Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_086509903.1 BZY95_RS10660 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_002151265.1:WP_086509903.1 Length = 264 Score = 176 bits (447), Expect = 3e-49 Identities = 94/256 (36%), Positives = 147/256 (57%), Gaps = 2/256 (0%) Query: 4 KNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVA 63 + +I+++ G V I NRP LNA+ A E+ AA+ + D V VI+TG G+AF Sbjct: 7 ETLIVDRRGAVMEIRFNRPHRLNAVVEAFYSELLAALAEAERDPEVRCVILTGEGRAFCV 66 Query: 64 GADIAE--MKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIR 121 GAD+ E T + R++ LGN + + KPVIAA+NG+ALG G E++++CD Sbjct: 67 GADMKEHGSAQRTLFQRRRYLQLGNDVCEAILRHPKPVIAAVNGYALGAGAEMAVACDFI 126 Query: 122 IASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKV 181 + + +A+ G PE +G G G ++ L + +G+ MA++L+YTG+ I+ EA R+GL Sbjct: 127 VMAEEAQIGFPETSIGTCVGGGVSKLLPQLVGLNMARQLLYTGRRIDGREAARVGLATSS 186 Query: 182 VEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDR 241 D + EA+AL +++ AP+++ M K +NQG +D+ + E + C T D Sbjct: 187 HAADAMPAEAQALAESLARQAPVSIAMLKRLVNQGSDTGLDSQLQQELDAVFTCSTTADW 246 Query: 242 VEGMTAFVEKRDKAFK 257 EG+ AF EKR FK Sbjct: 247 QEGVDAFAEKRTPQFK 262 Lambda K H 0.318 0.136 0.376 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: 150 Number of extensions: 3 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: 259 Length of database: 264 Length adjustment: 25 Effective length of query: 234 Effective length of database: 239 Effective search space: 55926 Effective search space used: 55926 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 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