Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_041099045.1 SUTH_RS10290 enoyl-CoA hydratase-related protein
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >NCBI__GCF_000828635.1:WP_041099045.1 Length = 268 Score = 90.1 bits (222), Expect = 6e-23 Identities = 70/205 (34%), Positives = 98/205 (47%), Gaps = 6/205 (2%) Query: 26 DEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAGGDI 85 D +GI ITLNRP+ LNAL M L A A + AVV++GAG + F AGGDI Sbjct: 11 DAASGIATITLNRPKALNALDMAMADGLRATTRHVAGDATVRAVVIQGAG-EHFMAGGDI 69 Query: 86 RALYDSFHAGTALHR----QFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHL 141 +A +++ A A R + + ++ + KPV+A + G V G G L A L Sbjct: 70 KAFHETLDAPAAERRALLERLIGEVHEAVTSIRTMEKPVIASVRGAVAGFGFSLMSACDL 129 Query: 142 RVLTERSRVAMPETGIGLVPDVGASHFLSKLPLA-LALYVGLTGVTLGAADTLLCKLADI 200 + + S + IG PD G+++ L +L A A+ + L G AA L L + Sbjct: 130 AIAADSSYFTLAYRHIGTSPDGGSTYALPRLVGAKQAMEIALLGERFNAARALELGLVNR 189 Query: 201 AVPAASLEHFEQTLAAINRTGDVLA 225 VPAA L Q LA G +A Sbjct: 190 VVPAAELAAATQALALELANGPTIA 214 Lambda K H 0.322 0.137 0.405 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: 220 Number of extensions: 13 Number of successful extensions: 3 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: 384 Length of database: 268 Length adjustment: 28 Effective length of query: 356 Effective length of database: 240 Effective search space: 85440 Effective search space used: 85440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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