Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate SM_b21129 SM_b21129 oxidoreductase
Query= reanno::Smeli:SMc00833 (405 letters) >FitnessBrowser__Smeli:SM_b21129 Length = 442 Score = 102 bits (255), Expect = 2e-26 Identities = 74/217 (34%), Positives = 104/217 (47%), Gaps = 8/217 (3%) Query: 7 PASEEGIASVVRSAAAERVTLAVVGGGTR-AGLGNPVRADRTLSTRRLSGIVTYDPAEMT 65 PAS +A +R A R + GG T AG NP D +S RLSGI D A T Sbjct: 29 PASVAEVADALRICNAHRQAVVPQGGLTGLAGGANPCAGDVAISLERLSGIEEIDAAAGT 88 Query: 66 MSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGA 125 M+ LAGTP+ + A G +L P+D G +GG A N G R G Sbjct: 89 MTVLAGTPLEVAQRAAEDAGFLL---PID----LGARGSCQVGGNLATNAGGIRVIRNGV 141 Query: 126 ARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPA 185 ARD++LG+ V G + + +++KN TG DL +L GS GTLGI+T ++ PLP Sbjct: 142 ARDNVLGLEAVLADGTVLSSMNKMIKNNTGYDLRQLFIGSEGTLGIITRAVLRLRPLPAG 201 Query: 186 AATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPES 222 T + + + A++ A + +S + ES Sbjct: 202 RLTALCALDSYENVVALLKRAQKELAGLSAYEAMWES 238 Score = 29.3 bits (64), Expect = 2e-04 Identities = 12/24 (50%), Positives = 15/24 (62%) Query: 375 PAVARLSERIRAQFDPSGIFNPGR 398 PA L RI+ DP+GI NPG+ Sbjct: 414 PAELELMRRIKNALDPNGILNPGK 437 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: 435 Number of extensions: 27 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: 2 Length of query: 405 Length of database: 442 Length adjustment: 32 Effective length of query: 373 Effective length of database: 410 Effective search space: 152930 Effective search space used: 152930 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