Align crotonase (EC 4.2.1.150) (characterized)
to candidate GFF2524 PS417_12870 enoyl-CoA hydratase
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__WCS417:GFF2524 Length = 270 Score = 147 bits (371), Expect = 2e-40 Identities = 93/266 (34%), Positives = 139/266 (52%), Gaps = 11/266 (4%) Query: 2 EFKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAF 61 E+ ++E GNVA + +NRP+ +NA+NAA EI I + D V AV+++G+GK F Sbjct: 3 EYHAFVVELIGNVAHVQINRPEKINAMNAAFWTEIIDIFQWIEDTDAVRAVVLSGAGKHF 62 Query: 62 VAGADIAEMKDLTAV----EGRKFSVLGNKI------FRKLENLEKPVIAAINGFALGGG 111 +G D+ + + GR +L KI F ++N KPV+AA+ G+ +GG Sbjct: 63 SSGIDLMMLASVANEFGKDVGRNARLLRRKILELQASFNAVDNCRKPVLAAVQGYCIGGA 122 Query: 112 CELSLSCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEE 171 +L +CD+R A+ A+F E+ +G+ G QRL R IG GM +EL YTG+ AEE Sbjct: 123 IDLISACDMRYAAEGAQFSIKEIDIGMAADVGTLQRLPRIIGDGMLRELAYTGRQFGAEE 182 Query: 172 ALRIGLVNKVV-EPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAE 230 A IGLVN+V + D LL + I +PIAV KA I+ ++ G+ Y A Sbjct: 183 ARSIGLVNRVYPDQDSLLAGVMEIAHEIAAKSPIAVTGTKAMISYMRDHTVNDGLEYVAT 242 Query: 231 VFGECFATEDRVEGMTAFVEKRDKAF 256 + D + A + K+ F Sbjct: 243 WNAAMLQSNDLRVAIAAHMSKQKPEF 268 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: 159 Number of extensions: 9 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: 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 17 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