Align 2-hydroxymuconate tautomerase; EC 5.3.2.6; 4-oxalocrotonate tautomerase; 4-OT (uncharacterized)
to candidate WP_086511264.1 BZY95_RS17985 4-oxalocrotonate tautomerase family protein
Query= curated2:Q93JW0 (63 letters) >NCBI__GCF_002151265.1:WP_086511264.1 Length = 65 Score = 40.4 bits (93), Expect = 2e-09 Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%) Query: 1 MPFAQIYMIEGRTEAQKKAVIEKVSQALVEATGAPMANVRVWIQEVPKENWGIAG 55 MP I R QK+ + ++++QA VE G P +V+V+ EV ENW AG Sbjct: 1 MPIVTIQQFP-RDLTQKRELAQRITQAFVEVYGTPEESVQVFFSEVDGENWAKAG 54 Lambda K H 0.315 0.129 0.370 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: 15 Number of extensions: 2 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 (19.3 bits) S2: 36 (18.5 bits)
This GapMind analysis is from Apr 09 2024. 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