Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate CA265_RS13720 CA265_RS13720 4-oxalocrotonate tautomerase
Query= BRENDA::Q01468 (63 letters) >FitnessBrowser__Pedo557:CA265_RS13720 Length = 72 Score = 38.1 bits (87), Expect = 1e-08 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 1/64 (1%) Query: 1 MPIAQIHIL-EGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELAS 59 MP +I + EG + EQK+TLI +++ IS LD ++I E+ +G GE S Sbjct: 1 MPYVKIEVTREGVTREQKQTLISGITKLISEVLDKDPKLTHIVIQEIELDDWGYAGEQVS 60 Query: 60 KVRR 63 +R+ Sbjct: 61 VLRK 64 Lambda K H 0.317 0.134 0.352 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: 63 Length of database: 72 Length adjustment: 5 Effective length of query: 58 Effective length of database: 67 Effective search space: 3886 Effective search space used: 3886 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 (19.8 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