Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate AO356_30355 AO356_30355 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30355 Length = 264 Score = 108 bits (269), Expect = 1e-28 Identities = 79/247 (31%), Positives = 117/247 (47%), Gaps = 4/247 (1%) Query: 17 LVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLENR 76 +V L+ P +NAL M + AL + + + I VITGA + FC+GG+L R Sbjct: 13 MVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGGDLGRRAAES 72 Query: 77 AK-DPSVQAQSIDLLA---EWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDA 132 A+ DP+ + I L + A+ KP+IAAV+GAA GAG L+L CD+ A++ A Sbjct: 73 AEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRFASESA 132 Query: 133 KFVMSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTA 192 +F +Y RVGL P GG + L + + A E+L G + A LG+VN++ Sbjct: 133 RFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVFSDDEL 192 Query: 193 RDAAVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISA 252 + +A L P IK L+ + L L + + E I A Sbjct: 193 MQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQSTDDYKEAIKA 252 Query: 253 FLEKRAP 259 + EKR P Sbjct: 253 YKEKRKP 259 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: 130 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 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