Align 4-carboxymuconolactone decarboxylase; CMD; EC 4.1.1.44 (uncharacterized)
to candidate GFF1359 Psest_1394 Uncharacterized homolog of gamma-carboxymuconolactone decarboxylase subunit
Query= curated2:P20370 (134 letters) >FitnessBrowser__psRCH2:GFF1359 Length = 146 Score = 55.8 bits (133), Expect = 2e-13 Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 1/116 (0%) Query: 5 QRYKQGLEVRTEVLGEKHVNRSLENLNDFNQDFQNFISRFAWGEVWSRPGLPRHTRSLVT 64 +R+++G+EV + G LE L + I+++A G+VW R L TR L Sbjct: 26 ERHERGVEVMDHLSGGAG-QPVLEALREDYLFLAEGITQYALGDVWGRSELDDRTRQLAV 84 Query: 65 IAVLLALGREDELRMHLRACFNNGVTKDELKELILHCSLYAGLPASNAAMHMAEEV 120 IA A G +++H GVT++ELKE++ ++ AG P + A EV Sbjct: 85 IAAFAAQGNLQYMKVHAGYALRLGVTREELKEVVYLTTVTAGFPRAIDAAQALREV 140 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: 49 Number of extensions: 2 Number of successful extensions: 1 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: 146 Length adjustment: 15 Effective length of query: 119 Effective length of database: 131 Effective search space: 15589 Effective search space used: 15589 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