Align BadH (characterized)
to candidate WP_059149763.1 V474_RS01280 SDR family oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001046635.1:WP_059149763.1 Length = 250 Score = 181 bits (459), Expect = 1e-50 Identities = 101/250 (40%), Positives = 144/250 (57%), Gaps = 7/250 (2%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63 L K AVITG G GIG R A++ A IAV+DLN + A + I AGG A A+ D Sbjct: 5 LDGKVAVITGAGSGIGRGIALRLAEDKAAIAVWDLNPEGAAETVKLIEAAGGKALAIVAD 64 Query: 64 IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123 +D+ ++ AA T GP+ ILVNNAG F PF E++++I INL G + Sbjct: 65 CSDKAAIRAAADETRAKFGPITILVNNAGIAPFTPFMDIPEDEFDKVIRINLKGPWLVTR 124 Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183 ++P M+ + GRI+NI S + + GS ++ Y A KGGL+ +K LA E + GIT N++ Sbjct: 125 EIVPDMLAAQWGRIINITSSSTQSGSFAQSHYVASKGGLLGLTKALALELGKTGITANMI 184 Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243 PG DT +L A EA+ ++P+GRLG+ D+A A AF S++A ++TGQ Sbjct: 185 PPGSIDTPMLRSAPIDA-------EAYGASLPVGRLGQVADIAAAAAFLASEEASYMTGQ 237 Query: 244 VLSVSGGLTM 253 +S +GG M Sbjct: 238 TISTNGGRYM 247 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: 175 Number of extensions: 8 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: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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