Align methylmalonyl-CoA epimerase (EC 5.1.99.1) (characterized)
to candidate GFF3998 Psest_4071 4-hydroxyphenylpyruvate dioxygenase and related hemolysins
Query= metacyc::MONOMER-17285 (139 letters) >FitnessBrowser__psRCH2:GFF3998 Length = 641 Score = 47.8 bits (112), Expect = 3e-10 Identities = 32/104 (30%), Positives = 52/104 (50%), Gaps = 7/104 (6%) Query: 5 IDHIG--LVVADLDAAIDFYRTAYDVTEWERIELPERHALIGVARF----GDVLIELIAP 58 IDH+ L L + + FYR+ +D + + LP+ + L+ G V + L Sbjct: 442 IDHMATALPAESLASWVLFYRSLFDFEADDELLLPDPYGLMKCRAMRSPCGRVRLPLNTS 501 Query: 59 TSDQASFARFLRE-KGPGMHHIAYRVDDIYAALATLQARGLPLI 101 A+ L +G G+HH+A+ DDI+A +A QA G+PL+ Sbjct: 502 QDRDTVIAQALSSYRGAGVHHVAFACDDIFAEVARAQAAGVPLL 545 Lambda K H 0.326 0.142 0.432 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: 233 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 139 Length of database: 641 Length adjustment: 26 Effective length of query: 113 Effective length of database: 615 Effective search space: 69495 Effective search space used: 69495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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