Align 4-carboxymuconolactone decarboxylase (EC 4.1.1.44) (characterized)
to candidate CCNA_02494 CCNA_02494 3-oxoadipate enol-lactonase/4-carboxymuconolactone decarboxylase
Query= BRENDA::Q6SJB9 (125 letters) >FitnessBrowser__Caulo:CCNA_02494 Length = 393 Score = 101 bits (251), Expect = 1e-26 Identities = 51/119 (42%), Positives = 71/119 (59%), Gaps = 1/119 (0%) Query: 5 YDNGMKVRRRVLGDAYVDRAEAGKTAFEAPFQTLITEGAWGTVWASDGISDRERSMLTLA 64 ++ G+ RRRVLGDA+VD++ A +TAF A +Q +IT AW +W G+ R R +L LA Sbjct: 274 FEAGLVTRRRVLGDAWVDKSLAKRTAFTADYQAMITRYAWNEIWGRPGLDHRTRRLLVLA 333 Query: 65 LLAALGNFDEIPMHIRATARTGASKQDVL-EAFQHVAIYAGVPRANQALKLARQTYDEM 122 + A+L ++E +H+RA G QD L E +AIYAGVP AN A A E+ Sbjct: 334 ICASLARWEEFRLHVRAGLEQGGFTQDELKEVLMQIAIYAGVPAANTAFTEAADVMSEL 392 Lambda K H 0.318 0.131 0.376 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: 114 Number of extensions: 9 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: 125 Length of database: 393 Length adjustment: 22 Effective length of query: 103 Effective length of database: 371 Effective search space: 38213 Effective search space used: 38213 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: 45 (21.9 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