GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praC in Azospirillum brasilense Sp245

Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate AZOBR_RS18455 AZOBR_RS18455 4-oxalocrotonate tautomerase

Query= BRENDA::A2SL37
         (71 letters)



>FitnessBrowser__azobra:AZOBR_RS18455
          Length = 62

 Score = 43.1 bits (100), Expect = 4e-10
 Identities = 20/56 (35%), Positives = 34/56 (60%)

Query: 1  MPIIQMNLLEGRTVEQKRNAVAAITEAVVRTLDVRPDQVRILINELGVEHFSVAGQ 56
          MP+I + L EGRT+EQKR    A+T+A V  L   P+ V ++ +++    ++  G+
Sbjct: 1  MPLINVQLFEGRTLEQKRAYAKALTDASVAVLGCSPEAVDVIFHDVKKSDWASGGK 56


Lambda     K      H
   0.319    0.130    0.339 

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: 18
Number of extensions: 1
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: 71
Length of database: 62
Length adjustment: 5
Effective length of query: 66
Effective length of database: 57
Effective search space:     3762
Effective search space used:     3762
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: 37 (20.0 bits)
S2: 37 (18.9 bits)

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