Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_068864712.1 I603_RS10325 crotonase/enoyl-CoA hydratase family protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_001677335.1:WP_068864712.1 Length = 265 Score = 171 bits (432), Expect = 2e-47 Identities = 106/262 (40%), Positives = 143/262 (54%), Gaps = 8/262 (3%) Query: 6 IILEKDGNVASITLNRPKALNALNAATLKEIDAAIND-IAEDDNVYAVIITGSGKAFVAG 64 I + ++G V +TL+R + +N L A + A+I D I D VI+TG+G+AF AG Sbjct: 4 IRIAREGPVTILTLDRAETMNPLGAPGDGDAFASIADAINRDMECRVVILTGAGRAFSAG 63 Query: 65 ADIAEMKDLTAVEGRKFSVLGN-------KIFRKLENLEKPVIAAINGFALGGGCELSLS 117 DI M+D T G + + ++ R L L PVIAA+NG A+G GC+++ Sbjct: 64 GDIKAMRDKTGTFGGTAPAISDGYRDNIHRMLRALHGLRVPVIAAVNGPAIGLGCDVACL 123 Query: 118 CDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGL 177 DIRIAS AKFG + LGI PG GGT L R IG+ A EL YTG VI+A A GL Sbjct: 124 ADIRIASENAKFGVTFLKLGIIPGDGGTWILPRVIGMSRAAELFYTGDVIDAATAKEWGL 183 Query: 178 VNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA 237 V++VV PD L++EA+AL I P A+R K + QG Q DT + A Sbjct: 184 VSRVVAPDALMDEARALAGRIAAMPPHALRQSKMLLRQGQQVSYDTALEMAANTQAMMHT 243 Query: 238 TEDRVEGMTAFVEKRDKAFKNK 259 T D EG+ A + KR F+ + Sbjct: 244 TADHAEGVAALIAKRVPDFRGE 265 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: 179 Number of extensions: 10 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: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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