GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaC in Burkholderia phytofirmans PsJN

Align 3-hydroxyanthranilate 3,4-dioxygenase; 3-hydroxyanthranilate oxygenase; 3-HAO; 3-hydroxyanthranilic acid dioxygenase; HAD; EC 1.13.11.6 (characterized)
to candidate BPHYT_RS07265 BPHYT_RS07265 3-hydroxyanthranilate 3,4-dioxygenase

Query= SwissProt::Q1LCS4
         (174 letters)



>FitnessBrowser__BFirm:BPHYT_RS07265
          Length = 174

 Score =  346 bits (887), Expect = e-100
 Identities = 153/173 (88%), Positives = 166/173 (95%)

Query: 1   MLTYGAPFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFY 60
           MLTYG PFNF RWID+HAHLLKPPVGN+QVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFY
Sbjct: 1   MLTYGKPFNFQRWIDDHAHLLKPPVGNQQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFY 60

Query: 61  QLRGNAYLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDG 120
           QLRGNAYL+LW+DG+RER DLKEGD+FLLPPHVRHSPQRPEAGS CLVIERQRPAG++DG
Sbjct: 61  QLRGNAYLHLWIDGKRERVDLKEGDVFLLPPHVRHSPQRPEAGSVCLVIERQRPAGVVDG 120

Query: 121 FEWYCDACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCGQVHPGRA 173
           FEWYCDACGHLV+RVEVQLKSIV+DLPPLF +FYASE+KRRC HCG VHPG+A
Sbjct: 121 FEWYCDACGHLVYRVEVQLKSIVSDLPPLFNAFYASEEKRRCGHCGHVHPGKA 173


Lambda     K      H
   0.324    0.143    0.481 

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: 239
Number of extensions: 3
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: 174
Length of database: 174
Length adjustment: 19
Effective length of query: 155
Effective length of database: 155
Effective search space:    24025
Effective search space used:    24025
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: 41 (22.0 bits)
S2: 44 (21.6 bits)

Align candidate BPHYT_RS07265 BPHYT_RS07265 (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.4131762.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    7.5e-84  265.7   0.1    8.4e-84  265.5   0.1    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07265  BPHYT_RS07265 3-hydroxyanthranil


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07265  BPHYT_RS07265 3-hydroxyanthranilate 3,4-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.5   0.1   8.4e-84   8.4e-84       1     159 []       8     167 ..       8     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.5 bits;  conditional E-value: 8.4e-84
                                TIGR03037   1 lnlkkwidehkellkppvgnkqiwqdselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvleeGkve 70 
                                              +n+++wid+h++llkppvgn+q+wqds++ivtvvGGpn+rtd+h+d+ eeffyql+G+++l+++ +Gk+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS07265   8 FNFQRWIDDHAHLLKPPVGNQQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNAYLHLWIDGKRE 77 
                                              7********************************************************************* PP

                                TIGR03037  71 dvpireGdifllppkvphspqra.agsiglvierkrkegeldalqwfcaecgeklyraevklesivkdlp 139
                                              +v+++eGd+fllpp+v+hspqr+ ags++lvier+r+ g  d+++w+c+ cg+ +yr+ev+l+siv+dlp
  lcl|FitnessBrowser__BFirm:BPHYT_RS07265  78 RVDLKEGDVFLLPPHVRHSPQRPeAGSVCLVIERQRPAGVVDGFEWYCDACGHLVYRVEVQLKSIVSDLP 147
                                              ***********************99********************************************* PP

                                TIGR03037 140 pvfekfyssedartckkcGe 159
                                              p+f++fy+se+ r+c +cG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07265 148 PLFNAFYASEEKRRCGHCGH 167
                                              *******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (159 nodes)
Target sequences:                          1  (174 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: 11.60
//
[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:

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:

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:

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:

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