Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 8501126 DvMF_1862 FAD linked oxidase domain protein (RefSeq)
Query= reanno::Phaeo:GFF2924 (366 letters) >FitnessBrowser__Miya:8501126 Length = 461 Score = 96.3 bits (238), Expect = 1e-24 Identities = 111/399 (27%), Positives = 162/399 (40%), Gaps = 62/399 (15%) Query: 19 PLAVSGGGTRGLSTG-------GETLSVAGLNGVTLYEPGALTLVVQAGTSVEEVQALLA 71 P+ V G GT LS G G + LN + L VV+ G + A +A Sbjct: 66 PITVRGAGTN-LSGGTIPDPREGIVILTNSLNRIIEINEEDLYAVVEPGVVTAKFAAEVA 124 Query: 72 GENQRLAFEPMDHRGLLGTKGTPTIGGVFAANVSGPRRIQCGAARDFLLGVRFVDGRGDV 131 +R F P D G++ T+GG A N G R ++ G +D+++G+ F D G + Sbjct: 125 ---KRGLFYPPDP----GSQAVSTLGGNVAENAGGLRGLKYGVTKDYVMGIEFFDVNGGL 177 Query: 132 LSNGGRVMKNVTGYDLVKLMAGSHGTLGVLSEVSLKVLP---CSEACATVTVHVADLTSA 188 + G R +K VTGY+L LM S GTLGV S + LK++P S+A V V + A Sbjct: 178 VKTGSRTVKCVTGYNLAGLMVASEGTLGVFSNIVLKLVPPPQASKAMMAVFDDVNKASEA 237 Query: 189 VAAMSTALGSPY--------------DVTGAAYDPEAGAV-YIRVEGFEASVTYRAEALK 233 VA + A P D T A +A A+ I V+G V AE ++ Sbjct: 238 VAGIIAAHVVPCTLEFMDQATIRYVDDFTKAGLPRDAQAILLIEVDGHAGQVAEDAEKVE 297 Query: 234 MALGKFG--EVSLALGAGD--ALWEGIRNV--AAFHDRPGDVWRISVKPSDAV-ALAPAL 286 L K G E+ +A A + LWE RN A +P V + P + A+ A+ Sbjct: 298 KVLNKVGATEIKVAKDAAEKFKLWEARRNALPALARAKPTTVLEDATVPRSKIPAMVKAI 357 Query: 287 E--------AEGLLFDWGGGLIWALVPAGR-------------DLRFRLTVPGHATLVRA 325 + G G G + + R D F + + H TL Sbjct: 358 NDIAAKYNISIGTFGHAGDGNLHPTILCDRRDKHEFERVEHAVDEIFDVALSLHGTLSGE 417 Query: 326 SAQTRAELGQFQPQPGPLA-AISGGLRRQFDPRGILNPG 363 A+ + + S ++R DP+ ILNPG Sbjct: 418 HGIGMAKSKWMEKETSKATIEFSRNMKRAIDPKYILNPG 456 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: 371 Number of extensions: 21 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 366 Length of database: 461 Length adjustment: 31 Effective length of query: 335 Effective length of database: 430 Effective search space: 144050 Effective search space used: 144050 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