Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_041308077.1 MVAN_RS23045 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000015305.1:WP_041308077.1 Length = 264 Score = 162 bits (409), Expect = 9e-45 Identities = 101/260 (38%), Positives = 152/260 (58%), Gaps = 11/260 (4%) Query: 7 ILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGA 65 + E+ GNV IT+NRP+A NA+NA+ + A+ +D + AVI+TG+G K+F AGA Sbjct: 9 LTERRGNVLIITINRPEARNAVNASVSIGVGNALQAAQDDPEIRAVILTGAGDKSFCAGA 68 Query: 66 D---IAEMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRI 122 D I+ ++L E ++ G ++KP IAA+NG ALGGG EL+L+ D+ + Sbjct: 69 DLKAISRGENLFHPEHTEWGFAGYV----RHFIDKPTIAAVNGTALGGGTELALASDLVV 124 Query: 123 ASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVV 182 A +AKFG PEV G+ G GG R+ + +A ELIYTG+ I++ +ALR GL+N+VV Sbjct: 125 AEERAKFGLPEVKRGLIAGAGGVFRIVEQLPRKVALELIYTGEPISSADALRWGLINQVV 184 Query: 183 EPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGE---CFATE 239 +++ A AL + I NAP+AV+ K + + + + + FGE TE Sbjct: 185 PDGTVVDAALALAERITCNAPLAVQASKRVSYGAVDGVVGSEEPFWKQTFGEFSTLLKTE 244 Query: 240 DRVEGMTAFVEKRDKAFKNK 259 D +EG AF +KR+ +K K Sbjct: 245 DAMEGPLAFAQKREPVWKAK 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: 168 Number of extensions: 10 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