Alignments for a candidate for kynA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Cupriavidus basilensis 4G11

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate RR42_RS15390 RR42_RS15390 tryptophan 2,3-dioxygenase

Query= reanno::Cup4G11:RR42_RS15390
         (291 letters)



>FitnessBrowser__Cup4G11:RR42_RS15390
          Length = 291

 Score =  598 bits (1542), Expect = e-176
 Identities = 291/291 (100%), Positives = 291/291 (100%)

Query: 1   MSNHKGCPMSGAGATETSDASWHDAQMDFAKDMSYGDYLALDQILNAQHPLSPEHNEMLF 60
           MSNHKGCPMSGAGATETSDASWHDAQMDFAKDMSYGDYLALDQILNAQHPLSPEHNEMLF
Sbjct: 1   MSNHKGCPMSGAGATETSDASWHDAQMDFAKDMSYGDYLALDQILNAQHPLSPEHNEMLF 60

Query: 61  IVQHQTSELWMKLALHELRAARECVRQDQLPPAFKMLTRVSRIMEQLVQAWNVLATMTPP 120
           IVQHQTSELWMKLALHELRAARECVRQDQLPPAFKMLTRVSRIMEQLVQAWNVLATMTPP
Sbjct: 61  IVQHQTSELWMKLALHELRAARECVRQDQLPPAFKMLTRVSRIMEQLVQAWNVLATMTPP 120

Query: 121 EYSAMRPYLGMSSGFQSFQYREIEFILGNKNAAMLRPHAHQPQHLALLEEALRTPSLYDE 180
           EYSAMRPYLGMSSGFQSFQYREIEFILGNKNAAMLRPHAHQPQHLALLEEALRTPSLYDE
Sbjct: 121 EYSAMRPYLGMSSGFQSFQYREIEFILGNKNAAMLRPHAHQPQHLALLEEALRTPSLYDE 180

Query: 181 AIRLMARRGFAIDAACIERDWTRPAGENASVEAAWLEVYRKPEAHWELYELGEKFVDLED 240
           AIRLMARRGFAIDAACIERDWTRPAGENASVEAAWLEVYRKPEAHWELYELGEKFVDLED
Sbjct: 181 AIRLMARRGFAIDAACIERDWTRPAGENASVEAAWLEVYRKPEAHWELYELGEKFVDLED 240

Query: 241 AFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRKMLDVVLFPELWKLRTDL 291
           AFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRKMLDVVLFPELWKLRTDL
Sbjct: 241 AFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRKMLDVVLFPELWKLRTDL 291


Lambda     K      H
   0.322    0.134    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: 509
Number of extensions: 9
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: 291
Length of database: 291
Length adjustment: 26
Effective length of query: 265
Effective length of database: 265
Effective search space:    70225
Effective search space used:    70225
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: 48 (23.1 bits)

Align candidate RR42_RS15390 RR42_RS15390 (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.8672.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.8e-141  455.0   0.3   4.3e-141  454.9   0.3    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS15390  RR42_RS15390 tryptophan 2,3-diox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS15390  RR42_RS15390 tryptophan 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  454.9   0.3  4.3e-141  4.3e-141       1     264 []      28     291 .]      28     291 .] 1.00

  Alignments for each domain:
  == domain 1  score: 454.9 bits;  conditional E-value: 4.3e-141
                                 TIGR03036   1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaalka 69 
                                               df+++msYgdYl+ld++l+aq+pls++h+emlfivqhq+selw+kl+lhel+aa++++r+d+l++a+k+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15390  28 DFAKDMSYGDYLALDQILNAQHPLSPEHNEMLFIVQHQTSELWMKLALHELRAARECVRQDQLPPAFKM 96 
                                               8******************************************************************** PP

                                 TIGR03036  70 laRvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpell 138
                                               l+Rvsri+eqlv+aW+vLat+tP eys++R++lg ssGfqs+qyReief+lGnknaa+l+ph+++p++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS15390  97 LTRVSRIMEQLVQAWNVLATMTPPEYSAMRPYLGMSSGFQSFQYREIEFILGNKNAAMLRPHAHQPQHL 165
                                               ********************************************************************* PP

                                 TIGR03036 139 aeleaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaek 207
                                               a le+al++PslYde++rl+arrGfai+a+++erd+t+pa +n++veaawlevYr++e++welyel+ek
  lcl|FitnessBrowser__Cup4G11:RR42_RS15390 166 ALLEEALRTPSLYDEAIRLMARRGFAIDAACIERDWTRPAGENASVEAAWLEVYRKPEAHWELYELGEK 234
                                               ********************************************************************* PP

                                 TIGR03036 208 lvDledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                               +vDled+fr+WRfrh+ttveR+iGfkrGtGG++Gv+yL+k+ldv+lfPelwk+Rt+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS15390 235 FVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRKMLDVVLFPELWKLRTDL 291
                                               *******************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (291 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.11
//
[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