Alignments for a candidate for kynA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kynA in Halomonas desiderata SP1

Align Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (characterized)
to candidate WP_086508296.1 BZY95_RS01805 tryptophan 2,3-dioxygenase

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



>NCBI__GCF_002151265.1:WP_086508296.1
          Length = 290

 Score =  310 bits (795), Expect = 2e-89
 Identities = 154/281 (54%), Positives = 189/281 (67%), Gaps = 2/281 (0%)

Query: 11  GAGATETSDASWHDAQMDFAKDMSYGDYLALDQILNAQHPLSPEHNEMLFIVQHQTSELW 70
           G   + + D S      D  + MSYGDYL L+ +L+AQ P + EH+EMLFIV HQ SELW
Sbjct: 7   GQARSASVDLSQEGVHWD--QPMSYGDYLQLEPLLSAQRPGTAEHDEMLFIVIHQVSELW 64

Query: 71  MKLALHELRAARECVRQDQLPPAFKMLTRVSRIMEQLVQAWNVLATMTPPEYSAMRPYLG 130
           +K  LHE  AA   +  D+L PAFKMLTRV+RI  Q++ AW VL TMTP +Y+  R  LG
Sbjct: 65  LKQCLHEAHAAAAHIASDRLRPAFKMLTRVARIQAQMINAWEVLVTMTPADYARFRDSLG 124

Query: 131 MSSGFQSFQYREIEFILGNKNAAMLRPHAHQPQHLALLEEALRTPSLYDEAIRLMARRGF 190
            SSGFQSFQYRE+EF+LGNKNAAM+  H   P+    L E L  PSLYD +++L+ARRGF
Sbjct: 125 QSSGFQSFQYRELEFLLGNKNAAMIEVHRRHPERYRRLSEVLHAPSLYDISLQLLARRGF 184

Query: 191 AIDAACIERDWTRPAGENASVEAAWLEVYRKPEAHWELYELGEKFVDLEDAFRQWRFRHV 250
           A+  + + RDW+ P      VE AW ++YR    +WELYEL EK VD E  F QWRF H+
Sbjct: 185 ALPDSVVARDWSEPYRPCDEVEQAWADIYRDTGRYWELYELAEKLVDTEYHFHQWRFSHL 244

Query: 251 TTVERVIGFKRGTGGTEGVSYLRKMLDVVLFPELWKLRTDL 291
            TVER+IG K GTGGT G SYL K LD+  FPELW +RT L
Sbjct: 245 KTVERIIGQKPGTGGTGGASYLAKALDLQFFPELWSVRTTL 285


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: 338
Number of extensions: 10
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: 290
Length adjustment: 26
Effective length of query: 265
Effective length of database: 264
Effective search space:    69960
Effective search space used:    69960
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 WP_086508296.1 BZY95_RS01805 (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.31398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-124  401.0   0.3   1.3e-124  400.8   0.3    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086508296.1  BZY95_RS01805 tryptophan 2,3-dio


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508296.1  BZY95_RS01805 tryptophan 2,3-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.8   0.3  1.3e-124  1.3e-124       3     264 .]      24     285 ..      22     285 .. 0.99

  Alignments for each domain:
  == domain 1  score: 400.8 bits;  conditional E-value: 1.3e-124
                                 TIGR03036   3 sesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaalkala 71 
                                               ++ msYgdYl+l+ llsaq+p + +hdemlfiv+hqvselwlk  lhe +aaa+++ +d+l++a+k+l+
  lcl|NCBI__GCF_002151265.1:WP_086508296.1  24 DQPMSYGDYLQLEPLLSAQRPGTAEHDEMLFIVIHQVSELWLKQCLHEAHAAAAHIASDRLRPAFKMLT 92 
                                               678****************************************************************** PP

                                 TIGR03036  72 RvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpellae 140
                                               Rv+ri+ q+++aW+vL t+tPa+y++fR++lg+ssGfqs+qyRe+efllGnknaa++++h+++pe +++
  lcl|NCBI__GCF_002151265.1:WP_086508296.1  93 RVARIQAQMINAWEVLVTMTPADYARFRDSLGQSSGFQSFQYRELEFLLGNKNAAMIEVHRRHPERYRR 161
                                               ********************************************************************* PP

                                 TIGR03036 141 leaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklv 209
                                               l+++l++PslYd +l+llarrGfa+p++v+ rd+++p++ ++eve+aw  +Yrd+ ++welyelaeklv
  lcl|NCBI__GCF_002151265.1:WP_086508296.1 162 LSEVLHAPSLYDISLQLLARRGFALPDSVVARDWSEPYRPCDEVEQAWADIYRDTGRYWELYELAEKLV 230
                                               ********************************************************************* PP

                                 TIGR03036 210 DledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264
                                               D+e +f++WRf hl+tveRiiG k GtGG+ G++yL kald ++fPelw+vRt+l
  lcl|NCBI__GCF_002151265.1:WP_086508296.1 231 DTEYHFHQWRFSHLKTVERIIGQKPGTGGTGGASYLAKALDLQFFPELWSVRTTL 285
                                               *****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (264 nodes)
Target sequences:                          1  (290 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: 00:00:00.01
# Mc/sec: 7.47
//
[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 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