Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate RR42_RS23450 RR42_RS23450 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__Cup4G11:RR42_RS23450 Length = 264 Score = 131 bits (330), Expect = 1e-35 Identities = 83/245 (33%), Positives = 125/245 (51%), Gaps = 4/245 (1%) Query: 18 VLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLN---RLLE 74 V+ L+ P RNA+ DM I+AL+ V D ++RA+VITG FCAGG+++ R +E Sbjct: 17 VIALNRPEKRNAMSDDMRTEFIDALERVAADKAVRALVITGNGKGFCAGGDVSGMKRRME 76 Query: 75 NRAKDPSVQAQSIDLLAEWISAL-RLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAK 133 + S + L KP +AAV+GAAAG G AL CD ++A++ A Sbjct: 77 APQGEVGFNGWSRQQRVHYTQKLLHTMPKPTVAAVNGAAAGLGADTALCCDFVIASEHAS 136 Query: 134 FVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTAR 193 F SY GL PDGGG +FL + + A E++ G+ + E+G+V++++ + Sbjct: 137 FSWSYINRGLIPDGGGMYFLPRRVGLAKAKELVFTGRKVAIEEAKEIGIVDRVSHADSLV 196 Query: 194 DAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAF 253 AVAWA EL + SP ++A KT++ + P + E E + AF Sbjct: 197 ADAVAWAKELSQGSPTAIALGKTIMNQSYELPADQIFAQGSQAQGICYTSAEHRESVLAF 256 Query: 254 LEKRA 258 L K A Sbjct: 257 LNKLA 261 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: 141 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: 264 Length adjustment: 25 Effective length of query: 237 Effective length of database: 239 Effective search space: 56643 Effective search space used: 56643 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