Align 2-hydroxymuconate tautomerase (EC 5.3.2.6) (characterized)
to candidate AZOBR_RS18455 AZOBR_RS18455 4-oxalocrotonate tautomerase
Query= BRENDA::A2SL37 (71 letters) >FitnessBrowser__azobra:AZOBR_RS18455 Length = 62 Score = 43.1 bits (100), Expect = 4e-10 Identities = 20/56 (35%), Positives = 34/56 (60%) Query: 1 MPIIQMNLLEGRTVEQKRNAVAAITEAVVRTLDVRPDQVRILINELGVEHFSVAGQ 56 MP+I + L EGRT+EQKR A+T+A V L P+ V ++ +++ ++ G+ Sbjct: 1 MPLINVQLFEGRTLEQKRAYAKALTDASVAVLGCSPEAVDVIFHDVKKSDWASGGK 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: 18 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: 62 Length adjustment: 5 Effective length of query: 66 Effective length of database: 57 Effective search space: 3762 Effective search space used: 3762 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