Align BadH (characterized)
to candidate WP_036258924.1 DL86_RS05195 acetoacetyl-CoA reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000746085.1:WP_036258924.1 Length = 241 Score = 143 bits (360), Expect = 4e-39 Identities = 90/247 (36%), Positives = 130/247 (52%), Gaps = 9/247 (3%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66 + AV++GG GIG A + G K+A D E A + G + D+++ Sbjct: 3 RVAVVSGGSRGIGAAISKGLHAAGYKVAATYAGND--EAAANFKAETG--IPVYKWDVSN 58 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 + LGP++IL+NNAG F K P +W +I NL +M V+ Sbjct: 59 YKECAEGLKKVGDDLGPIEILINNAGITRDTMFHKMTPEQWFDVINTNLNSLFNMTRPVI 118 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 GM ER GRIVNI+S + G G+ Y A K G + F+K+LA+E+A GITVN VCPG Sbjct: 119 EGMRERGFGRIVNISSINGQKGQMGQTNYTASKAGDIGFTKSLAQENAGKGITVNAVCPG 178 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 T ++ A E L ++ IPL RLG+P+++A + F ++++GFITG LS Sbjct: 179 YIATDMVK-----AVPKEVLEKSVLPLIPLRRLGEPEEVARVVVFLVAEESGFITGSTLS 233 Query: 247 VSGGLTM 253 V+GG M Sbjct: 234 VNGGQYM 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: 155 Number of extensions: 3 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: 255 Length of database: 241 Length adjustment: 24 Effective length of query: 231 Effective length of database: 217 Effective search space: 50127 Effective search space used: 50127 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 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