Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate AZOBR_RS19800 AZOBR_RS19800 4-carboxymuconolactone decarboxylase
Query= curated2:P20370 (134 letters) >FitnessBrowser__azobra:AZOBR_RS19800 Length = 139 Score = 82.0 bits (201), Expect = 3e-21 Identities = 42/120 (35%), Positives = 73/120 (60%), Gaps = 2/120 (1%) Query: 3 DEQRYKQGLEVRTEVLGEKHVNRSLENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSL 62 +E R ++G E+ G ++ + +L D DF ++ F +G+++SRPGL +R + Sbjct: 9 EESRLERGQRALAEIDGAAG-HKVVASLADIAPDFATYVFEFPFGDIYSRPGLDLRSREI 67 Query: 63 VTIAVLLALGRE-DELRMHLRACFNNGVTKDELKELILHCSLYAGLPASNAAMHMAEEVF 121 TIA L A+G +L++H+ A N G+T+DE+ E+++ S+YAG PA+ + A+EVF Sbjct: 68 ATIAALAAMGNAAPQLKVHIEAGLNVGLTRDEIVEVLIQMSVYAGFPAALNGLFAAKEVF 127 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: 48 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: 139 Length adjustment: 15 Effective length of query: 119 Effective length of database: 124 Effective search space: 14756 Effective search space used: 14756 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