Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate SMa0559 SMa0559 4-carboxymuconolactone decarboxylase
Query= curated2:P20370 (134 letters) >FitnessBrowser__Smeli:SMa0559 Length = 247 Score = 65.9 bits (159), Expect = 4e-16 Identities = 28/83 (33%), Positives = 55/83 (66%) Query: 40 FISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACFNNGVTKDELKELIL 99 + + + + ++W RP L RSLVTIA L+++G+ +++ HL +NG+++++ E+I Sbjct: 161 YTTDYLFRDLWLRPDLAPRDRSLVTIAALISVGQVEQITFHLNKALDNGLSEEQAAEVIT 220 Query: 100 HCSLYAGLPASNAAMHMAEEVFK 122 H + YAG P + +A+ +A+ VF+ Sbjct: 221 HLAFYAGWPNAMSALPVAKAVFE 243 Score = 64.3 bits (155), Expect = 1e-15 Identities = 33/94 (35%), Positives = 48/94 (51%) Query: 38 QNFISRFAWGEVWSRPGLPRHTRSLVTIAVLLALGREDELRMHLRACFNNGVTKDELKEL 97 + + + +G+VW RPGL R RSLVTIA L+A G L + NGV E+ E Sbjct: 32 EQYTQQRLYGDVWQRPGLNRRDRSLVTIAALIARGEAPALTYYADQALENGVKPSEISET 91 Query: 98 ILHCSLYAGLPASNAAMHMAEEVFKDLGIAPEKV 131 I H + Y+G + A + E F GI +++ Sbjct: 92 ITHLAYYSGWGKAMATVGPVSEAFAKRGIGQDQL 125 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: 85 Number of extensions: 3 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: 247 Length adjustment: 19 Effective length of query: 115 Effective length of database: 228 Effective search space: 26220 Effective search space used: 26220 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