Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate AO353_00510 AO353_00510 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00510 Length = 715 Score = 79.7 bits (195), Expect = 2e-19 Identities = 61/175 (34%), Positives = 88/175 (50%), Gaps = 22/175 (12%) Query: 24 VNVLDMETMKEIISAIDEVEG----VDVIVFSGEGKSFSAGAEIKEHFPD-KAPEMIRWF 78 VN + T+ E+ SA+D ++ VIV SG+ F GA+I E + K P+ Sbjct: 29 VNKFNRLTLNELRSAVDAIKADASVKGVIVSSGKDV-FIVGADITEFVDNFKLPD----- 82 Query: 79 TQLIDKVLRCKAI----------TVAAVKGFALGGGFELAIACDFVLASKNAKLGVPEIT 128 +L+ L I TVAA+ G ALGGG E+ +A D+ + S AK+G+PE+ Sbjct: 83 AELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADYRVMSTTAKIGLPEVK 142 Query: 129 LAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEES 182 L YP LPR+IG NA E I G+ E A ++G V+ V E +E+ Sbjct: 143 LGIYPGFGGTVRLPRIIGADNAIEWIAAGKENRPEDALKVGAVDAVVAPEQLQEA 197 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: 437 Number of extensions: 24 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: 252 Length of database: 715 Length adjustment: 32 Effective length of query: 220 Effective length of database: 683 Effective search space: 150260 Effective search space used: 150260 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 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