Align BadH (characterized)
to candidate WP_057507496.1 ABB28_RS04570 NAD(P)-dependent oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_001431535.1:WP_057507496.1 Length = 253 Score = 156 bits (394), Expect = 4e-43 Identities = 90/246 (36%), Positives = 129/246 (52%), Gaps = 7/246 (2%) Query: 7 KTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCDIAD 66 KT ++TG G GIG AT R F+ GA + + D + +AG + V D++D Sbjct: 6 KTVIVTGAGSGIGAATARAFSNAGANVVLADRDHPDVAALAGELAAERTLVHDV--DVSD 63 Query: 67 RTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHHAVL 126 V A + T G +D++ NNAG + P T +W R++A+NLTG A L Sbjct: 64 EAQVQALVDATVKRFGGLDVIFNNAGILVEGPAEDTSLEDWNRIVAVNLTGVFLGCRAAL 123 Query: 127 PGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVVCPG 186 P + +R G IVN AS + Y A KG + ++ LA ++ RHG+ VN VCP Sbjct: 124 PEL-RKRKGCIVNTASVSGLAADRNMPAYNAVKGAVANLTRALAIDNGRHGVRVNAVCPT 182 Query: 187 PTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQVLS 246 T T++ A+ A L+ F IP+GRLG+P+D+A A+ SD AGFITG L Sbjct: 183 FTRTSMTAEKEKDKA----LVTNFLNRIPMGRLGEPEDIANAVLLLASDHAGFITGVNLP 238 Query: 247 VSGGLT 252 V GG++ Sbjct: 239 VDGGVS 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: 11 Number of successful extensions: 4 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: 253 Length adjustment: 24 Effective length of query: 231 Effective length of database: 229 Effective search space: 52899 Effective search space used: 52899 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