Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate BWI76_RS14810 BWI76_RS14810 carboxymuconolactone decarboxylase
Query= curated2:P20370 (134 letters) >FitnessBrowser__Koxy:BWI76_RS14810 Length = 266 Score = 69.3 bits (168), Expect = 4e-17 Identities = 32/100 (32%), Positives = 58/100 (58%) Query: 28 ENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACFNN 87 +N+ + F ++ + ++W RPGL RSLVT++ L+A G+ ++ HL +N Sbjct: 166 QNVGAISPGLVKFTTQPLFLDLWQRPGLKPRDRSLVTVSALIAAGQSAQIGYHLNRAMDN 225 Query: 88 GVTKDELKELILHCSLYAGLPASNAAMHMAEEVFKDLGIA 127 G+T +E E++ H + YAG P + +A+ + EV + G+A Sbjct: 226 GLTAEEAGEVVAHAAFYAGWPNAFSAVAVVSEVLRARGLA 265 Score = 64.7 bits (156), Expect = 9e-16 Identities = 32/106 (30%), Positives = 61/106 (57%) Query: 26 SLENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACF 85 S+E++ F S ++W+R L R RS+VT+A+L+A + EL+ ++ Sbjct: 37 SVEDVQSVAPALARFGSEVLTEDLWARNELSRRDRSIVTVAILIARHQPAELKHYVDVAL 96 Query: 86 NNGVTKDELKELILHCSLYAGLPASNAAMHMAEEVFKDLGIAPEKV 131 +NGVT E+ E++ H + Y+G P + +A+ + +++F GI E++ Sbjct: 97 DNGVTAAEISEIVTHLAFYSGWPNAMSAVAVTKDIFIARGIGREQL 142 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: 97 Number of extensions: 6 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: 2 Length of query: 134 Length of database: 266 Length adjustment: 20 Effective length of query: 114 Effective length of database: 246 Effective search space: 28044 Effective search space used: 28044 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: 44 (21.6 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