GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaC in Rhodanobacter denitrificans 2APBS1

Align 3-hydroxyanthranilate 3,4-dioxygenase; 3-hydroxyanthranilate oxygenase; 3-HAO; 3-hydroxyanthranilic acid dioxygenase; HAD; EC 1.13.11.6 (characterized)
to candidate WP_015447353.1 R2APBS1_RS06780 3-hydroxyanthranilate 3,4-dioxygenase

Query= SwissProt::Q1LCS4
         (174 letters)



>NCBI__GCF_000230695.2:WP_015447353.1
          Length = 173

 Score =  172 bits (436), Expect = 3e-48
 Identities = 86/167 (51%), Positives = 104/167 (62%), Gaps = 2/167 (1%)

Query: 7   PFNFPRWIDEHAHLLKPPVGNRQVWQDSDFIVTVVGGPNHRTDYHDDPLEEFFYQLRGNA 66
           P N  RWIDEH HLL+PPVGN+ +  D DFI+ +VGGPN RTDYH D   EFFYQL G  
Sbjct: 6   PINLQRWIDEHRHLLQPPVGNKCI-VDGDFIIMIVGGPNARTDYHYDEGPEFFYQLEGEI 64

Query: 67  YLNLWVDGRRERADLKEGDIFLLPPHVRHSPQRPEAGSACLVIERQRPAGMLDGFEWYCD 126
            L +  DG      L+ G+IF LPP V HSP R  AGS  LVIER+R AG  DG  W+C+
Sbjct: 65  TLKVQDDGVARDIPLRAGEIFYLPPRVPHSPNR-AAGSIGLVIERRRIAGEKDGLMWFCE 123

Query: 127 ACGHLVHRVEVQLKSIVTDLPPLFESFYASEDKRRCPHCGQVHPGRA 173
            C H ++     L SI  D PP+FE +Y S + R C  CG ++P  A
Sbjct: 124 RCNHKLYEEHFVLDSIEHDFPPVFERYYRSREARTCAACGHLNPAPA 170


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: 167
Number of extensions: 5
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: 174
Length of database: 173
Length adjustment: 19
Effective length of query: 155
Effective length of database: 154
Effective search space:    23870
Effective search space used:    23870
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 WP_015447353.1 R2APBS1_RS06780 (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.2159930.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-78  248.5   0.0    1.6e-78  248.4   0.0    1.0  1  NCBI__GCF_000230695.2:WP_015447353.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015447353.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.4   0.0   1.6e-78   1.6e-78       1     159 []       7     164 ..       7     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.4 bits;  conditional E-value: 1.6e-78
                             TIGR03037   1 lnlkkwidehkellkppvgnkqiwqdselivtvvGGpnkrtdfhvdeseeffyqlkGemvlkvleeGkvedvp 73 
                                           +nl++wideh++ll+ppvgnk+i  d ++i+++vGGpn+rtd+h+de++effyql+Ge++lkv+++G ++d+p
  NCBI__GCF_000230695.2:WP_015447353.1   7 INLQRWIDEHRHLLQPPVGNKCI-VDGDFIIMIVGGPNARTDYHYDEGPEFFYQLEGEITLKVQDDGVARDIP 78 
                                           7**********************.899********************************************** PP

                             TIGR03037  74 ireGdifllppkvphspqraagsiglvierkrkegeldalqwfcaecgeklyraevklesivkdlppvfekfy 146
                                           +r+G+if lpp+vphsp+raagsiglvier+r  ge+d+l+wfc++c++kly++++ l+si++d+ppvfe++y
  NCBI__GCF_000230695.2:WP_015447353.1  79 LRAGEIFYLPPRVPHSPNRAAGSIGLVIERRRIAGEKDGLMWFCERCNHKLYEEHFVLDSIEHDFPPVFERYY 151
                                           ************************************************************************* PP

                             TIGR03037 147 ssedartckkcGe 159
                                           +s++artc  cG+
  NCBI__GCF_000230695.2:WP_015447353.1 152 RSREARTCAACGH 164
                                           ************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (159 nodes)
Target sequences:                          1  (173 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: 11.89
//
[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:

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