Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_011384978.1 AMB_RS13070 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_000009985.1:WP_011384978.1 Length = 256 Score = 120 bits (301), Expect = 3e-32 Identities = 79/259 (30%), Positives = 138/259 (53%), Gaps = 7/259 (2%) Query: 4 ELLTSRPTESESTLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFF 63 E+L +P +S ++L ++ P A+NAL+ ++ E + ++ DPS+RA+V+TG F Sbjct: 3 EVLLEKPFDS--VVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEAF 60 Query: 64 CAGGNLNRLLENRAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALAC 123 AG ++ + E A + + ++ LL W A+ KPVIAAV+G A G G L + Sbjct: 61 AAGADIKDMAEVGAIE--LMQRNNHLL--W-RAIANCPKPVIAAVNGYAWGGGCELVMHA 115 Query: 124 DLIVAADDAKFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVV 183 D+IVA ++A F +VG+ P GG+ L +A+ + A +++ G+ I ++G+ Sbjct: 116 DIIVAGENASFSQPEVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQMGLA 175 Query: 184 NKLTKPGTARDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHH 243 + + D A+ A + ++ P ++A+IK ++ A L L+ ER F Sbjct: 176 SVVVPDAEVVDKALEIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLLFAS 235 Query: 244 REGLEGISAFLEKRAPVYK 262 + EG+ AF+EKR P Y+ Sbjct: 236 ADQKEGMKAFIEKRKPTYQ 254 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: 151 Number of extensions: 7 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: 256 Length adjustment: 24 Effective length of query: 238 Effective length of database: 232 Effective search space: 55216 Effective search space used: 55216 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