Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate H281DRAFT_01662 H281DRAFT_01662 4-oxalocrotonate tautomerase
Query= BRENDA::A9W9U6 (72 letters) >FitnessBrowser__Burk376:H281DRAFT_01662 Length = 70 Score = 43.1 bits (100), Expect = 4e-10 Identities = 19/61 (31%), Positives = 32/61 (52%) Query: 1 MLLLRITMLEGRSTEQKAELARALSAAAAAAFDVPLAEVRLIIQEVPPTHWTVGGISMAE 60 M ++ I+++EGR + +A++ VPL +R+ EVP THW +G + E Sbjct: 1 MPIIHISLVEGRDAQAVKACLKAIARTVHETLGVPLDSIRVFANEVPSTHWAIGERTKDE 60 Query: 61 L 61 L Sbjct: 61 L 61 Lambda K H 0.316 0.126 0.338 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: 10 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: 72 Length of database: 70 Length adjustment: 6 Effective length of query: 66 Effective length of database: 64 Effective search space: 4224 Effective search space used: 4224 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: 37 (19.9 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