Alignments for a candidate for kynA in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Nocardioides daejeonensis MJ31

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 WP_110206803.1 DNK54_RS09975 tryptophan 2,3-dioxygenase

Query= SwissProt::Q8PDA8
         (298 letters)



>NCBI__GCF_003194585.1:WP_110206803.1
          Length = 282

 Score =  332 bits (850), Expect = 8e-96
 Identities = 165/282 (58%), Positives = 203/282 (71%)

Query: 1   MPVDKNLRDLEPGIHTDLEGRLTYGGYLRLDQLLSAQQPLSEPAHHDEMLFIIQHQTSEL 60
           M    N R+LE  + TD   R++YGGYL L  LLSAQ+PLS+P HHDE+LFI+QHQT+EL
Sbjct: 1   MGAQDNTRELEESVVTDFSDRMSYGGYLDLGTLLSAQRPLSDPEHHDELLFIVQHQTTEL 60

Query: 61  WLKLLAHELRAAIVHLQRDEVWQCRKVLARSKQVLRQLTEQWSVLETLTPSEYMGFRDVL 120
           WLKL+ HEL AA   LQ+DE+    K +AR K V + L +QWSVL TLTPSEY+ FR VL
Sbjct: 61  WLKLVLHELTAACRWLQQDELGHALKAIARVKHVQKTLADQWSVLATLTPSEYVEFRGVL 120

Query: 121 GPSSGFQSLQYRYIEFLLGNKNPQMLQVFAYDPAGQARLREVLEAPSLYEEFLRYLARFG 180
           G SSGFQS QYR +EF LGNKN  ML+VF  DPA Q  +R  LEAPSLY+EFLR+L R G
Sbjct: 121 GNSSGFQSWQYRAVEFTLGNKNAAMLKVFDADPAAQTMVRAALEAPSLYDEFLRHLGRRG 180

Query: 181 HAIPQQYQARDWTAAHVADDTLRPVFERIYENTDRYWREYSLCEDLVDVETQFQLWRFRH 240
           + +P++ ++RD T A      L PVF  IY +   +W  Y  CE+LVD+E  FQLWRFRH
Sbjct: 181 YPVPEEIRSRDVTRAWTFRPDLVPVFTAIYADAQTHWSAYETCEELVDLEDNFQLWRFRH 240

Query: 241 MRTVMRVIGFKRGTGGSSGVGFLQQALALTFFPELFDVRTSV 282
           ++TV R+IG K GTGGSSG  FL++AL LTFFPEL+ VRT +
Sbjct: 241 LKTVERIIGMKGGTGGSSGAPFLRRALDLTFFPELYAVRTQL 282


Lambda     K      H
   0.323    0.138    0.423 

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: 290
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: 298
Length of database: 282
Length adjustment: 26
Effective length of query: 272
Effective length of database: 256
Effective search space:    69632
Effective search space used:    69632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate WP_110206803.1 DNK54_RS09975 (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.844015.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-122  393.6   0.0   2.3e-122  393.5   0.0    1.0  1  NCBI__GCF_003194585.1:WP_110206803.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003194585.1:WP_110206803.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.5   0.0  2.3e-122  2.3e-122       1     264 []      17     282 .]      17     282 .] 0.99

  Alignments for each domain:
  == domain 1  score: 393.5 bits;  conditional E-value: 2.3e-122
                             TIGR03036   1 dfsesmsYgdYlkldellsaqkpls..edhdemlfivqhqvselwlklilheleaaaralradeleaalkala 71 
                                           dfs++msYg Yl+l +llsaq+pls  e+hde+lfivqhq++elwlkl+lhel+aa r+l++del  alka+a
  NCBI__GCF_003194585.1:WP_110206803.1  17 DFSDRMSYGGYLDLGTLLSAQRPLSdpEHHDELLFIVQHQTTELWLKLVLHELTAACRWLQQDELGHALKAIA 89 
                                           8************************888********************************************* PP

                             TIGR03036  72 RvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpellaeleaa 144
                                           Rv++++++l+++W+vLatltP+ey efR  lg+ssGfqs+qyR++ef lGnknaa+lk++++dp +++ ++aa
  NCBI__GCF_003194585.1:WP_110206803.1  90 RVKHVQKTLADQWSVLATLTPSEYVEFRGVLGNSSGFQSWQYRAVEFTLGNKNAAMLKVFDADPAAQTMVRAA 162
                                           ************************************************************************* PP

                             TIGR03036 145 leePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklvDledlfrr 217
                                           le+PslYde+lr l rrG+++p+e+ +rdvt++++++++++ +++++Y+da+++w++ye +e+lvDled+f+ 
  NCBI__GCF_003194585.1:WP_110206803.1 163 LEAPSLYDEFLRHLGRRGYPVPEEIRSRDVTRAWTFRPDLVPVFTAIYADAQTHWSAYETCEELVDLEDNFQL 235
                                           ************************************************************************* PP

                             TIGR03036 218 WRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                           WRfrhl+tveRiiG+k GtGGssG+ +L++ald ++fPel++vRt+l
  NCBI__GCF_003194585.1:WP_110206803.1 236 WRFRHLKTVERIIGMKGGTGGSSGAPFLRRALDLTFFPELYAVRTQL 282
                                           *********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (282 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: 12.44
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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