Alignments for a candidate for nbaC in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for nbaC in Stenotrophomonas chelatiphaga DSM 21508

Align 3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6) (characterized)
to candidate WP_057507930.1 ABB28_RS06855 3-hydroxyanthranilate 3,4-dioxygenase

Query= metacyc::MONOMER-15634
         (181 letters)



>NCBI__GCF_001431535.1:WP_057507930.1
          Length = 170

 Score =  164 bits (415), Expect = 8e-46
 Identities = 76/167 (45%), Positives = 109/167 (65%), Gaps = 2/167 (1%)

Query: 6   IQKPINLWKFIEEHKDQLKPPVNNKVIWKDAEIMVMLLGGPNKRRDFHVDPSEELFYQLK 65
           +  PINL  ++EEH+  LKPPV NK+I +D + +VM++GGPN R DFH+D   E FYQL+
Sbjct: 2   LASPINLMGWVEEHRHLLKPPVGNKMI-EDGDFIVMVVGGPNSRTDFHIDEGPEWFYQLE 60

Query: 66  GDCYVEIINNEGKREVITVREGEMFLLPPNVPHSPHRVADTIGIVIERNRKKGELESFVW 125
           G+  +++   +G+   I +R GE+FLLP NVPHSP R A  IG+V+ER R   E +  VW
Sbjct: 61  GEMVLKV-QEDGQVRDIPIRAGEIFLLPGNVPHSPRRPAGGIGLVVERKRLPHERDGVVW 119

Query: 126 YCDKCDHMMHRVTIQLTNIEVQVKQAIEEFNSSLELRTCKNCGYVMP 172
           +C++C+H +H     L NIE  + +    +   L+LRTC  CG+V P
Sbjct: 120 HCERCNHKLHEEWFTLQNIETDLPKVFARYQGDLQLRTCSACGHVDP 166


Lambda     K      H
   0.320    0.137    0.430 

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: 148
Number of extensions: 9
Number of successful extensions: 3
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: 181
Length of database: 170
Length adjustment: 19
Effective length of query: 162
Effective length of database: 151
Effective search space:    24462
Effective search space used:    24462
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 (21.8 bits)
S2: 44 (21.6 bits)

Align candidate WP_057507930.1 ABB28_RS06855 (3-hydroxyanthranilate 3,4-dioxygenase)
to HMM TIGR03037 (nbaC: 3-hydroxyanthranilate 3,4-dioxygenase (EC 1.13.11.6))

# 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/TIGR03037.hmm
# target sequence database:        /tmp/gapView.4148215.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03037  [M=159]
Accession:   TIGR03037
Description: anthran_nbaC: 3-hydroxyanthranilate 3,4-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.4e-77  245.2   0.1    1.6e-77  245.1   0.1    1.0  1  NCBI__GCF_001431535.1:WP_057507930.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001431535.1:WP_057507930.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   0.1   1.6e-77   1.6e-77       1     159 []       6     163 ..       6     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 1.6e-77
                             TIGR03037   1 lnlkkwidehkellkppvgnkqiwqdselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvleeGkvedvp 73 
                                           +nl  w++eh++llkppvgnk+i +d ++iv+vvGGpn rtdfh+de++e+fyql+Gemvlkv+e+G+v+d+p
  NCBI__GCF_001431535.1:WP_057507930.1   6 INLMGWVEEHRHLLKPPVGNKMI-EDGDFIVMVVGGPNSRTDFHIDEGPEWFYQLEGEMVLKVQEDGQVRDIP 77 
                                           799********************.************************************************* PP

                             TIGR03037  74 ireGdifllppkvphspqraagsiglvierkrkegeldalqwfcaecgeklyraevklesivkdlppvfekfy 146
                                           ir+G+ifllp +vphsp+r+ag iglv+erkr ++e+d+++w+c++c++kl+++ ++l++i++dlp+vf ++ 
  NCBI__GCF_001431535.1:WP_057507930.1  78 IRAGEIFLLPGNVPHSPRRPAGGIGLVVERKRLPHERDGVVWHCERCNHKLHEEWFTLQNIETDLPKVFARYQ 150
                                           ************************************************************************* PP

                             TIGR03037 147 ssedartckkcGe 159
                                           ++ ++rtc+ cG+
  NCBI__GCF_001431535.1:WP_057507930.1 151 GDLQLRTCSACGH 163
                                           ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (159 nodes)
Target sequences:                          1  (170 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: 11.95
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 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