Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate 3608683 Dshi_2076 FAD linked oxidase domain protein (RefSeq)
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__Dino:3608683 Length = 472 Score = 67.8 bits (164), Expect = 6e-16 Identities = 83/285 (29%), Positives = 118/285 (41%), Gaps = 50/285 (17%) Query: 19 IRHATGTRTPLRLRGGGSKDFYGQ----HPQGTLLDTRAYSGIVDYDPPELVITARCGTP 74 +R A + P+ GGG+ GQ P +L R I P E V+ A G Sbjct: 57 VRLAQAHKVPIIPYGGGTGLVGGQIAPAGPVPVILSLRRMRSIRAVYPEENVLVADAGAV 116 Query: 75 LAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGT 134 LA+++ A + ++ S ++GS ATIGG +A G G RD LG Sbjct: 117 LAEVQQAARDVGRLFPL-----SLASEGS--ATIGGVLATNAGGVNVLRYGNARDLCLGL 169 Query: 135 RVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFAL 194 + G + ++ KN GYD+ L+ G+ GTLG+I +L++ P+P + Sbjct: 170 EAVMPDGAIWHGLTRLRKNNMGYDLRHLLIGAEGTLGIITGAALRLSPLPQRHGVGLLVV 229 Query: 195 DE-AAALDRLN---------------------DWGGQPLPIAAS------AWH-----DG 221 D AAALD L ++ + +P + AW G Sbjct: 230 DSPAAALDLLALAGEVAGDTISAFELISGRGFEFFAETMPEMRAPLDPVPAWSVLIDLAG 289 Query: 222 VLHLRLSGAAAAL--RAARARLGGEAVDA---AQADALWRALREH 261 GA L RAA A L + V A AQADALW ALRE+ Sbjct: 290 ASGFDPEGALETLFARAAEAGLVSDGVIAQSEAQADALW-ALREN 333 Lambda K H 0.321 0.136 0.414 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: 400 Number of extensions: 22 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: 2 Length of query: 374 Length of database: 472 Length adjustment: 32 Effective length of query: 342 Effective length of database: 440 Effective search space: 150480 Effective search space used: 150480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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