Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate BPHYT_RS10815 BPHYT_RS10815 crotonase
Query= BRENDA::D3RXI0 (252 letters) >FitnessBrowser__BFirm:BPHYT_RS10815 Length = 268 Score = 115 bits (289), Expect = 7e-31 Identities = 81/255 (31%), Positives = 130/255 (50%), Gaps = 6/255 (2%) Query: 1 MEYKKIKVEKDERVARIKIANPPVNVLDM---ETMKEIISAIDEVEGVDVIVFSGEGKSF 57 +E I+++ A I + PP+NV+ M + ++ A+D+ V VIV +G+ F Sbjct: 15 LEGFSIEIDAQRERADIILHRPPLNVISMHARDQLRAAFEALDDDPRVRVIVVRAKGEHF 74 Query: 58 SAGAEIKEHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLAS 117 S+G +IK F + +PE + I RC +AA +GF G GFEL++ACDF +A+ Sbjct: 75 SSGGDIKG-FLEASPETVSKLAWNIAAPARCSKPVIAANRGFCFGVGFELSLACDFRIAT 133 Query: 118 KNAKLGVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFED 176 +PE L P A L +M+G ++++ I ++A+E G+ + D Sbjct: 134 DTTFYALPEQKLGQIPGSGGSARLQQMVGIGRTKDIVMRSRRIPGKQAYEWGIAVECVAD 193 Query: 177 ENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVE 236 E + + V+ L S +A R KK LL TE LS+ + S+L S+D E Sbjct: 194 SELEAATDALVDELRAFSPLAQRTAKK-LLNDTEDAPLSIAIELEGHCYSRLRASDDFRE 252 Query: 237 GLKAFLEKRKPEWKG 251 G++AF KRKP ++G Sbjct: 253 GVEAFHGKRKPVFRG 267 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: 148 Number of extensions: 10 Number of successful extensions: 5 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: 268 Length adjustment: 24 Effective length of query: 228 Effective length of database: 244 Effective search space: 55632 Effective search space used: 55632 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