Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate WP_011427992.1 RHE_RS24720 4-oxalocrotonate tautomerase
Query= BRENDA::Q01468 (63 letters) >NCBI__GCF_000092045.1:WP_011427992.1 Length = 61 Score = 53.1 bits (126), Expect = 3e-13 Identities = 25/60 (41%), Positives = 38/60 (63%) Query: 1 MPIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK 60 MPI + + GR+DEQK +RE + A +L P SV ++ITE+AK + +GG+L S+ Sbjct: 1 MPILHLQMHPGRTDEQKRAFVREATRAAVDTLACPPESVEILITEVAKDSWAVGGKLKSE 60 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: 16 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: 61 Length adjustment: 4 Effective length of query: 59 Effective length of database: 57 Effective search space: 3363 Effective search space used: 3363 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 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