Alignments for a candidate for catA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for catA in Burkholderia phytofirmans PsJN

Align catechol 1,2-dioxygenase 2; EC 1.13.11.1 (characterized)
to candidate BPHYT_RS10670 BPHYT_RS10670 catechol 1,2-dioxygenase

Query= CharProtDB::CH_014953
         (275 letters)



>FitnessBrowser__BFirm:BPHYT_RS10670
          Length = 302

 Score =  515 bits (1327), Expect = e-151
 Identities = 249/261 (95%), Positives = 257/261 (98%)

Query: 1   MNKQAIDALLQKINDSAINEGNPRTKQIVNRIVRDLFYTIEDLDVQPDEFWTALNYLGDA 60
           MNKQAIDALL KINDSA +EGNPRTKQIVNRIV+DLFYTIEDLDVQP EFWTALNYLGDA
Sbjct: 1   MNKQAIDALLNKINDSATSEGNPRTKQIVNRIVQDLFYTIEDLDVQPAEFWTALNYLGDA 60

Query: 61  GRSGELGLLAAGLGFEHFLDLRMDEAEAKAGVEGGTPRTIEGPLYVAGAPVSDGHARLDD 120
           G+SGELGLLAAGLGFEHFLDLR+DEAEAKAG+EGGTPRTIEGPLYVAGAP+SDGHARLDD
Sbjct: 61  GKSGELGLLAAGLGFEHFLDLRLDEAEAKAGIEGGTPRTIEGPLYVAGAPLSDGHARLDD 120

Query: 121 GTDPGQTLVMRGRVFGEDGKPLANALVEVWHANHLGNYSYFDKSQPAFNLRRSIRTDAEG 180
           GTDPGQTLVMRGRV GEDGKPLA+ALVEVWHANHLGNYSYFDKSQPAFNLRRSIRTDAEG
Sbjct: 121 GTDPGQTLVMRGRVLGEDGKPLAHALVEVWHANHLGNYSYFDKSQPAFNLRRSIRTDAEG 180

Query: 181 KYSFRSVVPVGYSVPPQGQTQLLLDQLGRHGHRPAHIHFFVSAPGFRKLTTQINIDGDPY 240
           KYSFRSVVPVGYSVPPQGQTQLLLDQLGRHGHRPAHIHFFVSAPGFRKLTTQINIDGDPY
Sbjct: 181 KYSFRSVVPVGYSVPPQGQTQLLLDQLGRHGHRPAHIHFFVSAPGFRKLTTQINIDGDPY 240

Query: 241 LWDDFAFATRDGLVPAVRQAE 261
           LWDDFAFATRDGLVPAV+QAE
Sbjct: 241 LWDDFAFATRDGLVPAVKQAE 261


Lambda     K      H
   0.319    0.138    0.418 

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: 420
Number of extensions: 7
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: 275
Length of database: 302
Length adjustment: 26
Effective length of query: 249
Effective length of database: 276
Effective search space:    68724
Effective search space used:    68724
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate BPHYT_RS10670 BPHYT_RS10670 (catechol 1,2-dioxygenase)
to HMM TIGR02439 (catA: catechol 1,2-dioxygenase (EC 1.13.11.1))

# 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/TIGR02439.hmm
# target sequence database:        /tmp/gapView.1327.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02439  [M=285]
Accession:   TIGR02439
Description: catechol_proteo: catechol 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.7e-144  466.0   0.0     2e-144  465.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS10670  BPHYT_RS10670 catechol 1,2-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS10670  BPHYT_RS10670 catechol 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.8   0.0    2e-144    2e-144       2     285 .]       3     283 ..       2     283 .. 0.99

  Alignments for each domain:
  == domain 1  score: 465.8 bits;  conditional E-value: 2e-144
                                TIGR02439   2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaG 71 
                                              ++ ++all+k++   +++gn+r+kqiv+r+++dlf +iedld+++ efw+a++yl+++G+++elgllaaG
  lcl|FitnessBrowser__BFirm:BPHYT_RS10670   3 KQAIDALLNKINDSATSEGNPRTKQIVNRIVQDLFYTIEDLDVQPAEFWTALNYLGDAGKSGELGLLAAG 72 
                                              689******************************************************************* PP

                                TIGR02439  72 lGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGk 141
                                              lG+ehfldlrld+a+akag+eggtPrtieGPlyvaGap+s+G+arlddg+  d ++tlv++G+vl ++Gk
  lcl|FitnessBrowser__BFirm:BPHYT_RS10670  73 LGFEHFLDLRLDEAEAKAGIEGGTPRTIEGPLYVAGAPLSDGHARLDDGT--DPGQTLVMRGRVLGEDGK 140
                                              **************************************************..668*************** PP

                                TIGR02439 142 piagakvevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrh 211
                                              p+a a vevwhan+ Gnys+fdksq  fnlrr+i+tdaeGky++rsvvPvGy+vppqg+tq ll++lGrh
  lcl|FitnessBrowser__BFirm:BPHYT_RS10670 141 PLAHALVEVWHANHLGNYSYFDKSQPAFNLRRSIRTDAEGKYSFRSVVPVGYSVPPQGQTQLLLDQLGRH 210
                                              ********************************************************************** PP

                                TIGR02439 212 GerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfaeief 281
                                              G+rPah+hffvsapg+rklttqin++gd+yl+ddfafatr+glv++vk+ e+a+ +  +gv+g+fa i+f
  lcl|FitnessBrowser__BFirm:BPHYT_RS10670 211 GHRPAHIHFFVSAPGFRKLTTQINIDGDPYLWDDFAFATRDGLVPAVKQAEGAEGKP-YGVDGNFALIDF 279
                                              ***************************************************999988.************ PP

                                TIGR02439 282 dlel 285
                                              d++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS10670 280 DFTL 283
                                              **87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (285 nodes)
Target sequences:                          1  (302 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: 00:00:00.01
# Mc/sec: 6.64
//
[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