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

GapMind for catabolism of small carbon sources

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

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 H281DRAFT_04144 H281DRAFT_04144 Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-dioxygenase apoenzyme

Query= SwissProt::Q1LK00
         (299 letters)



>FitnessBrowser__Burk376:H281DRAFT_04144
          Length = 313

 Score =  446 bits (1148), Expect = e-130
 Identities = 212/297 (71%), Positives = 247/297 (83%), Gaps = 2/297 (0%)

Query: 5   KGCPMGHG-AAPQNGDG-GDSGDTGNGWHGAQMDFARDMSYGDYLGLDQILSAQHPLSPD 62
           +GCP GHG AAP + +     G + +GWH AQ+DF+  MSYGDYL L  +L AQHPLSPD
Sbjct: 17  QGCPFGHGRAAPPSAEAPATEGASADGWHDAQLDFSESMSYGDYLSLGTVLDAQHPLSPD 76

Query: 63  HNEMLFIVQHQTTELWMKLMLHELRAARDGVKSDQLQPAFKMLARVSRIMDQLVQAWNVL 122
           HNEMLFI+QHQT+ELWMKL L+ELRAA   V  D+L PAFKMLARVSRIM+QLVQAW+VL
Sbjct: 77  HNEMLFIIQHQTSELWMKLALYELRAALGAVHRDELPPAFKMLARVSRIMEQLVQAWSVL 136

Query: 123 ATMTPPEYSAMRPYLGASSGFQSYQYREIEFILGNKNAAMLRPHAHRPEHLELVETALHT 182
           ATMTP EY++MRPYLG+SSGFQSYQYR+IEF+LGNKN  ML+PHAHR E L  V+ +L +
Sbjct: 137 ATMTPSEYTSMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHAHRAEVLAEVKASLES 196

Query: 183 PSMYDEAIRLMARRGFQIDPEVVERDWTQPTQYNASVEAAWLEVYRNPSAHWELYELGEK 242
           PS YDE ++L+ARRGF I P  + RDWTQPT ++ASVEAAWLEVYRNPS HWELYE+ E+
Sbjct: 197 PSFYDEVVKLLARRGFAISPSRLTRDWTQPTVHDASVEAAWLEVYRNPSKHWELYEMAEE 256

Query: 243 FVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRRMLDVVLFPELWKLRTDL 299
            VDLEDAFRQWRFRHVTTVER+IGFK+GTGGT G  YLR+MLDVVLFPELW +RT L
Sbjct: 257 LVDLEDAFRQWRFRHVTTVERIIGFKQGTGGTSGAPYLRKMLDVVLFPELWHVRTML 313


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: 387
Number of extensions: 5
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: 313
Length adjustment: 27
Effective length of query: 272
Effective length of database: 286
Effective search space:    77792
Effective search space used:    77792
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 H281DRAFT_04144 H281DRAFT_04144 (Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-dioxygenase apoenzyme)
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.11063.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.4e-136  439.3   0.5   2.7e-136  439.1   0.5    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04144  H281DRAFT_04144 Tryptophan 2,3-d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04144  H281DRAFT_04144 Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-di
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.1   0.5  2.7e-136  2.7e-136       1     264 []      50     313 .]      50     313 .] 1.00

  Alignments for each domain:
  == domain 1  score: 439.1 bits;  conditional E-value: 2.7e-136
                                    TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaa 66 
                                                  dfsesmsYgdYl+l ++l+aq+pls+dh+emlfi+qhq+selw+kl+l+el+aa  a+++del++a
  lcl|FitnessBrowser__Burk376:H281DRAFT_04144  50 DFSESMSYGDYLSLGTVLDAQHPLSPDHNEMLFIIQHQTSELWMKLALYELRAALGAVHRDELPPA 115
                                                  8***************************************************************** PP

                                    TIGR03036  67 lkalaRvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphe 132
                                                  +k+laRvsri+eqlv+aW+vLat+tP+ey+++R++lg+ssGfqsyqyR+iefllGnkn+++lkph+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04144 116 FKMLARVSRIMEQLVQAWSVLATMTPSEYTSMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHA 181
                                                  ****************************************************************** PP

                                    TIGR03036 133 kdpellaeleaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaeke 198
                                                  +++e+lae++a+le+Ps+Ydev++llarrGfai  ++l rd+t+p+ ++++veaawlevYr+++k+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04144 182 HRAEVLAEVKASLESPSFYDEVVKLLARRGFAISPSRLTRDWTQPTVHDASVEAAWLEVYRNPSKH 247
                                                  ****************************************************************** PP

                                    TIGR03036 199 welyelaeklvDledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                                  welye+ae+lvDled+fr+WRfrh+ttveRiiGfk+GtGG+sG+ yL+k+ldv+lfPelw+vRt l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04144 248 WELYEMAEELVDLEDAFRQWRFRHVTTVERIIGFKQGTGGTSGAPYLRKMLDVVLFPELWHVRTML 313
                                                  ***************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (313 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: 00:00:00.01
# Mc/sec: 8.18
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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