Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate BPHYT_RS28020 BPHYT_RS28020 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__BFirm:BPHYT_RS28020 Length = 272 Score = 103 bits (258), Expect = 3e-27 Identities = 79/261 (30%), Positives = 124/261 (47%), Gaps = 34/261 (13%) Query: 11 DERVARIKIANPPVNVLDMETMKEIISAIDEVEG---VDVIVFSGEG-KSFSAGAEIKEH 66 D VA++ + PP N E + ++ ++ + G V IV +G+G K FSAGA++ Sbjct: 9 DGAVAQLTLKRPPANAFTPEGLLQLQQTVERLNGEARVRAIVITGDGPKFFSAGADLNT- 67 Query: 67 FPDKAPEMIRW----FTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKL 122 F D E+ R F + + + + +AA+ G+A+GGG E A+ACD +A ++A L Sbjct: 68 FADGNREVARTAAARFGAAFETLQNARPVVIAAINGYAMGGGLECALACDIRIAEQHALL 127 Query: 123 GVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEE 181 +PE + P LP ++G A +ILTGE + A A IGLV +V E + Sbjct: 128 ALPETAVGLLPCGCGTQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEVVEKGAARD 187 Query: 182 SVNDFVNSLLEKSSVALRLTK-----------KALLFSTEKE-YLSLFDVINDVYLSQLV 229 + + S A+ +K +A + E+E ++ LFD Sbjct: 188 AALVMAARVATLSPQAVGFSKTLIHQGRSGVPRAAALALERERFVDLFD----------- 236 Query: 230 KSEDAVEGLKAFLEKRKPEWK 250 D EG+ AFLEKR P W+ Sbjct: 237 -GADQREGVNAFLEKRPPRWQ 256 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: 158 Number of extensions: 11 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: 272 Length adjustment: 25 Effective length of query: 227 Effective length of database: 247 Effective search space: 56069 Effective search space used: 56069 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