Align BadH (characterized)
to candidate WP_043743408.1 AMB_RS04300 beta-ketoacyl-ACP reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000009985.1:WP_043743408.1 Length = 240 Score = 141 bits (356), Expect = 1e-38 Identities = 91/248 (36%), Positives = 128/248 (51%), Gaps = 12/248 (4%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKI-AVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIA 65 + A++TGG GIG + G K+ A + N +AA K A +++ D+ Sbjct: 3 RLAIVTGGTRGIGREISVTLKKAGYKVVANYGGNDEAAAKFT-----AETGIPSMKWDVG 57 Query: 66 DRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAV 125 + +AAIA GPV+I+VNNAG + WE +I NLT +M Sbjct: 58 SYPACEAAIAKIVAEHGPVEIIVNNAGITRDATLHRMSYQMWEEVIHTNLTSCFNMARLA 117 Query: 126 LPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCP 185 + M ER GRIVNI S + G G+ YAA K G+ F+K LA+E A ITVN + P Sbjct: 118 IDSMRERGFGRIVNIGSINGQAGQYGQVNYAAAKSGIHGFTKALAQEGAAKNITVNAIAP 177 Query: 186 GPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVL 245 G DT ++ V P ++E IP+GRLG+ +D+A + F +D+A FITG L Sbjct: 178 GYVDTDMVRAV------PPAVLEKIIAKIPVGRLGRAEDIARCVMFLIADEADFITGSTL 231 Query: 246 SVSGGLTM 253 SV+GG M Sbjct: 232 SVNGGQHM 239 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: 166 Number of extensions: 7 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: 240 Length adjustment: 24 Effective length of query: 231 Effective length of database: 216 Effective search space: 49896 Effective search space used: 49896 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 17 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