Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_083510176.1 AU252_RS00745 enoyl-CoA hydratase-related protein
Query= metacyc::MONOMER-13469 (259 letters) >NCBI__GCF_001484605.1:WP_083510176.1 Length = 279 Score = 153 bits (386), Expect = 4e-42 Identities = 103/255 (40%), Positives = 145/255 (56%), Gaps = 12/255 (4%) Query: 6 IILEKDGNVASITLNRPKALNALNAATLKEIDAAINDIAEDDNVYAVIITGSG-KAFVAG 64 + E+ G+V +T+NRP+A NA+N ++ + A+ E + AV+ITGSG KAF AG Sbjct: 22 VTAEEIGHVFLVTINRPEARNAVNPDVIRGVGRALEHAEECPGIRAVVITGSGDKAFCAG 81 Query: 65 ADIAEMKDLTAVE-GRKFSVLGNKIFRKLENLEKPVIAAINGFALGGGCELSLSCDIRIA 123 AD+ E G F K ++ KP IAAINGFALGGG E+ L+ D+ IA Sbjct: 82 ADLKSAAVGAFGEIPEGMEQWGFAGFVK-HHISKPTIAAINGFALGGGTEIVLASDLAIA 140 Query: 124 SSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGLVNKVVE 183 SS+A FG PEV LGI G GG R + + +A E++ TG+ + A+ AL IGLVN+VV Sbjct: 141 SSEAVFGLPEVKLGIFAGAGGAFRAGQQVPKKIAMEMLLTGQPLPAQRALEIGLVNRVVP 200 Query: 184 PDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVA------YEAEVFGECFA 237 P+++L A L I NAP+AV+ K N +++ A +EA+ + Sbjct: 201 PEEVLPAALELARQICENAPLAVQTTKRIANGITDGTVESDQADWARSEWEAQ---KLMR 257 Query: 238 TEDRVEGMTAFVEKR 252 + D +EGM AF EKR Sbjct: 258 STDFMEGMRAFAEKR 272 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: 168 Number of extensions: 13 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: 279 Length adjustment: 25 Effective length of query: 234 Effective length of database: 254 Effective search space: 59436 Effective search space used: 59436 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