Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_012384881.1 BIND_RS09620 FAD-binding protein
Query= reanno::Smeli:SMc00833 (405 letters) >NCBI__GCF_000019845.1:WP_012384881.1 Length = 437 Score = 307 bits (787), Expect = 3e-88 Identities = 188/408 (46%), Positives = 241/408 (59%), Gaps = 25/408 (6%) Query: 7 PASEEGIASVVRSAAAERVTLAVVGGGTRAGLGNPVRADRTLSTRRLSGIVTYDPAEMTM 66 P E+ + +VV +A A RV L ++G G++ G G PV A+R +S LSGI Y+P+E+ + Sbjct: 20 PRDEKDVVAVVEAAVANRVPLEIMGLGSKRGFGAPVTAERHISLSGLSGITLYEPSELVL 79 Query: 67 SALAGTPVAEVEAALHAKGQMLSFEPMDHRPIFATTGEP-----TIGGVFAANVSGPRRY 121 A AGTP+ E+ A L GQ L+FEPMD+ ++ + TIGG A N SGPRR Sbjct: 80 RAHAGTPMREIRALLDQNGQELAFEPMDYGDLYGAPKDDKAKGGTIGGTIAVNASGPRRI 139 Query: 122 VAGAARDSLLGVRFVNGRGEPIKAGGRVMKNVTGLDLVKLMAGSYGTLGILTEVTFKVLP 181 AGAARD LLG + V+GR E K+GGRVMKNVTG DL KL+AGS+GTL I+TEVT KVLP Sbjct: 140 RAGAARDHLLGFKAVSGRAESFKSGGRVMKNVTGYDLSKLLAGSHGTLAIMTEVTVKVLP 199 Query: 182 LPPAAATVVVSGLNDAEAAAVMAEAMAQPVEVSGASHLPE-SVRSRFLDGALPDGAATVL 240 P +V+ + L + +A A++ EA P EVS + LPE SV LP G VL Sbjct: 200 RPENEESVIATNLTEDQALALLREASGLPYEVSSFACLPEGSVL------GLPRGPIAVL 253 Query: 241 RLEGLAASVAIRAEKL---GEKLSRF--GRISQLDEAQTRTLWAEIRDVKPYADGTRRPL 295 RLEG S+ R E+L K +RF G+ L A +R WA IRD P + Sbjct: 254 RLEGPDLSIQKRKEELITTFRKNTRFAKGQYDILKAAVSREFWAAIRDALPITT-CGGQV 312 Query: 296 WRISVAPSAGHQLVAALRLQTGVDA---FYDWQGGLVWLRMEADPEAEL--LRRYIGAVG 350 WR+S APS LV A+ GV FYDW GGL+WL +EA P A +R + Sbjct: 313 WRLSTAPSEAAPLVTAIH-AAGVPILRWFYDWAGGLIWLCVEATPHAHAPSIRAAVDRF- 370 Query: 351 GGHAALLRAGEEARGRIPAFEPQPPAVARLSERIRAQFDPSGIFNPGR 398 GGHA L+RA +E R IP F PQPPA+A LS R++ FDP + N R Sbjct: 371 GGHATLIRAEDEVRAAIPVFHPQPPALAALSRRVKHGFDPLSLLNRHR 418 Lambda K H 0.318 0.134 0.387 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: 533 Number of extensions: 30 Number of successful extensions: 7 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: 405 Length of database: 437 Length adjustment: 32 Effective length of query: 373 Effective length of database: 405 Effective search space: 151065 Effective search space used: 151065 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 24 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