Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate Dsui_2351 Dsui_2351 uncharacterized protein, gamma-carboxymuconolactone decarboxylase subunit like protein
Query= curated2:P20370 (134 letters) >FitnessBrowser__PS:Dsui_2351 Length = 124 Score = 77.4 bits (189), Expect = 7e-20 Identities = 40/122 (32%), Positives = 70/122 (57%), Gaps = 2/122 (1%) Query: 5 QRYKQGLEVRTEVLGEKHVNRSLENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSLVT 64 +RY +GL E+ G+ + + +L DF ++ F +G+++SRPGL R + Sbjct: 4 ERYARGLAKLQEIDGQAG-EKVVASLAGIAPDFARYLIEFPFGDIYSRPGLDLRAREIAV 62 Query: 65 IAVLLALGRE-DELRMHLRACFNNGVTKDELKELILHCSLYAGLPASNAAMHMAEEVFKD 123 +A L ALG +L++H++ N GV++ E+ E I+ ++YAG PA+ + A+EVF + Sbjct: 63 VAALTALGNAAPQLKVHIQGALNVGVSRQEVVETIMQMAVYAGFPAALNGLFAAQEVFAE 122 Query: 124 LG 125 G Sbjct: 123 AG 124 Lambda K H 0.320 0.135 0.403 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: 43 Number of extensions: 3 Number of successful extensions: 2 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: 134 Length of database: 124 Length adjustment: 14 Effective length of query: 120 Effective length of database: 110 Effective search space: 13200 Effective search space used: 13200 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: 41 (21.8 bits) S2: 41 (20.4 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