Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_011779219.1 MVAN_RS09980 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000015305.1:WP_011779219.1 Length = 270 Score = 152 bits (384), Expect = 7e-42 Identities = 102/267 (38%), Positives = 148/267 (55%), Gaps = 26/267 (9%) Query: 3 FKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFV 62 + I E DG+ A+ITLNRP+ALNAL+ + E+ AA ++ DD+++ +I+TG+G+AF Sbjct: 6 YDTIGYEVDGHKATITLNRPEALNALSPHMINELRAAYDEAENDDDIWLMIVTGTGRAFC 65 Query: 63 AGADIAEMKD----------LTAVEGRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGC 112 GAD+ E+ + L+ + + G FR+ + KPV+AAING G G Sbjct: 66 TGADVKEIPEDGKVIYERPYLSTYDQWEAPQEGTPPFRR---MAKPVLAAINGICCGAGL 122 Query: 113 ELSLSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGK--VINAE 170 + + DI IAS KA F P V +G+ RLARA+ +A + GK ++AE Sbjct: 123 DWVTTGDIVIASDKATFFDPHVSIGLVAA-REMVRLARALPRSVALRMALMGKHERMSAE 181 Query: 171 EALRIGLVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAE 230 A +G++ +VVE DKLLE A + D + NAP+AVR + AI++ L + E E Sbjct: 182 RAYELGMITEVVEHDKLLERAHEIADIVNSNAPLAVRGTRLAIHKTLDLPL-----LEGE 236 Query: 231 VFGECF-----ATEDRVEGMTAFVEKR 252 + E F TED EG AFVEKR Sbjct: 237 ILAETFRERVVRTEDAQEGPLAFVEKR 263 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: 10 Number of successful extensions: 5 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: 270 Length adjustment: 25 Effective length of query: 234 Effective length of database: 245 Effective search space: 57330 Effective search space used: 57330 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