Align BadH (characterized)
to candidate WP_053939027.1 WG78_RS16965 acetoacetyl-CoA reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001294205.1:WP_053939027.1 Length = 244 Score = 154 bits (390), Expect = 1e-42 Identities = 88/244 (36%), Positives = 130/244 (53%), Gaps = 6/244 (2%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66 + A++TGG GGIG A CR+ A G ++A E+ AG A C++AD Sbjct: 3 RLALVTGGMGGIGTAICRQLADAGYQVATTYSRTGRQEQWLADATAAGYAFHAFECNVAD 62 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 S A A LG VDILVNNAG F K +W+ ++ NL ++ + Sbjct: 63 YASCSAMAAALREKLGEVDILVNNAGITRDATFRKLSQPDWDAVMGTNLDSLFNVSKQFV 122 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 M ER GR++NI+S + G G+ Y+A K G+ F+ LA+E AR G+TVN + PG Sbjct: 123 DSMSERGWGRVINISSINGQKGQFGQTNYSAAKAGMHGFTMALAQEVARKGVTVNTISPG 182 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 T ++ V P ++ E IP+GRLGKP+++A I + S+ AGF+TG ++ Sbjct: 183 YIATEMVMAV------PVEIRERIVGQIPVGRLGKPEEVASLIVWLASEMAGFVTGANIA 236 Query: 247 VSGG 250 ++GG Sbjct: 237 INGG 240 Lambda K H 0.318 0.135 0.398 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: 177 Number of extensions: 9 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: 255 Length of database: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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: 46 (22.3 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