Align BadH (characterized)
to candidate WP_004671535.1 RHE_RS29990 SDR family oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000092045.1:WP_004671535.1 Length = 255 Score = 156 bits (394), Expect = 4e-43 Identities = 85/247 (34%), Positives = 128/247 (51%), Gaps = 3/247 (1%) Query: 4 LQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRCD 63 L + ++TGGG GIG AT FA+ GA + V D+N DAA +VA I G A VR D Sbjct: 3 LNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEI---GSKAFGVRVD 59 Query: 64 IADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMHH 123 ++ ++ + TT G VD+LVNNAG+ W+R++++N+ G Sbjct: 60 VSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSK 119 Query: 124 AVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNVV 183 V+P M G I+N S A + Y A KG + + ++ +A +HA+ GI VN V Sbjct: 120 YVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAV 179 Query: 184 CPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDAGFITGQ 243 PG D+ + + A +P KL F + R+G +++A A+ F SD + F TG Sbjct: 180 APGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGS 239 Query: 244 VLSVSGG 250 +L+V GG Sbjct: 240 ILTVDGG 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: 159 Number of extensions: 9 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: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 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