Align BadH (characterized)
to candidate SMc00268 SMc00268 oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >FitnessBrowser__Smeli:SMc00268 Length = 252 Score = 153 bits (386), Expect = 4e-42 Identities = 92/253 (36%), Positives = 137/253 (54%), Gaps = 12/253 (4%) Query: 2 ARLQNKTAVITGGGG--GIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEA 59 A L+ AVITG G+G AT R FA+ GA +A+ DL+ A + A ++ G Sbjct: 4 ALLEGNFAVITGAASRRGLGKATARLFAEHGATVAILDLDEADAREAAASL---GPRHVG 60 Query: 60 VRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGAL 119 + C++ D SV + + G +DILVNNAG + P ++ ++ +NL G L Sbjct: 61 MACNVTDLASVRTVMDALVSQWGRIDILVNNAGITQPLKIMEIAPENYDAVLDVNLRGTL 120 Query: 120 HMHHAVLPGMVERRHGRIVNIASDAARVGSS--GEAVYAACKGGLVAFSKTLAREHARHG 177 + AV+P M R+ G+IVN++S +A+ G G Y+A K G++ +K +ARE A Sbjct: 121 YCSQAVIPHMRSRKQGKIVNLSSVSAQRGGGIFGGPHYSAAKAGVLGLTKAMARELAPDN 180 Query: 178 ITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAFFGSDDA 237 + VN +CPG + D+T G PEKL E IP+GR G DD+AG F SD + Sbjct: 181 VRVNAICPG----FIATDITGGLLTPEKL-EEIKAGIPMGRPGTADDVAGCALFLASDLS 235 Query: 238 GFITGQVLSVSGG 250 ++TG + V+GG Sbjct: 236 AYVTGSEVDVNGG 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: 188 Number of extensions: 15 Number of successful extensions: 6 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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 17 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