Align BadH (characterized)
to candidate WP_068009499.1 PsAD2_RS18845 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001623255.1:WP_068009499.1 Length = 245 Score = 166 bits (419), Expect = 5e-46 Identities = 91/253 (35%), Positives = 140/253 (55%), Gaps = 9/253 (3%) Query: 1 MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60 M L+ K+A++TG GGIG A R +GA + + E +A D G Sbjct: 1 MFNLEGKSALVTGATGGIGEAIARSLHTQGATVTLSGTREAKLEALAA---DLGDRVHIK 57 Query: 61 RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120 +++DR SVD I +G +DILVNNAG F + + EW++++ +NL+ Sbjct: 58 AANLSDRDSVDELIPAAEEFMGGLDILVNNAGITRDNIFMRMKDEEWDQVLEVNLSATFR 117 Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180 + A + GM++RRHGRI+ I S G++G+ Y+A K G++ SK+LA+E A ITV Sbjct: 118 ICRAAIKGMMKRRHGRIIGITSIVGVTGNAGQVNYSAAKAGMIGMSKSLAQEVASRKITV 177 Query: 181 NVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFI 240 N + PG TA+ ++ EK ++ +P GRLG D++A A + SD+AG++ Sbjct: 178 NTIAPGFIATAMTDELN------EKQRDSILGNVPAGRLGTADEIASAAVYLASDEAGYV 231 Query: 241 TGQVLSVSGGLTM 253 TGQ L V+GG+ M Sbjct: 232 TGQTLHVNGGMAM 244 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: 172 Number of extensions: 6 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: 245 Length adjustment: 24 Effective length of query: 231 Effective length of database: 221 Effective search space: 51051 Effective search space used: 51051 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