Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_076481536.1 BW971_RS16050 crotonase/enoyl-CoA hydratase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_900156495.1:WP_076481536.1 Length = 264 Score = 138 bits (348), Expect = 1e-37 Identities = 88/251 (35%), Positives = 134/251 (53%), Gaps = 6/251 (2%) Query: 13 NVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADIAEMKD 72 ++A ITL+RP ALNA+N+A + A+ A+D +V V++TG+G+AF AGAD+ + Sbjct: 16 HIAVITLDRPDALNAVNSALAVGLGNALEAAAQDMDVRVVVVTGTGRAFCAGADLKALAA 75 Query: 73 LTAVEGRKFSVLGNK-IFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAKFGQ 131 ++ G I R + KPVIAA+NGFALGGG EL L+ D+ + A G Sbjct: 76 GDRIDDPDHPERGFAGIVRHW--IPKPVIAAVNGFALGGGTELVLAADLAVIDETASLGL 133 Query: 132 PEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLLEEA 191 PEV G+ GG R+ R + +A E+ TG+ I+A A +GLVN+V L+ A Sbjct: 134 PEVRRGLIAAAGGLLRVHRQVSPKVANEIALTGQPISAVRAHELGLVNRVARQGTALDTA 193 Query: 192 KALVDAIIVNAPIAVRMCKAAINQGLQCD---IDTGVAYEAEVFGECFATEDRVEGMTAF 248 + L I NAP++V K +++ + + D E ++ D EG AF Sbjct: 194 RELAATIAANAPVSVAQSKWLMHETAKDEQGWDDRAWELNQEALVRVLSSADAREGPRAF 253 Query: 249 VEKRDKAFKNK 259 EKR+ ++ + Sbjct: 254 AEKREPRWEGR 264 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: 158 Number of extensions: 8 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: 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