Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_012047279.1 BBTA_RS35265 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_000015165.1:WP_012047279.1 Length = 264 Score = 139 bits (349), Expect = 8e-38 Identities = 92/249 (36%), Positives = 131/249 (52%), Gaps = 5/249 (2%) Query: 17 LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENR 76 L +T++ P RNAL+ DM +EA DP +RAV++ GA FC GG++ + E + Sbjct: 16 LTITMNRPERRNALNSDMTKGLVEAAHRAADDPEVRAVLLKGAGGTFCVGGDVKAMAEAK 75 Query: 77 AKDPSVQAQSIDLLAEWISALRL---SSKPVIAAVDGAAAGAGFSLALACDLIVAADDAK 133 PS + + + L E + RL KPV+A +DGAAAGAG S+ALACDL VAA AK Sbjct: 76 GA-PSFETK-VSTLRERMEVSRLLHQMQKPVVAQIDGAAAGAGLSIALACDLRVAAASAK 133 Query: 134 FVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTAR 193 ++A+VGL+ D GG++FL Q L A E+ + + A LG+V K+ Sbjct: 134 ITTAFAKVGLSGDFGGTYFLTQLLGSAKARELYLTSPILSAQEALALGMVTKVVPDAEVD 193 Query: 194 DAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAF 253 AA A A L + ++ IK + A T L AE + + E AF Sbjct: 194 AAARALALSLAEGPSVTLGYIKRNINNAETMTLEACFDAEAVHHSRCSDTEDHKEAAKAF 253 Query: 254 LEKRAPVYK 262 +EKRAPV++ Sbjct: 254 VEKRAPVFR 262 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: 134 Number of extensions: 4 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 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