Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_058929179.1 AU252_RS01275 enoyl-CoA hydratase-related protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_001484605.1:WP_058929179.1 Length = 262 Score = 159 bits (402), Expect = 6e-44 Identities = 95/261 (36%), Positives = 151/261 (57%), Gaps = 9/261 (3%) Query: 4 KNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFV 62 + ++ E VA IT+NRP++ NAL+ A + + AED++V+A+++TG+G +AF Sbjct: 6 EEVLFEIRDRVAYITMNRPESRNALSQAVVARLAEVFTVAAEDNDVWAIVLTGAGDRAFC 65 Query: 63 AGADIAEMKDLTAVEGRKFSV----LGNKIFRKLENLEKPVIAAINGFALGGGCELSLSC 118 AG D+ E+ + A EGR+F V +F + + KP IA++NG A+ GG EL+L+C Sbjct: 66 AGGDLKELNQI-AQEGRRFPVPMTGTERNLFELVLEVGKPTIASLNGPAVAGGFELALAC 124 Query: 119 DIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLV 178 DIRIA+ + G PE G+ F T L R + +A ++YTG+++ EAL GLV Sbjct: 125 DIRIAAEHSTIGMPEAKRGMGANFA-TVLLPRLVPRSVALSMLYTGELMAPSEALHWGLV 183 Query: 179 NKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFAT 238 N V D+L +E + V +I+ NAP+A+R K + +G + + A V + + Sbjct: 184 NAVHPADQLAKETEEFVRSIVANAPLALRRYKEMVTKGWELSVQ--AALRLNVGPNPYLS 241 Query: 239 EDRVEGMTAFVEKRDKAFKNK 259 DR EG+ AF+EKR ++ K Sbjct: 242 ADREEGVRAFIEKRAPRWEGK 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: 147 Number of extensions: 10 Number of successful extensions: 4 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: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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 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