Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Ga0059261_2632 Ga0059261_2632 FAD binding domain
Query= reanno::Smeli:SMc00833 (405 letters) >FitnessBrowser__Korea:Ga0059261_2632 Length = 364 Score = 277 bits (709), Expect = 3e-79 Identities = 166/372 (44%), Positives = 207/372 (55%), Gaps = 28/372 (7%) Query: 27 LAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMTMSALAGTPVAEVEAALHAKGQ 86 L + GGG++ +G P A + + R SGIV YDP E+ ++ AGTP+A++EA + +GQ Sbjct: 20 LRLRGGGSKDAIGAPCDA-QVVDMRGFSGIVDYDPPELVLTVGAGTPLAQIEALVVGEGQ 78 Query: 87 MLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGAARDSLLGVRFVNGRGEPIKAG 146 ML+F+P DH + G TIGGV AA V+GP R G ARD LLG V+GRGE AG Sbjct: 79 MLAFDPFDHGAMLGNDGGATIGGVVAAGVAGPARLSRGGARDHLLGFTAVSGRGERFVAG 138 Query: 147 GRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPAAATVVVSGLNDAEAAAVMAEA 206 +V+KNVTG DL KLMAGS+G L LTEVT KVLP P T+ + GL+ A A A MA A Sbjct: 139 AKVVKNVTGYDLPKLMAGSWGRLAALTEVTLKVLPAPRTRLTLAMRGLDAAGAVAAMARA 198 Query: 207 MAQPVEVSGASHLPESVRSRFLDGALPDGAATVLRLEGLAASVAIRAEKLGEKLSRFGRI 266 + EV+ A+HLP+ A T LRL+G A SVA RA L E F I Sbjct: 199 LGSAAEVTAAAHLPD----------WRGEAVTALRLDGFAESVAARAAMLPE----FDAI 244 Query: 267 SQLDEAQTRTLWAEIRDVKPYADGTRRPLWRISVAPSAGHQLVAALRLQTGVDAFYDWQG 326 D LW +RD P PLWR+ VAP ++AAL DW G Sbjct: 245 EDAD-----ALWRAVRDASPLP--REWPLWRLIVAPGKAPGVIAAL---PDAQWLLDWAG 294 Query: 327 GLVWLRMEADPEAELLRRYIGAVGGGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRA 386 GL+WL +A P A R GGHA L RA E R +PA PQP A+A + R+R Sbjct: 295 GLIWLTSDAGPVA---IRTAAEAAGGHATLWRASEAMRRAVPALHPQPGALAAIEARVRR 351 Query: 387 QFDPSGIFNPGR 398 FDP G+F GR Sbjct: 352 AFDPGGVFETGR 363 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: 498 Number of extensions: 28 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: 405 Length of database: 364 Length adjustment: 30 Effective length of query: 375 Effective length of database: 334 Effective search space: 125250 Effective search space used: 125250 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 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