Align BadK (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Dyella79:N515DRAFT_1164 Length = 260 Score = 171 bits (434), Expect = 1e-47 Identities = 102/250 (40%), Positives = 145/250 (58%), Gaps = 2/250 (0%) Query: 11 QGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIAS 69 +G V IIT+NRPD LNALN ++ L A DD + +V+AG +AF AGADIA Sbjct: 11 RGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDKAFVAGADIAE 70 Query: 70 MAAWSYSDVYG-SNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKF 128 M ++ G S R +I ++ KPV+A + G A GGG ELA+AC + +A A+F Sbjct: 71 MNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACHLRVASEKARF 130 Query: 129 ALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRD 188 PEI LGL+PG GGTQRL R G+ A+++CL+ + A+ A G+V+RVV + L + Sbjct: 131 GQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVNRVVAPEALDE 190 Query: 189 ETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFL 248 ALA +AA + A + +++ + E L +G+ FE + F++ D REG AFL Sbjct: 191 TVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTEDMREGTTAFL 250 Query: 249 EKRAPCFSHR 258 EKR F R Sbjct: 251 EKRKAEFKGR 260 Lambda K H 0.321 0.135 0.389 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: 134 Number of extensions: 7 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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