Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate Dsui_3414 Dsui_3414 FAD/FMN-dependent dehydrogenase
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__PS:Dsui_3414 Length = 366 Score = 379 bits (972), Expect = e-110 Identities = 203/362 (56%), Positives = 249/362 (68%), Gaps = 19/362 (5%) Query: 22 ATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELVITARCGTPLAQIEAA 81 A PL LRGGGSKDFYG+ QG +LDTR++ G+V Y+P ELV+T + GT LA++EA Sbjct: 15 AASAGAPLLLRGGGSKDFYGRPVQGDILDTRSHRGVVAYEPTELVVTVKAGTSLAELEAV 74 Query: 82 LAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGALRDFVLGTRVMDGRG 141 LAE+ Q LA EPPHF G D AT+GG VAAGLSGPRR GA+RDFVLG R+MDG+G Sbjct: 75 LAEKGQYLACEPPHF-----GPD-ATVGGMVAAGLSGPRRAQAGAVRDFVLGVRLMDGQG 128 Query: 142 DVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFDDATLRFALDEAAALD 201 L+FGGQVMKNVAGYDV RL++GSLG LGL+LEVSLKVLP P +AT+R +A AL Sbjct: 129 QALNFGGQVMKNVAGYDVPRLLAGSLGQLGLLLEVSLKVLPRPVAEATIRLETSQAKALA 188 Query: 202 RLNDWGGQPLPIAASAWHDG------VLHLRLSGAAAALRAARARLGGEAVDAAQADALW 255 +N WGG+PLPI+A+ W D + +RLSGA AA+ AA+A LGG V+A A A W Sbjct: 189 LMNQWGGKPLPISATVWSDAGHPDGEAITVRLSGARAAVAAAQAALGGALVEAGPASAFW 248 Query: 256 RALREHSHAFFAPVQAGR--ALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLGGSDSAAD 313 +RE +H FF ALWR+AVP+TA L LPG L+EWGG QRW + S A+ Sbjct: 249 AGVREQTHPFFTGAGGANESALWRLAVPSTAPQLDLPGRTLVEWGGAQRWLV----SDAE 304 Query: 314 SAIVRAAAKAAGGHATLFRNGDKAVG-VFTPLSAPVAAIHQRLKATFDPAGIFNPQRMYA 372 +R A + AGGHATLFR A F PL++P+ IH+RLKATFDP G+F R+Y Sbjct: 305 PRRIREAVEKAGGHATLFRGPAAARDQAFHPLASPLLDIHRRLKATFDPRGVFAAGRLYE 364 Query: 373 GL 374 GL Sbjct: 365 GL 366 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: 437 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: 374 Length of database: 366 Length adjustment: 30 Effective length of query: 344 Effective length of database: 336 Effective search space: 115584 Effective search space used: 115584 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: 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