Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 3609511 Dshi_2895 FAD linked oxidase domain protein (RefSeq)
Query= reanno::Phaeo:GFF2924 (366 letters) >FitnessBrowser__Dino:3609511 Length = 378 Score = 431 bits (1109), Expect = e-125 Identities = 233/376 (61%), Positives = 272/376 (72%), Gaps = 13/376 (3%) Query: 2 TPQSEAELAQIIVGATAPLAVSGGGTR--GLSTGGETLSVAGLNGVTLYEPGALTLVVQA 59 TP SEAELA++I GA APL + GGGTR G GE LS A L+G+ LYEPGALTLV QA Sbjct: 3 TPGSEAELAEVIAGADAPLRIRGGGTRPIGKPVAGEVLSTAALSGIGLYEPGALTLVAQA 62 Query: 60 GTSVEEVQALLAGENQRLAFEPMDHRGLLGTKGTPTIGGVFAANVSGPRRIQCGAARDFL 119 GT + EV+A LA E QRL FEPMDHRGLLG+ G PT+GGV A NVSGPRRIQ GA RD L Sbjct: 63 GTPLAEVEAALAAERQRLPFEPMDHRGLLGSAGEPTLGGVVAGNVSGPRRIQAGACRDSL 122 Query: 120 LGVRFVDGRGDVLSNGGRVMKNVTGYDLVKLMAGSHGTLGVLSEVSLKVLPCSEACATVT 179 +GVRFV G G V+ NGGRVMKNVTGYDLVKLMAGSHGTLGVL+EVS KVLP +E AT+T Sbjct: 123 IGVRFVTGEGAVVKNGGRVMKNVTGYDLVKLMAGSHGTLGVLTEVSFKVLPQTETEATLT 182 Query: 180 VHVADLTSAVAAMSTALGSPYDVTGAAYDP---EAGAVYIRVEGFEASVTYRAEALKMAL 236 V D +AVAA+S ALG+PY+V+GAA+ P + ++R+EGFE SV YR L L Sbjct: 183 VTGLDDATAVAALSRALGAPYEVSGAAHLPRGADGPETHVRIEGFETSVIYRTGKLTELL 242 Query: 237 GKFGEVSLAL--GAGDALWEGIRNVAAFHDRPGDVWRISVKPSDAVALAPALEAEGLLFD 294 GKFG V + A + W IR+VAAFH GDVWRISVKP D A+ AL + +++D Sbjct: 243 GKFGPVRVEADPAASRSTWVAIRDVAAFHGTAGDVWRISVKPCDGPAVGAALGGD-VIYD 301 Query: 295 WGGGLIWALVPAGRDLRFRLT-----VPGHATLVRASAQTRAELGQFQPQPGPLAAISGG 349 WGGGL+WA V GRD+R L GHATL+RA+ TRA FQP+P PLAAIS G Sbjct: 302 WGGGLVWAHVAPGRDVRGALAGLPGGFSGHATLIRAAEATRAAQPVFQPEPAPLAAISAG 361 Query: 350 LRRQFDPRGILNPGLM 365 LR +FDP+GILNPGLM Sbjct: 362 LRAKFDPKGILNPGLM 377 Lambda K H 0.318 0.136 0.401 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: 535 Number of extensions: 24 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: 366 Length of database: 378 Length adjustment: 30 Effective length of query: 336 Effective length of database: 348 Effective search space: 116928 Effective search space used: 116928 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: 49 (23.5 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