504 201 LAQEIVGVTIAQKKGDPITVSQDEHPR-ETSLETLAKLKGVVRPDGTVTAGNASGVNDGAAALLLA 265
                                                  ***************************.************************************** PP

                                    TIGR02430 266 seeavkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqala 331
                                                   ee++kr+gltprar+l++a+aGv+pr+mG+gp+pa++kl+ar++++++++dvielneafa+q++a
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504 266 NEETAKRFGLTPRARVLGIATAGVAPRIMGMGPAPAAQKLMARLNMTIDQFDVIELNEAFASQGIA 331
                                                  ****************************************************************** PP

                                    TIGR02430 332 vlrelgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvi 397
                                                  vlr lg+adddarvnpnGGaialGhplG+sGarlv+ta++ql++++gr+al+t+ciGvGqGia++i
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504 332 VLRTLGVADDDARVNPNGGAIALGHPLGMSGARLVTTAMYQLQRTQGRFALCTMCIGVGQGIAIAI 397
                                                  ****************************************************************** PP

                                    TIGR02430 398 erv 400
                                                  erv
  lcl|FitnessBrowser__Burk376:H281DRAFT_01504 398 ERV 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: 7.35
//
[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