Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate AZOBR_RS05730 AZOBR_RS05730 2-hydroxy-acid oxidase
Query= reanno::Smeli:SMc00833 (405 letters) >FitnessBrowser__azobra:AZOBR_RS05730 Length = 417 Score = 298 bits (763), Expect = 2e-85 Identities = 173/414 (41%), Positives = 239/414 (57%), Gaps = 23/414 (5%) Query: 6 EPASEEGIASVVRSAAAERVTLAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMT 65 +P S A VR A +E L V G G++ GLG P++ TL LSG+V Y+ E+ Sbjct: 7 KPDSAAQAADAVRWALSEGTPLDVAGSGSKRGLGRPIQTAYTLDLSGLSGVVAYEAEELV 66 Query: 66 MSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATT-GEPTIGGVFAANVSGPRRYVAG 124 ++A AGTP+AE+ L + Q +FEP D P+F G+ T+GGV + ++GPRR AG Sbjct: 67 LTARAGTPMAEILPMLAERRQQFAFEPQDLGPLFGRPEGQGTLGGVISCGLAGPRRISAG 126 Query: 125 AARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPP 184 +ARD LG+ VNGRG+ K GG+V+KNVTG D+ KLMAGS+GTL +LTE+T KVLP Sbjct: 127 SARDHTLGIEGVNGRGDLYKGGGKVVKNVTGYDVPKLMAGSFGTLTVLTELTVKVLPASE 186 Query: 185 AAATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPESV--RSRFLDGALPDGAATVLRL 242 T++++G DA A A + A+ P +VSGA+HLP +V RS A GA T++R+ Sbjct: 187 DVRTLLLAGREDAGAVAALTAALQSPYDVSGAAHLPAAVAARSHVRAVAAVGGAVTLVRV 246 Query: 243 EGLAASVAIRAEKLGEKLSRFGRISQLDEAQTRTLWAEIRDV-------KPYADG----- 290 EG SV R L E+L G + LD ++ +W E+RDV P + G Sbjct: 247 EGFGPSVIARVAALKEEL---GADAVLDRDESLAVWKEVRDVAYFGPTPSPASAGEGWGG 303 Query: 291 --TRRPLWRISVAPSAGHQLVAALRLQTGVDAFYDWQGGLVWLRMEADPEAELLRRYIGA 348 R +W+ISV PS G ++ ++R + ++DW GGL+W + P+A R GA Sbjct: 304 GEDSRHIWKISVQPSEGPRVAESIRWALDAELYFDWGGGLIWAAVAPTPDAASAIR--GA 361 Query: 349 VG-GGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRAQFDPSGIFNPGRAAA 401 +G GHA L+RA E+ R F P P V LS R++ FDP GI NPGR A Sbjct: 362 LGTAGHATLVRAPEDVRTTTEVFHPLPDPVKALSRRVKESFDPCGILNPGRMYA 415 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: 538 Number of extensions: 31 Number of successful extensions: 5 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: 405 Length of database: 417 Length adjustment: 31 Effective length of query: 374 Effective length of database: 386 Effective search space: 144364 Effective search space used: 144364 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: 50 (23.9 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