Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS31645 BPHYT_RS31645 FAD-binding protein
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__BFirm:BPHYT_RS31645 Length = 499 Score = 820 bits (2117), Expect = 0.0 Identities = 398/499 (79%), Positives = 447/499 (89%) Query: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 M+ YDER+DGAL DK+ ++A+LQA +PDL +LH EDL+P+ECDGL+AYR TP+LV Sbjct: 1 MSYHYDERIDGALATHDKSTVVAQLQALIPDLQLLHEQEDLRPFECDGLAAYRATPMLVA 60 Query: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 LP+++EQVE LLK + + +PVVARGAGTGLSGGALPL++GILLVMARFN+ILEVDP Sbjct: 61 LPDKVEQVEALLKFANAQKIPVVARGAGTGLSGGALPLDKGILLVMARFNRILEVDPEAG 120 Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 ARVQPGVRNLAISQA AP+ LYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTV+N+L Sbjct: 121 IARVQPGVRNLAISQAVAPHGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVNNIL 180 Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 K++ILT++GER+TLGS+ALD+PGFD LALFTGSEGMLGIVTEVTVKLL KPQ AKVLLA+ Sbjct: 181 KLEILTIDGERITLGSEALDAPGFDFLALFTGSEGMLGIVTEVTVKLLTKPQSAKVLLAS 240 Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 FD +EKAG AV II AG+IPGGLEMMDNL+IRAAEDFIHAGYPVDAEAILLCE+DGVE+ Sbjct: 241 FDDIEKAGAAVARIIGAGVIPGGLEMMDNLAIRAAEDFIHAGYPVDAEAILLCEVDGVES 300 Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 DV +D RV +L AGAT++RLAKDEAER RFWAGRKNAFPAVGRISPDYYCMDGTIPR Sbjct: 301 DVQEDVERVEALLSAAGATDIRLAKDEAERQRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 RELP VLKGI DLS ++GLRVANVFHAGDGNMHPLILFDAN PGE ERAE LG KILELC Sbjct: 361 RELPRVLKGIEDLSNEYGLRVANVFHAGDGNMHPLILFDANAPGETERAEMLGAKILELC 420 Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 V VGGSITGEHGVGREKINQMC+QFN DEL FHA+KAAFDP+GLLNPGKN+PTLHRCAE Sbjct: 421 VAVGGSITGEHGVGREKINQMCAQFNHDELDFFHALKAAFDPAGLLNPGKNVPTLHRCAE 480 Query: 481 FGRMHIHNGQLPFPELERF 499 FG MH+H+G LPFPELERF Sbjct: 481 FGSMHVHHGALPFPELERF 499 Lambda K H 0.320 0.140 0.412 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: 901 Number of extensions: 27 Number of successful extensions: 1 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: 499 Length of database: 499 Length adjustment: 34 Effective length of query: 465 Effective length of database: 465 Effective search space: 216225 Effective search space used: 216225 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: 52 (24.6 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