Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate HSERO_RS19100 HSERO_RS19100 FAD-binding protein
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__HerbieS:HSERO_RS19100 Length = 359 Score = 406 bits (1043), Expect = e-118 Identities = 214/368 (58%), Positives = 262/368 (71%), Gaps = 16/368 (4%) Query: 7 DQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELV 66 D A L +FR+ I PL++RGGG+KD+YGQ P G LLDTRAYSGI+DY+P ELV Sbjct: 8 DLDAVLASFRERILAGR----PLQIRGGGTKDWYGQTPSGELLDTRAYSGIIDYEPTELV 63 Query: 67 ITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGA 126 ITARCGTPL++I+AALA+ QMLA+EPP F AT+GG VAAGLSGP R + GA Sbjct: 64 ITARCGTPLSEIDAALAQHNQMLAWEPPSFG------GAATVGGMVAAGLSGPARASAGA 117 Query: 127 LRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFD 186 +RDFVLG +MD +G+ L FGGQVMKNVAGYD+SRL++GSLGTLGLILEVSLKVLP P Sbjct: 118 VRDFVLGAVLMDAQGEPLHFGGQVMKNVAGYDISRLLAGSLGTLGLILEVSLKVLPRPIA 177 Query: 187 DATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAV 246 +T F +++ AL LN GQPLP+ ASAW VL +RLSGA AA+ +A A+LGG Sbjct: 178 SSTRVFEINQEGALRLLNQSAGQPLPLVASAWVGNVLTIRLSGAQAAVDSAIAKLGG--T 235 Query: 247 DAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLG 306 + + D W LRE +H FFA +A LWR+++P+ AAP+ LPG QLIEWGG QRW Sbjct: 236 ELSNPDDYWTDLREQTHPFFADAEA--PLWRLSLPSVAAPIDLPGRQLIEWGGAQRWL-- 291 Query: 307 GSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFDPAGIFN 366 + D+ +RAAA A GGHA+L R GDKA+GVF PL V +H+RLK FDP GIFN Sbjct: 292 RPEGNVDAVTIRAAALAVGGHASLHRGGDKAIGVFHPLQPAVETLHRRLKQQFDPQGIFN 351 Query: 367 PQRMYAGL 374 P R+YA L Sbjct: 352 PGRLYASL 359 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: 444 Number of extensions: 20 Number of successful extensions: 5 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: 374 Length of database: 359 Length adjustment: 30 Effective length of query: 344 Effective length of database: 329 Effective search space: 113176 Effective search space used: 113176 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