Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_092483962.1 BM299_RS10985 FAD-linked oxidase C-terminal domain-containing protein
Query= reanno::Smeli:SMc00833 (405 letters) >NCBI__GCF_900115975.1:WP_092483962.1 Length = 458 Score = 102 bits (253), Expect = 3e-26 Identities = 85/289 (29%), Positives = 125/289 (43%), Gaps = 20/289 (6%) Query: 7 PASEEGIASVVRSAAAERVTLAVVGGGTRAGLGN-PVRADRTLSTRRLSGIVTYDPAEMT 65 P + +A +VR A + + G GT G+ P + R++ I+ ++ Sbjct: 45 PGNAREVAEIVRLANEKGFPIFPRGAGTGLSGGSVPAEQGLAMVLSRMNRILEISRDDLL 104 Query: 66 MSALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATTGEPTIGGVFAANVSGPRRYVAGA 125 G + A+ +G +P + TIGG A N GPR + G Sbjct: 105 AVVEPGVVTGRLHRAVEKEGLFYPPDPSSLQTC-------TIGGNVAENAGGPRAFKYGV 157 Query: 126 ARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLPLPPA 185 RD +LG+ V GE I GGR +KNVTG DL L+ GS GTLGI+T +T +++P P A Sbjct: 158 TRDYVLGLEVVTPTGEIINTGGRTVKNVTGYDLTGLLTGSEGTLGIITRITLRLVPKPRA 217 Query: 186 AATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPESVRSRFLDGAL------PDGAATV 239 T ++ N E AA AM + + L + + R ++ L GA + Sbjct: 218 VQT-ALAVYNRVEDAASTVTAMIRRGIIPATLELMDRITIRCVENYLRLGLPMDAGAILL 276 Query: 240 LRLEGLAASVAIRAEKLGEKLSRFGRISQL----DEAQTRTLWAEIRDV 284 + ++GL A VA KL E R L D A+ LW R V Sbjct: 277 IEVDGLPAQVA-EEMKLVEDACRQNSCRALQTATDAAERERLWKARRAV 324 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: 455 Number of extensions: 26 Number of successful extensions: 1 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: 458 Length adjustment: 32 Effective length of query: 373 Effective length of database: 426 Effective search space: 158898 Effective search space used: 158898 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 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