Align BadH (characterized)
to candidate WP_066329803.1 BLR17_RS09120 SDR family oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_900100165.1:WP_066329803.1 Length = 254 Score = 137 bits (344), Expect = 3e-37 Identities = 80/252 (31%), Positives = 133/252 (52%), Gaps = 6/252 (2%) Query: 1 MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAV 60 M L++K A+ITGGG GIG A FA++GA++ + +L ++A+ I GG A Sbjct: 1 MFSLKDKKAIITGGGSGIGKAISVLFAKQGAEVHIIELTAESAQSTVDEITAEGGKVFAH 60 Query: 61 RCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALH 120 C++A V A T +G + ILVNNAG T +++R++ +N+ G + Sbjct: 61 ACNVAKHDEVVA----TFEKIGNIHILVNNAGIAHVGKVDTTPEADFDRIMDVNVKGVYN 116 Query: 121 MHHAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITV 180 A +P + G IVN+AS A+ VG S Y+ KG +++ + ++AR++ I Sbjct: 117 CLFASIPQFRKSGGGSIVNMASIASWVGISDRFAYSTAKGAVMSMTLSVARDYINENIRC 176 Query: 181 NVVCPGPTDTALLAD--VTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAG 238 N + P T + + N ++ + +K+ P+GR+GKP+++A F S++AG Sbjct: 177 NSISPARVHTPFVDGFIAKNYPGNEAEIFDKLSKSQPIGRMGKPEEIATLALFLASEEAG 236 Query: 239 FITGQVLSVSGG 250 FITG + GG Sbjct: 237 FITGSDYPIDGG 248 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: 156 Number of extensions: 4 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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: 47 (22.7 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