Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate BPHYT_RS09010 BPHYT_RS09010 4-carboxymuconolactone decarboxylase
Query= curated2:P20370 (134 letters) >FitnessBrowser__BFirm:BPHYT_RS09010 Length = 152 Score = 69.7 bits (169), Expect = 2e-17 Identities = 39/118 (33%), Positives = 65/118 (55%), Gaps = 2/118 (1%) Query: 6 RYKQGLEVRTEVLGEKHVNRSLENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSLVTI 65 RY +G E ++ G + + L DF + F +G+++SRP L R + TI Sbjct: 8 RYTRGWEKLKQIDGSTG-EQVIAALAPIAPDFGRLLIEFGFGDIYSRPQLDLRAREIATI 66 Query: 66 AVLLALG-REDELRMHLRACFNNGVTKDELKELILHCSLYAGLPASNAAMHMAEEVFK 122 A L LG + +L++H+ A N G T++E+ E+ + +LYAG PA+ A+ A E+F+ Sbjct: 67 ASLATLGCAQLQLKVHIEAALNVGCTREEIVEVFMQMALYAGFPAALNALFAAREIFE 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: 44 Number of extensions: 2 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: 152 Length adjustment: 16 Effective length of query: 118 Effective length of database: 136 Effective search space: 16048 Effective search space used: 16048 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: 42 (20.8 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