Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate AZOBR_RS15730 AZOBR_RS15730 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__azobra:AZOBR_RS15730 Length = 266 Score = 213 bits (543), Expect = 3e-60 Identities = 120/245 (48%), Positives = 156/245 (63%), Gaps = 1/245 (0%) Query: 17 LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENR 76 L LT+++P RN++ P + A A D+ DP + AVV+TGA+ FC+GGNL L E R Sbjct: 20 LRLTINDPATRNSIGPALMEAARAAFDAAAADPGVGAVVLTGAEGAFCSGGNLKWLKEAR 79 Query: 77 AKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFVM 136 D ++ I +LR KPVIAAV+G A GAGF LALACDLIVAA+DA F + Sbjct: 80 GGDRESVRAGVESFHAMIRSLRACPKPVIAAVEGPAGGAGFPLALACDLIVAAEDAVFTL 139 Query: 137 SYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDAA 196 SY +V LT DGGG+ LA+ALP QLA E+L EG +GA RL +LG++N+LT PG A A Sbjct: 140 SYIKVALTSDGGGTASLARALPPQLAAEILFEGGRVGAPRLAQLGMINRLTAPGGALAEA 199 Query: 197 VAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLEK 256 AWA+ L ++ R K L+ A L++ L ERD FV SL + E EG++AF EK Sbjct: 200 TAWAERLAAGPTAALGRAKGLLEVA-YGGLADQLDRERDAFVESLFNDEAGEGVTAFFEK 258 Query: 257 RAPVY 261 RAPV+ Sbjct: 259 RAPVF 263 Lambda K H 0.317 0.132 0.377 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: 184 Number of extensions: 6 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: 262 Length of database: 266 Length adjustment: 25 Effective length of query: 237 Effective length of database: 241 Effective search space: 57117 Effective search space used: 57117 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