Align BadK (characterized)
to candidate WP_058860024.1 AS188_RS15810 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001482365.1:WP_058860024.1 Length = 264 Score = 181 bits (459), Expect = 1e-50 Identities = 104/255 (40%), Positives = 151/255 (59%), Gaps = 2/255 (0%) Query: 2 SSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRA 60 S+ + T + R+ ++T+NRP+V NALN ++D + AL AF+ + + A+V G +A Sbjct: 7 SATTVTTTVRDRIAVVTVNRPEVRNALNFGVLDGIEAALDAFERREDVDAVVFTGAGEKA 66 Query: 61 FAAGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 F AGADI+ + ++ D + + R ++ I+ + P +AAV G A GGG ELA++CDI Sbjct: 67 FVAGADISQLIGYTLQDGLRAR-MQRLYDRIQDLELPTIAAVNGFALGGGNELAMSCDIR 125 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 IA +A+F LPE LG+LPGAGGTQRL R +G +A +M L+ R ++AEEA R GLV+ V Sbjct: 126 IAAANARFGLPETNLGILPGAGGTQRLSRLVGLGRAQEMILTGRIIDAEEALRIGLVTSV 185 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 V + L D A A TI A A+ K + E+ G+L ER +A+ + Sbjct: 186 VPAEELMDTAHATARTILAKGPLAVRLAKLVVRNGAETDQRTGLLLERLAQSLLYAADEK 245 Query: 241 REGIQAFLEKRAPCF 255 EG AFLEKR F Sbjct: 246 AEGASAFLEKRPARF 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: 124 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: 264 Length adjustment: 25 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 24 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