Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate H281DRAFT_02585 H281DRAFT_02585 FAD/FMN-containing dehydrogenase
Query= reanno::Smeli:SMc00833 (405 letters) >FitnessBrowser__Burk376:H281DRAFT_02585 Length = 461 Score = 84.7 bits (208), Expect = 5e-21 Identities = 64/184 (34%), Positives = 86/184 (46%), Gaps = 10/184 (5%) Query: 7 PASEEGIASVVRSAAAERVTLAVVGGGTR-AGLGNPVRADRTLSTRRLSGIVTYDPAEMT 65 P S E +A +R A + GG T G N + + LS R++ IV D T Sbjct: 47 PRSTEDVARALRVCHAFSQPVVTQGGLTGLVGGANALGGEVALSLERMNRIVEVDRTSAT 106 Query: 66 MSALAGTPVAEV-EAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAG 124 M+ AG P+ V EAAL A + P+D G TIGG A N G R G Sbjct: 107 MTVEAGVPLQVVQEAALDAG----FYFPLD----LGARGSCTIGGNLATNAGGNRVIKYG 158 Query: 125 AARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPP 184 RD +LG+ V GE +++KN +G DL L+ GS GTL ++T ++ P P Sbjct: 159 MMRDQVLGIEAVLANGEVTSGMHKMIKNNSGYDLRHLLIGSEGTLAVITRAVLRLRPRPT 218 Query: 185 AAAT 188 A AT Sbjct: 219 AVAT 222 Lambda K H 0.318 0.134 0.387 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: 412 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 405 Length of database: 461 Length adjustment: 32 Effective length of query: 373 Effective length of database: 429 Effective search space: 160017 Effective search space used: 160017 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: 51 (24.3 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