Alignments for a candidate for nbaC in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for nbaC in Cupriavidus basilensis 4G11

Align 3-hydroxyanthranilate 3,4-dioxygenase; 3-hydroxyanthranilate oxygenase; 3-HAO; 3-hydroxyanthranilic acid dioxygenase; HAD; EC 1.13.11.6 (characterized)
to candidate RR42_RS05080 RR42_RS05080 3-hydroxyanthranilate 3,4-dioxygenase

Query= SwissProt::Q83V26
         (185 letters)



>FitnessBrowser__Cup4G11:RR42_RS05080
          Length = 186

 Score =  299 bits (765), Expect = 2e-86
 Identities = 136/179 (75%), Positives = 157/179 (87%)

Query: 2   MFTFGKPLNFQRWLDDHSDLLRPPVGNQQVWQDSDFIVTVVGGPNFRTDFHDDPMEEFFY 61
           MF +G PLNF RWLD+H+ LL+PPVGNQQVWQD+D IVTVVGGPN RTDFHDDP+EEFFY
Sbjct: 1   MFIYGMPLNFPRWLDEHAHLLKPPVGNQQVWQDADTIVTVVGGPNQRTDFHDDPLEEFFY 60

Query: 62  QFKGNAYLNIMDRGQMDRVELKEGDIFLLPPHLRHSPQRPEAGSRCLVIERQRPKGMLDG 121
           QFKGNA+L+IMDRG+ +RV+LKEGDIFLLP H+RHSPQRPEA SRCLVIERQRP+G++DG
Sbjct: 61  QFKGNAWLDIMDRGKRERVDLKEGDIFLLPAHVRHSPQRPEADSRCLVIERQRPEGVVDG 120

Query: 122 FEWYCLSCNGLVYRVDVQLNSIVTDLPPLFDIFYGNVGLRKCPQCGQVHPGKAAIEAVA 180
           FEWYC +C+ LVYRV+VQL SIVTDLPPLF  FY N  LR+C QCG VHPG+A+  A A
Sbjct: 121 FEWYCPACSALVYRVEVQLKSIVTDLPPLFAGFYDNAALRRCGQCGTVHPGRASAPAPA 179


Lambda     K      H
   0.325    0.145    0.475 

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: 198
Number of extensions: 6
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: 185
Length of database: 186
Length adjustment: 19
Effective length of query: 166
Effective length of database: 167
Effective search space:    27722
Effective search space used:    27722
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 44 (21.6 bits)

Align candidate RR42_RS05080 RR42_RS05080 (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.24336.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      1e-79  252.2   0.0    1.2e-79  252.0   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS05080  RR42_RS05080 3-hydroxyanthranila


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS05080  RR42_RS05080 3-hydroxyanthranilate 3,4-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.0   0.0   1.2e-79   1.2e-79       1     159 []       8     167 ..       8     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 252.0 bits;  conditional E-value: 1.2e-79
                                 TIGR03037   1 lnlkkwidehkellkppvgnkqiwqdselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvleeGkv 69 
                                               ln+ +w+deh++llkppvgn+q+wqd++ ivtvvGGpn+rtdfh+d+ eeffyq+kG++ l +++ Gk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05080   8 LNFPRWLDEHAHLLKPPVGNQQVWQDADTIVTVVGGPNQRTDFHDDPLEEFFYQFKGNAWLDIMDRGKR 76 
                                               79******************************************************************* PP

                                 TIGR03037  70 edvpireGdifllppkvphspqra.agsiglvierkrkegeldalqwfcaecgeklyraevklesivkd 137
                                               e+v+++eGdifllp++v+hspqr+ a+s++lvier+r+eg  d+++w+c+ c+  +yr+ev+l+siv+d
  lcl|FitnessBrowser__Cup4G11:RR42_RS05080  77 ERVDLKEGDIFLLPAHVRHSPQRPeADSRCLVIERQRPEGVVDGFEWYCPACSALVYRVEVQLKSIVTD 145
                                               ************************9******************************************** PP

                                 TIGR03037 138 lppvfekfyssedartckkcGe 159
                                               lpp+f  fy + ++r+c +cG+
  lcl|FitnessBrowser__Cup4G11:RR42_RS05080 146 LPPLFAGFYDNAALRRCGQCGT 167
                                               ********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (159 nodes)
Target sequences:                          1  (186 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.80
//
[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