Align crotonase (EC 4.2.1.150) (characterized)
to candidate Echvi_0069 Echvi_0069 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-13469 (259 letters) >FitnessBrowser__Cola:Echvi_0069 Length = 260 Score = 136 bits (342), Expect = 5e-37 Identities = 84/260 (32%), Positives = 136/260 (52%), Gaps = 6/260 (2%) Query: 1 MEFKNIILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKA 60 M++K I + + I ++RP NALN L+E+ AA + A+ + V V++TG G A Sbjct: 1 MDYKYIRSSVNNHCQEIAIDRPAVFNALNFEVLEELKAAFDQAAQAETVRCVVLTGGGGA 60 Query: 61 FVAGADIAEMKDLTAVEGRKFSVLGNKIFRKL----ENLEKPVIAAINGFALGGGCELSL 116 F +G D+ + T ++G F + K + L NL KP+I +NG A+G GC L+L Sbjct: 61 FCSGQDLKAVG--TDLDGIPFKEIIRKYYNPLIIQMRNLSKPIICKLNGAAVGAGCSLAL 118 Query: 117 SCDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIG 176 + D+ IAS +A + +G+ G L + +G +A EL TG+ + AEEA R+G Sbjct: 119 ATDVIIASKEAYLAEMFAHIGLVMDAGSNYFLPKRVGYPLAFELATTGRKVYAEEAERLG 178 Query: 177 LVNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECF 236 LVNK +E L E V+ + + A+ M K + + ++ + EA + Sbjct: 179 LVNKAIEHSALDETVAQYVEVYVNASGSAIGMIKEMLRKSNGMSLEEVLEMEAVYQEKAG 238 Query: 237 ATEDRVEGMTAFVEKRDKAF 256 + +D EG+T+F+EKR F Sbjct: 239 SHQDFKEGVTSFLEKRKPRF 258 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: 143 Number of extensions: 8 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 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