Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate BPHYT_RS24200 BPHYT_RS24200 4-oxalocrotonate tautomerase
Query= BRENDA::A2SL37 (71 letters) >FitnessBrowser__BFirm:BPHYT_RS24200 Length = 61 Score = 50.4 bits (119), Expect = 2e-12 Identities = 24/56 (42%), Positives = 38/56 (67%) Query: 1 MPIIQMNLLEGRTVEQKRNAVAAITEAVVRTLDVRPDQVRILINELGVEHFSVAGQ 56 MP ++ L EGR+VEQKR V AIT+A +L V P+ V I++ ++ E+++ AG+ Sbjct: 1 MPTFRIELFEGRSVEQKRQFVEAITKATCESLGVEPNSVDIILTDVKRENWATAGR 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: 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: 71 Length of database: 61 Length adjustment: 5 Effective length of query: 66 Effective length of database: 56 Effective search space: 3696 Effective search space used: 3696 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.
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:
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