Alignments for a candidate for kynA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Pseudomonas fluorescens GW456-L13

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate PfGW456L13_4292 Tryptophan 2,3-dioxygenase (EC 1.13.11.11)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4292
         (284 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292
          Length = 284

 Score =  582 bits (1500), Expect = e-171
 Identities = 284/284 (100%), Positives = 284/284 (100%)

Query: 1   MSQCPYSPANQTEEWHNAELNFSDSMSYGDYLDLGRILSAQHPLSPDHNEMLFIIQHQTS 60
           MSQCPYSPANQTEEWHNAELNFSDSMSYGDYLDLGRILSAQHPLSPDHNEMLFIIQHQTS
Sbjct: 1   MSQCPYSPANQTEEWHNAELNFSDSMSYGDYLDLGRILSAQHPLSPDHNEMLFIIQHQTS 60

Query: 61  ELWMKLMLHELNAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYHAIRP 120
           ELWMKLMLHELNAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYHAIRP
Sbjct: 61  ELWMKLMLHELNAAREHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYHAIRP 120

Query: 121 FLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLQALEKAIATPSLYDEAIRLMAS 180
           FLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLQALEKAIATPSLYDEAIRLMAS
Sbjct: 121 FLGQSSGFQSFQYREIEFILGNKSATLLRPHAHRPELLQALEKAIATPSLYDEAIRLMAS 180

Query: 181 AGLTIDPQRFERDPTSPTAHDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFRQWRF 240
           AGLTIDPQRFERDPTSPTAHDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFRQWRF
Sbjct: 181 AGLTIDPQRFERDPTSPTAHDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFRQWRF 240

Query: 241 RHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 284
           RHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL
Sbjct: 241 RHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 284


Lambda     K      H
   0.321    0.135    0.416 

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: 460
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: 284
Length of database: 284
Length adjustment: 26
Effective length of query: 258
Effective length of database: 258
Effective search space:    66564
Effective search space used:    66564
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 PfGW456L13_4292 (Tryptophan 2,3-dioxygenase (EC 1.13.11.11))
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.13159.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     6e-133  428.2   0.0   6.8e-133  428.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292  Tryptophan 2,3-dioxygenase (EC 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292  Tryptophan 2,3-dioxygenase (EC 1.13.11.11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.0   0.0  6.8e-133  6.8e-133       1     264 []      21     284 .]      21     284 .] 0.99

  Alignments for each domain:
  == domain 1  score: 428.0 bits;  conditional E-value: 6.8e-133
                                               TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaa 55 
                                                             +fs+smsYgdYl+l ++lsaq+pls+dh+emlfi+qhq+selw+kl+lhel+aa+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292  21 NFSDSMSYGDYLDLGRILSAQHPLSPDHNEMLFIIQHQTSELWMKLMLHELNAAR 75 
                                                             69***************************************************** PP

                                               TIGR03036  56 ralradeleaalkalaRvsrileqlveaWdvLatltPaeysefRealgessGfqs 110
                                                             +++r +el++a+k+laRvsri++qlv+aW+vLat+tP+ey+++R++lg+ssGfqs
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292  76 EHVRLGELPPAFKMLARVSRIFDQLVHAWTVLATMTPTEYHAIRPFLGQSSGFQS 130
                                                             ******************************************************* PP

                                               TIGR03036 111 yqyReiefllGnknaallkphekdpellaeleaaleePslYdevlrllarrGfai 165
                                                             +qyReief+lGnk+a+ll+ph+++pell+ le+a+++PslYde++rl+a +G++i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292 131 FQYREIEFILGNKSATLLRPHAHRPELLQALEKAIATPSLYDEAIRLMASAGLTI 185
                                                             ******************************************************* PP

                                               TIGR03036 166 paevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklvDledlfrrWRf 220
                                                             + ++ erd t+p+ ++++veaaw+ vY+d++++w+ly+laekl+Dled+fr+WRf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292 186 DPQRFERDPTSPTAHDASVEAAWRVVYTDPSRYWDLYQLAEKLIDLEDSFRQWRF 240
                                                             ******************************************************* PP

                                               TIGR03036 221 rhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                                             rh+ttveRiiGf+ GtGG++Gv yL+k+ld++lfPelw+vR++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4292 241 RHVTTVERIIGFQPGTGGTEGVGYLRKMLDTVLFPELWRVRSTL 284
                                                             *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (284 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: 11.07
//
[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