Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate RR42_RS19805 RR42_RS19805 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__Cup4G11:RR42_RS19805 Length = 258 Score = 96.3 bits (238), Expect = 6e-25 Identities = 83/256 (32%), Positives = 118/256 (46%), Gaps = 23/256 (8%) Query: 12 ERVARIKIANPPV-NVLDMETMKEIISAIDEV---EGVDVIVFSGEGKSFSAGAEIKEH- 66 E VA I + P V N L+ + E+ +A++ E V +V S G+ F AGA++ Sbjct: 11 EGVATITLNRPDVLNALNSALLLELRAAVERAAQDEAVRAVVLSANGRGFCAGADLAGRG 70 Query: 67 --FPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNA---- 120 D + + +I + + +V G A G G LA+A D VLA ++A Sbjct: 71 TGLQDSGTLLRERYHPIILALRNMPKPVITSVNGVAAGAGMSLALAGDVVLAGRSASFLQ 130 Query: 121 ---KLG-VPEITLAHYPPVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFED 176 K+G VP+ ++ LPR G A L + E I AE A IGLV KV ED Sbjct: 131 AFSKIGLVPDAGSTYF-------LPRYAGEMRARALAILAEKIDAEEAHRIGLVWKVHED 183 Query: 177 ENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVE 236 E L + + A L K+AL S + + + + S+ KSED E Sbjct: 184 EALPAETARLAAHLAQMPTFAYGLIKEALNASLQSDLPAQLE-REATLQSRASKSEDVKE 242 Query: 237 GLKAFLEKRKPEWKGR 252 G+ AFLEKRKP +KGR Sbjct: 243 GVAAFLEKRKPAFKGR 258 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: 123 Number of extensions: 9 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: 258 Length adjustment: 24 Effective length of query: 228 Effective length of database: 234 Effective search space: 53352 Effective search space used: 53352 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