Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_002115805.1:WP_085640004.1 Length = 695 Score = 108 bits (269), Expect = 4e-28 Identities = 57/171 (33%), Positives = 101/171 (59%), Gaps = 6/171 (3%) Query: 6 IKVEKDERVARIKIANPPVNVLDMETMKEIISAID--EVEGVDVIVFSGEGKSFSAGAEI 63 I+ +D +A I I NPPVN L + ++ A++ E +G + GEG+SF AGA+I Sbjct: 5 IRYNRDGDIAMIAIDNPPVNALGQAVRQGLVEAVEKAEADGARAALIYGEGRSFPAGADI 64 Query: 64 KEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLG 123 +E P + W + +++ + V+A+ G ALGGG E+A+A D+ +A+ AK+G Sbjct: 65 REF---GKPPLEPWLPDVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVG 121 Query: 124 VPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKV 173 +PE+ + P LPR++G + + ++I +G I+A AF++G++++V Sbjct: 122 LPEVLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRV 172 Lambda K H 0.318 0.136 0.382 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: 358 Number of extensions: 22 Number of successful extensions: 4 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: 252 Length of database: 695 Length adjustment: 31 Effective length of query: 221 Effective length of database: 664 Effective search space: 146744 Effective search space used: 146744 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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