Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 215 bits (547), Expect = 8e-61 Identities = 115/251 (45%), Positives = 159/251 (63%), Gaps = 1/251 (0%) Query: 10 KDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAGADIA 68 +D + +TLNRP NAL+AA L+EI+ I +I D N+ +++TG+G K F AGAD+ Sbjct: 10 QDDYIGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLK 69 Query: 69 EMKDLTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSKAK 128 E + +T E ++ + + F +E+L PVIA ING ALGGG EL+L+CD+RIA + A Sbjct: 70 ERRLMTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAA 129 Query: 129 FGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDKLL 188 G PE GL I PG GGTQRL R IG G AKE+I+TG + AEEA++IGL+ ++ D L+ Sbjct: 130 LGLPETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLM 189 Query: 189 EEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFATEDRVEGMTAF 248 +A L I N PIA++ K AI L D+ TG+ E E + TEDR+EG+ AF Sbjct: 190 NDAITLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKAF 249 Query: 249 VEKRDKAFKNK 259 EKR ++ K Sbjct: 250 QEKRTPHYRGK 260 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: 163 Number of extensions: 5 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: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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