Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_012757048.1 RLEG_RS07315 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_000023185.1:WP_012757048.1 Length = 259 Score = 161 bits (407), Expect = 1e-44 Identities = 98/255 (38%), Positives = 137/255 (53%), Gaps = 7/255 (2%) Query: 8 LEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAGADI 67 ++ DG+VA++T++RP+ LNAL+ LK + A +++ + NV A I+TG GK F AG DI Sbjct: 8 IDVDGHVATLTISRPEKLNALDLDMLKALADAADEVEANANVRAAILTGEGKGFSAGGDI 67 Query: 68 AEMKDLTAVE-GRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIASSK 126 + E G + G++IF +L L P+IAA+NG ALGGG EL+ DIR+A + Sbjct: 68 KAWGGMLPQEFGHLWVRHGHRIFERLATLRVPLIAALNGHALGGGLELAGVADIRLAEEQ 127 Query: 127 AKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVEPDK 186 K G PE GLG+ PG+ GTQRL R + + G++ AEEA +G+V+ VV Sbjct: 128 IKIGLPETGLGMVPGWSGTQRLVRRFSAQAVRRMALGGEIFTAEEARLLGIVDAVVPTGN 187 Query: 187 LLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA--TEDRVEG 244 L A+ I P A + K I D T V E G A T D EG Sbjct: 188 ALAAAREYAQRIAARGPAATEIAKLMIASANGEDNGTAV----EALGSILAAKTGDLKEG 243 Query: 245 MTAFVEKRDKAFKNK 259 + +F EKR FK + Sbjct: 244 VASFSEKRPATFKGE 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: 169 Number of extensions: 12 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: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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 Apr 09 2024. 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