GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacA in Chryseobacterium viscerum 687B-08

Align Galactose-6-phosphate isomerase subunit LacA; EC 5.3.1.26 (characterized)
to candidate WP_103234702.1 C1634_RS02900 ribose 5-phosphate isomerase B

Query= SwissProt::P23494
         (141 letters)



>NCBI__GCF_002899945.2:WP_103234702.1
          Length = 144

 Score = 74.3 bits (181), Expect = 7e-19
 Identities = 49/138 (35%), Positives = 71/138 (51%), Gaps = 4/138 (2%)

Query: 3   IVVGADLKGTRLKDVVKNFLVEEGFEVIDV---TKDGQDFVDVTLAVASEVNKDEQNLGI 59
           I + AD  G   K++VKN+L E  FEV D    + +  D+ D     A+ V   E  LGI
Sbjct: 5   IAIAADHAGYEYKEIVKNYLSER-FEVQDFGTFSTNSVDYPDFVHPAATSVENGENELGI 63

Query: 60  VIDAYGAGPFMVATKIKGMVAAEVSDERSAYMTRGHNNARMITVGAEIVGDELAKNIAKA 119
           +I   G G  + A K + +  A       A + R HN+A MI++ A  +  ELA  I   
Sbjct: 64  LICGSGNGVQITANKHQKIRCALCWMPEIATLARLHNDANMISMPARFISKELALEIVDK 123

Query: 120 FVNGKYDGGRHQVRVDML 137
           F++  ++GGRHQ RVD +
Sbjct: 124 FLSTDFEGGRHQNRVDKI 141


Lambda     K      H
   0.318    0.136    0.374 

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: 47
Number of extensions: 3
Number of successful extensions: 2
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: 141
Length of database: 144
Length adjustment: 16
Effective length of query: 125
Effective length of database: 128
Effective search space:    16000
Effective search space used:    16000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 42 (20.8 bits)

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