Align BadH (characterized)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Marino:GFF2263 Length = 247 Score = 157 bits (398), Expect = 1e-43 Identities = 88/250 (35%), Positives = 141/250 (56%), Gaps = 6/250 (2%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63 L+ KTA++TG GIG A R A +GA++ + AE + ++ AG + + Sbjct: 3 LEGKTALVTGATRGIGQAIARALAAQGAEVVGTATSEAGAESITNDLQSAGYKGYGMVMN 62 Query: 64 IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123 +AD S++A + T G ILVNNAG + + +W ++ NL+ Sbjct: 63 VADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKDDDWASVLETNLSSVYRTSK 122 Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183 AVL GM + + GRI+NI+S A +G++G+ Y A K G+ F+++LA+E + GIT N V Sbjct: 123 AVLRGMAKAKWGRIINISSVVAGMGNAGQGNYCAAKAGVEGFTRSLAKEMSNRGITANCV 182 Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243 PG DT D+T + ++ A + IP GRLG+P+++A +AF SD AG++TG+ Sbjct: 183 APGFIDT----DMTKKLDDKQR--GAMLEIIPAGRLGEPEEVAAVVAFLASDAAGYVTGE 236 Query: 244 VLSVSGGLTM 253 ++V+GG+ M Sbjct: 237 TINVNGGMYM 246 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: 164 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: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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