Alignments for a candidate for kynA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Pseudomonas fluorescens FW300-N2E3

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate AO353_05970 AO353_05970 tryptophan 2,3-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_05970
         (288 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05970
          Length = 288

 Score =  589 bits (1519), Expect = e-173
 Identities = 288/288 (100%), Positives = 288/288 (100%)

Query: 1   MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ 60
           MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ
Sbjct: 1   MSQCPYSSDQSPSNPPEEWHNAELNFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQ 60

Query: 61  HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH 120
           HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH
Sbjct: 61  HQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYH 120

Query: 121 AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR 180
           AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR
Sbjct: 121 AIRPFLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLAELEKAIATPSLYDESIR 180

Query: 181 LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR 240
           LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR
Sbjct: 181 LMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFR 240

Query: 241 QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 288
           QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL
Sbjct: 241 QWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 288


Lambda     K      H
   0.320    0.135    0.414 

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: 486
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: 288
Length of database: 288
Length adjustment: 26
Effective length of query: 262
Effective length of database: 262
Effective search space:    68644
Effective search space used:    68644
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: 47 (22.7 bits)

Align candidate AO353_05970 AO353_05970 (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.22228.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.9e-132  426.5   0.0   2.2e-132  426.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970  AO353_05970 tryptophan 2,3-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970  AO353_05970 tryptophan 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.3   0.0  2.2e-132  2.2e-132       1     264 []      25     288 .]      25     288 .] 0.99

  Alignments for each domain:
  == domain 1  score: 426.3 bits;  conditional E-value: 2.2e-132
                                     TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradelea 65 
                                                   +fs+smsYgdYl+l ++lsaq+pls+dh+emlfi+qhq+selw+kl+lhel+aa++++r +el++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970  25 NFSDSMSYGDYLDLGKILSAQHPLSPDHNEMLFIIQHQTSELWMKLMLHELKAAREHVRLGELPP 89 
                                                   69*************************************************************** PP

                                     TIGR03036  66 alkalaRvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkp 130
                                                   a+k+laRvsri++qlv+aW+vLat+tP+ey+++R++lg+ssGfqs+qyReief+lGnk+a+ll+p
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970  90 AFKMLARVSRIFDQLVHAWTVLATMTPTEYHAIRPFLGQSSGFQSFQYREIEFILGNKSATLLRP 154
                                                   ***************************************************************** PP

                                     TIGR03036 131 hekdpellaeleaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrda 195
                                                   h+++pellaele+a+++PslYde++rl+  +G+ai+ ++ erd ++p+ ++++veaaw+ vY+d+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970 155 HAHRPELLAELEKAIATPSLYDESIRLMVSAGLAIDPQRFERDPASPTAYDASVEAAWRVVYTDP 219
                                                   ***************************************************************** PP

                                     TIGR03036 196 ekewelyelaeklvDledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkv 260
                                                   +++w+ly+laekl+Dled+fr+WRfrh+ttveRiiGf+ GtGG++Gv yL+k+ld++lfPelw+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970 220 SRYWDLYQLAEKLIDLEDSFRQWRFRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRV 284
                                                   ***************************************************************** PP

                                     TIGR03036 261 Rtel 264
                                                   R++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05970 285 RSTL 288
                                                   *986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (288 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: 11.34
//
[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