GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praC in Desulfovibrio vulgaris Hildenborough

Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate 207912 DVU2421 4-oxalocrotonate tautomerase family protein

Query= BRENDA::O29588
         (63 letters)



>MicrobesOnline__882:207912
          Length = 65

 Score = 52.4 bits (124), Expect = 6e-13
 Identities = 26/63 (41%), Positives = 37/63 (58%)

Query: 1  MPVLIVYGPKLDVGKKREFVERLTSVAAEIYGMDRSAITILIHEPPAENVGVGGKLIADR 60
          MP++ V   +L +  +RE V  LT  AA I G+    I +++   PAE+  VGG L+ADR
Sbjct: 1  MPIITVQANQLSLETRRELVHELTQSAARIMGLPPETIVVVLECRPAEDYAVGGVLLADR 60

Query: 61 ERE 63
           RE
Sbjct: 61 HRE 63


Lambda     K      H
   0.318    0.140    0.393 

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: 14
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: 63
Length of database: 65
Length adjustment: 5
Effective length of query: 58
Effective length of database: 60
Effective search space:     3480
Effective search space used:     3480
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: 36 (19.4 bits)
S2: 36 (18.5 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