Align BadK (characterized)
to candidate WP_011425014.1 RHE_RS08795 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000092045.1:WP_011425014.1 Length = 259 Score = 114 bits (285), Expect = 2e-30 Identities = 87/260 (33%), Positives = 122/260 (46%), Gaps = 10/260 (3%) Query: 1 MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRA 60 M+S + + V I+T++RP+ LNAL+ ++ AL A A +A+ + V+ G + Sbjct: 1 MASGTVRVDVDRHVAILTISRPEKLNALDLDMLKALADAADAVEANPDLRVAVLTGEGKG 60 Query: 61 FAAGADIASMAAWS--YSDVYGSNFIT---RNWETIRQIRKPVLAAVAGLAYGGGCELAL 115 F+AG DI AW V+G ++ R +E + +R P++AA+ G A GGG ELA Sbjct: 61 FSAGGDIK---AWGGMLPQVFGHAWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAG 117 Query: 116 ACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYG 175 DI +A K LPE LG++PG GTQRL R G M L AEEA G Sbjct: 118 VADIRVAEEHIKIGLPETGLGMVPGWSGTQRLVRRFGAQAVRRMALGGEIFTAEEARLLG 177 Query: 176 LVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235 +V VV A IAA A+ K L A + G E Sbjct: 178 IVDAVVPTGNSVAAARQYAGRIAARGPAAVEIAK--LMIASANGEDNGTAVEALGSILAA 235 Query: 236 ASADAREGIQAFLEKRAPCF 255 + D +EG+ +F EKR F Sbjct: 236 KTGDLKEGVASFSEKRPATF 255 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: 135 Number of extensions: 5 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 Apr 09 2024. 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