Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_083510176.1 AU252_RS00745 enoyl-CoA hydratase-related protein
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_001484605.1:WP_083510176.1 Length = 279 Score = 108 bits (271), Expect = 9e-29 Identities = 80/259 (30%), Positives = 135/259 (52%), Gaps = 15/259 (5%) Query: 6 IKVEKDERVARIKIANPPV-NVLDMETMKEIISAIDEVE---GVDVIVFSGEG-KSFSAG 60 + E+ V + I P N ++ + ++ + A++ E G+ +V +G G K+F AG Sbjct: 22 VTAEEIGHVFLVTINRPEARNAVNPDVIRGVGRALEHAEECPGIRAVVITGSGDKAFCAG 81 Query: 61 AEIKEH----FPDKAPEMIRW-FTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVL 115 A++K F + M +W F + + T+AA+ GFALGGG E+ +A D + Sbjct: 82 ADLKSAAVGAFGEIPEGMEQWGFAGFVKHHI--SKPTIAAINGFALGGGTEIVLASDLAI 139 Query: 116 ASKNAKLGVPEITLAHYPPVAIAL-LPRMIGWKNAYELILTGEAITAERAFEIGLVNKVF 174 AS A G+PE+ L + A + + K A E++LTG+ + A+RA EIGLVN+V Sbjct: 140 ASSEAVFGLPEVKLGIFAGAGGAFRAGQQVPKKIAMEMLLTGQPLPAQRALEIGLVNRVV 199 Query: 175 EDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLS-LFDVINDVYLSQ-LVKSE 232 E + + + E + +A++ TK+ T+ S D + +Q L++S Sbjct: 200 PPEEVLPAALELARQICENAPLAVQTTKRIANGITDGTVESDQADWARSEWEAQKLMRST 259 Query: 233 DAVEGLKAFLEKRKPEWKG 251 D +EG++AF EKR P+W+G Sbjct: 260 DFMEGMRAFAEKRAPQWQG 278 Lambda K H 0.318 0.136 0.382 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: 173 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: 252 Length of database: 279 Length adjustment: 25 Effective length of query: 227 Effective length of database: 254 Effective search space: 57658 Effective search space used: 57658 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