Aligments for a candidate for kynA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for kynA in Pseudomonas simiae WCS417

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate GFF4633 PS417_23705 tryptophan 2,3-dioxygenase

Query= reanno::WCS417:GFF4633
         (285 letters)



>FitnessBrowser__WCS417:GFF4633
          Length = 285

 Score =  582 bits (1501), Expect = e-171
 Identities = 285/285 (100%), Positives = 285/285 (100%)

Query: 1   MSQCPFSADYQPPEEWHNAELNFSESMSYGDYLDLGKVLSAQHPLSPDHNEMLFIIQHQT 60
           MSQCPFSADYQPPEEWHNAELNFSESMSYGDYLDLGKVLSAQHPLSPDHNEMLFIIQHQT
Sbjct: 1   MSQCPFSADYQPPEEWHNAELNFSESMSYGDYLDLGKVLSAQHPLSPDHNEMLFIIQHQT 60

Query: 61  SELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWAVLATMTPSEYKSIR 120
           SELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWAVLATMTPSEYKSIR
Sbjct: 61  SELWMKLMLHELKAAREHVRLGELPPAFKMLARVSRIFDQLVHAWAVLATMTPSEYKSIR 120

Query: 121 PFLGQSSGFQSFQYREIEFILGNKSAALLRPHAHRPELLNELKVAIATPSLYDEAINLMI 180
           PFLGQSSGFQSFQYREIEFILGNKSAALLRPHAHRPELLNELKVAIATPSLYDEAINLMI
Sbjct: 121 PFLGQSSGFQSFQYREIEFILGNKSAALLRPHAHRPELLNELKVAIATPSLYDEAINLMI 180

Query: 181 QAGLAIDPKRAERDPTAATVHDESVEAAWREVYRDPSRYWDLYQLAEKFIDLEDSFRQWR 240
           QAGLAIDPKRAERDPTAATVHDESVEAAWREVYRDPSRYWDLYQLAEKFIDLEDSFRQWR
Sbjct: 181 QAGLAIDPKRAERDPTAATVHDESVEAAWREVYRDPSRYWDLYQLAEKFIDLEDSFRQWR 240

Query: 241 FRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 285
           FRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL
Sbjct: 241 FRHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 285


Lambda     K      H
   0.321    0.135    0.415 

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: 469
Number of extensions: 5
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: 285
Length of database: 285
Length adjustment: 26
Effective length of query: 259
Effective length of database: 259
Effective search space:    67081
Effective search space used:    67081
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate GFF4633 PS417_23705 (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.22162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-131  424.1   0.0   1.2e-131  423.9   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4633  PS417_23705 tryptophan 2,3-dioxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4633  PS417_23705 tryptophan 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.9   0.0  1.2e-131  1.2e-131       1     264 []      22     285 .]      22     285 .] 1.00

  Alignments for each domain:
  == domain 1  score: 423.9 bits;  conditional E-value: 1.2e-131
                           TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaalkalaRvsr 75 
                                         +fsesmsYgdYl+l ++lsaq+pls+dh+emlfi+qhq+selw+kl+lhel+aa++++r +el++a+k+laRvsr
  lcl|FitnessBrowser__WCS417:GFF4633  22 NFSESMSYGDYLDLGKVLSAQHPLSPDHNEMLFIIQHQTSELWMKLMLHELKAAREHVRLGELPPAFKMLARVSR 96 
                                         69************************************************************************* PP

                           TIGR03036  76 ileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpellaeleaaleePsl 150
                                         i++qlv+aW vLat+tP+ey+++R++lg+ssGfqs+qyReief+lGnk+aall+ph+++pell+el+ a+++Psl
  lcl|FitnessBrowser__WCS417:GFF4633  97 IFDQLVHAWAVLATMTPSEYKSIRPFLGQSSGFQSFQYREIEFILGNKSAALLRPHAHRPELLNELKVAIATPSL 171
                                         *************************************************************************** PP

                           TIGR03036 151 YdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklvDledlfrrWRfrhltt 225
                                         Yde+++l+ ++G+ai+ ++ erd t ++ ++e+veaaw+evYrd++++w+ly+laek++Dled+fr+WRfrh+tt
  lcl|FitnessBrowser__WCS417:GFF4633 172 YDEAINLMIQAGLAIDPKRAERDPTAATVHDESVEAAWREVYRDPSRYWDLYQLAEKFIDLEDSFRQWRFRHVTT 246
                                         *************************************************************************** PP

                           TIGR03036 226 veRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                         veRiiGf+ GtGG++Gv yL+k+ld++lfPelw+vR++l
  lcl|FitnessBrowser__WCS417:GFF4633 247 VERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 285
                                         ************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (285 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.51
//
[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, or view the source code.

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