Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate GFF12 HP15_12 enoyl-CoA hydratase/isomerase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Marino:GFF12 Length = 270 Score = 100 bits (249), Expect = 3e-26 Identities = 81/260 (31%), Positives = 130/260 (50%), Gaps = 19/260 (7%) Query: 6 IKVEKDERVARIKIANPP-VNVLDMETMKEIISAIDEVEG---VDVIVFSGEG-KSFSAG 60 + V +D V + + P +N ++ E + A+++ E + VIV GEG + AG Sbjct: 15 VNVCRDGNVGWVILNRPKQINAINDEIRVGVPEALEQFEKDKEIRVIVIRGEGERGLCAG 74 Query: 61 AEIKEHF-PD------KAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDF 113 A+IKE P+ K E RW I+ + + + A+ G+ +GGG ELA+ACD Sbjct: 75 ADIKERRGPENSLQVRKRMECARW----IESIDQTTKPVIVAIHGYCMGGGLELALACDI 130 Query: 114 VLASKNAKLGVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNK 172 AS NA + +PE L P L R++ +A +++L+G+ + A RA IGLV + Sbjct: 131 RYASPNAVMALPETGLGLIPGGGGTQRLSRVVAPGHALDMLLSGDRLDAARARSIGLVTR 190 Query: 173 VFE-DENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKS 231 V E E+ + V++ + K +A K+A S E E D+ D++ + L + Sbjct: 191 VAETQESLLQEVSELAQKIAMKPPLATTYVKRAARASLELELKRGLDLELDLF-ALLAPT 249 Query: 232 EDAVEGLKAFLEKRKPEWKG 251 EDA E AF E+R P + G Sbjct: 250 EDAREAASAFSERRSPNFIG 269 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: 132 Number of extensions: 10 Number of successful extensions: 3 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: 270 Length adjustment: 25 Effective length of query: 227 Effective length of database: 245 Effective search space: 55615 Effective search space used: 55615 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: 47 (22.7 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