Alignments for a candidate for kynA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Burkholderia phytofirmans PsJN

Align Tryptophan 2,3-dioxygenase; TDO; Tryptamin 2,3-dioxygenase; Tryptophan oxygenase; TO; TRPO; Tryptophan pyrrolase; Tryptophanase; EC 1.13.11.11 (characterized)
to candidate BPHYT_RS16035 BPHYT_RS16035 tryptophan 2,3-dioxygenase

Query= SwissProt::Q1LK00
         (299 letters)



>FitnessBrowser__BFirm:BPHYT_RS16035
          Length = 310

 Score =  448 bits (1153), Expect = e-131
 Identities = 212/295 (71%), Positives = 246/295 (83%), Gaps = 1/295 (0%)

Query: 5   KGCPMGHGAAPQNGDGGDSGDTGNGWHGAQMDFARDMSYGDYLGLDQILSAQHPLSPDHN 64
           +GCP GHGA   +     + D+G+GWH AQ+DF+  MSYGDYL L  +L AQHPLSPDHN
Sbjct: 17  QGCPFGHGAVASSV-ATPAADSGDGWHDAQLDFSESMSYGDYLSLGTVLDAQHPLSPDHN 75

Query: 65  EMLFIVQHQTTELWMKLMLHELRAARDGVKSDQLQPAFKMLARVSRIMDQLVQAWNVLAT 124
           EMLFI+QHQT+ELWMKL L+ELRAA   V  D+L PAFKMLARVSRIM+QLVQAW+VLAT
Sbjct: 76  EMLFIIQHQTSELWMKLALYELRAALQAVHRDELPPAFKMLARVSRIMEQLVQAWSVLAT 135

Query: 125 MTPPEYSAMRPYLGASSGFQSYQYREIEFILGNKNAAMLRPHAHRPEHLELVETALHTPS 184
           MTP EY+AMRPYLG+SSGFQSYQYR+IEF+LGNKN  ML+PHAHR + L  V+ +L  PS
Sbjct: 136 MTPSEYTAMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHAHRADVLAEVKASLEAPS 195

Query: 185 MYDEAIRLMARRGFQIDPEVVERDWTQPTQYNASVEAAWLEVYRNPSAHWELYELGEKFV 244
            YDE +RL+ARRGF I    +ERDWTQPT ++ASVEAAWLEVYRNPS HWELYE+ E+ V
Sbjct: 196 FYDEVVRLLARRGFAISAARLERDWTQPTVHDASVEAAWLEVYRNPSQHWELYEMAEELV 255

Query: 245 DLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRRMLDVVLFPELWKLRTDL 299
           DLEDAFRQWRFRHVTTVER+IGFK+GTGGT G +YLR+MLDVVLFPELW +RT L
Sbjct: 256 DLEDAFRQWRFRHVTTVERIIGFKQGTGGTSGATYLRKMLDVVLFPELWHVRTML 310


Lambda     K      H
   0.321    0.136    0.424 

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: 390
Number of extensions: 7
Number of successful extensions: 2
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: 299
Length of database: 310
Length adjustment: 27
Effective length of query: 272
Effective length of database: 283
Effective search space:    76976
Effective search space used:    76976
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: 48 (23.1 bits)

Align candidate BPHYT_RS16035 BPHYT_RS16035 (tryptophan 2,3-dioxygenase)
to HMM TIGR03036 (kynA: tryptophan 2,3-dioxygenase (EC 1.13.11.11))

# 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/TIGR03036.hmm
# target sequence database:        /tmp/gapView.32110.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03036  [M=264]
Accession:   TIGR03036
Description: trp_2_3_diox: tryptophan 2,3-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     5e-138  444.8   1.7   5.7e-138  444.6   1.7    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS16035  BPHYT_RS16035 tryptophan 2,3-dio


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS16035  BPHYT_RS16035 tryptophan 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.6   1.7  5.7e-138  5.7e-138       1     264 []      47     310 .]      47     310 .] 1.00

  Alignments for each domain:
  == domain 1  score: 444.6 bits;  conditional E-value: 5.7e-138
                                TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaalkal 70 
                                              dfsesmsYgdYl+l ++l+aq+pls+dh+emlfi+qhq+selw+kl+l+el+aa +a+++del++a+k+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS16035  47 DFSESMSYGDYLSLGTVLDAQHPLSPDHNEMLFIIQHQTSELWMKLALYELRAALQAVHRDELPPAFKML 116
                                              8********************************************************************* PP

                                TIGR03036  71 aRvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpellae 140
                                              aRvsri+eqlv+aW+vLat+tP+ey+++R++lg+ssGfqsyqyR+iefllGnkn+++lkph++++++lae
  lcl|FitnessBrowser__BFirm:BPHYT_RS16035 117 ARVSRIMEQLVQAWSVLATMTPSEYTAMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHAHRADVLAE 186
                                              ********************************************************************** PP

                                TIGR03036 141 leaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklvD 210
                                              ++a+le+Ps+Ydev+rllarrGfai a++lerd+t+p+ ++++veaawlevYr+++++welye+ae+lvD
  lcl|FitnessBrowser__BFirm:BPHYT_RS16035 187 VKASLEAPSFYDEVVRLLARRGFAISAARLERDWTQPTVHDASVEAAWLEVYRNPSQHWELYEMAEELVD 256
                                              ********************************************************************** PP

                                TIGR03036 211 ledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                              led+fr+WRfrh+ttveRiiGfk+GtGG+sG++yL+k+ldv+lfPelw+vRt l
  lcl|FitnessBrowser__BFirm:BPHYT_RS16035 257 LEDAFRQWRFRHVTTVERIIGFKQGTGGTSGATYLRKMLDVVLFPELWHVRTML 310
                                              ***************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (310 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 8.94
//
[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