Align BadH (characterized)
to candidate WP_011427206.1 RHE_RS20550 beta-ketoacyl-ACP reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000092045.1:WP_011427206.1 Length = 241 Score = 163 bits (412), Expect = 3e-45 Identities = 98/246 (39%), Positives = 135/246 (54%), Gaps = 11/246 (4%) Query: 6 NKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65 ++ A++TGG GIG A G ++A D + A A D G A + D++ Sbjct: 2 SRVALVTGGTRGIGAAISTALKNAGYRVAATYAGND---EKAHAFHDVTGVA-VFKWDVS 57 Query: 66 DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAV 125 D + I +GPV+ILVNNAG F K P +W +I NLTG +M H V Sbjct: 58 DYAACGEGITKVEGEIGPVEILVNNAGITRDAMFHKMTPQQWHEVINTNLTGLFNMTHQV 117 Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185 GM +R GRIVNI+S + G G+A Y+A K G + F+K LA+E A ITVN +CP Sbjct: 118 WSGMRDRSFGRIVNISSINGQKGQMGQANYSAAKAGDLGFTKALAQEGAAKNITVNAICP 177 Query: 186 GPTDTALLADVTSGAANPEKLI-EAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQV 244 G T ++ V PEK++ E IP+GRLG+P+++A + F SDDAGFITG Sbjct: 178 GYIGTEMVLAV------PEKVLNERIIPQIPVGRLGEPEEIARCVTFLVSDDAGFITGST 231 Query: 245 LSVSGG 250 L+ +GG Sbjct: 232 LTANGG 237 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: 179 Number of extensions: 5 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: 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