Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS03505 BPHYT_RS03505 FAD-binding protein
Query= reanno::Cup4G11:RR42_RS17310 (374 letters) >FitnessBrowser__BFirm:BPHYT_RS03505 Length = 362 Score = 421 bits (1082), Expect = e-122 Identities = 210/368 (57%), Positives = 268/368 (72%), Gaps = 13/368 (3%) Query: 7 DQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDYDPPELV 66 ++ + + + +R A+ LR+RGGG+KD+YGQ +G +LDTRAY GI+ YDP ELV Sbjct: 2 EEDDIVAVWSERVRSASAEGHALRIRGGGTKDWYGQTLEGDILDTRAYRGIIAYDPAELV 61 Query: 67 ITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPRRQAVGA 126 ITAR GTPL +IEAALAE QMLAFEPPHF A T GG +AAG++GPRR + GA Sbjct: 62 ITARAGTPLLEIEAALAEHHQMLAFEPPHFGPQA------TFGGCIAAGIAGPRRPSAGA 115 Query: 127 LRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKVLPVPFD 186 RDFVLG +M+G+G L FGGQV+KNVAGYDVSRLM+GSLGTLGLILE+S+KVLP+P Sbjct: 116 ARDFVLGAVIMNGQGQKLHFGGQVVKNVAGYDVSRLMAGSLGTLGLILELSIKVLPLPQA 175 Query: 187 DATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARARLGGEAV 246 +ATL+F ++ A+ +LN+WGG+PLPI ASAW G L +RL+GA AA+++A+ LGGE V Sbjct: 176 EATLKFDMNGTDAVRKLNEWGGRPLPITASAWRHGTLVVRLAGAEAAVKSAKMALGGEVV 235 Query: 247 DAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGGQRWWLG 306 DA +A+ W LRE + +FFA + ALWR+A+P+ PL LPG QL+EWGGGQRWW+ Sbjct: 236 DAVEAERFWAGLREQTDSFFAAIPPRAALWRLALPSITEPLQLPGAQLMEWGGGQRWWI- 294 Query: 307 GSDSAADSAIVRAAAKAAGGHATLFRNG---DKAVGVFTPLSAPVAAIHQRLKATFDPAG 363 + D+ VR +AK AGGHAT+FR G D+ GVFTPL AP+ IH+ LK FDPA Sbjct: 295 ---TDTDAQTVRISAKQAGGHATIFRAGHGYDRGAGVFTPLPAPLMKIHRGLKTAFDPAR 351 Query: 364 IFNPQRMY 371 IFN R+Y Sbjct: 352 IFNRGRLY 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: 474 Number of extensions: 20 Number of successful extensions: 3 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: 362 Length adjustment: 30 Effective length of query: 344 Effective length of database: 332 Effective search space: 114208 Effective search space used: 114208 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