Align BadK (characterized)
to candidate WP_058857336.1 AS188_RS01390 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001482365.1:WP_058857336.1 Length = 259 Score = 268 bits (685), Expect = 8e-77 Identities = 139/253 (54%), Positives = 183/253 (72%), Gaps = 1/253 (0%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65 I ET+GR GIITL+RP LNAL+ A + + A A DAD GIGAIV+ G+ +AFAAGA Sbjct: 8 IRVETRGRTGIITLHRPKALNALDAATLREVVAAAAAMDADPGIGAIVLTGSGKAFAAGA 67 Query: 66 DIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125 DI MA +S+++ +++ W+ ++R PV+ AVAG A GGGCELA+ CD++IA + Sbjct: 68 DIKEMADRGFSEMFRADWFA-GWDAFTRVRTPVVGAVAGYALGGGCELAMMCDVLIAADT 126 Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185 A+F PEI LG++PG GG+QRL RA+GKAKAMDM L+ R ++A EA+R GLVSRVV DR Sbjct: 127 ARFGQPEINLGVIPGMGGSQRLTRAVGKAKAMDMVLTGRQMDAAEAERAGLVSRVVPADR 186 Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245 L DE + +A TIAA S PA MA KE+++ AFE+ LA+G+LFERR H FA+ D +EG+ Sbjct: 187 LLDEALEVAGTIAAKSLPAAMAAKEAVSAAFETGLAQGVLFERRLFHGLFATEDQKEGMA 246 Query: 246 AFLEKRAPCFSHR 258 AF KR P F+HR Sbjct: 247 AFAAKREPRFTHR 259 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: 166 Number of extensions: 10 Number of successful extensions: 2 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 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