Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate GFF3080 HP15_3023 glycolate oxidase FAD binding subunit
Query= reanno::psRCH2:GFF3771 (353 letters) >FitnessBrowser__Marino:GFF3080 Length = 355 Score = 294 bits (753), Expect = 2e-84 Identities = 161/353 (45%), Positives = 217/353 (61%), Gaps = 10/353 (2%) Query: 7 DASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQAD--GVLLDTREHRGIVSYDPTELVV 64 D S QL +QV QA + L I G G+K+F+G +AD L+ EH GIV Y P ELV+ Sbjct: 3 DISQQLKEQVLQARDSGHKLNIVGGGTKAFMGREADTDAGTLNVGEHTGIVDYHPVELVL 62 Query: 65 TVRAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLG 124 TVRAGTPL+E+E L E GQ L EPPHFG +T+GG +A LSGP RPW+GSVRD VLG Sbjct: 63 TVRAGTPLSEIEATLAEEGQCLHFEPPHFGAASTIGGTLACNLSGPGRPWAGSVRDQVLG 122 Query: 125 SRVITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLE 184 R++ G+G+HLRFGG+VMKNVAGYD+SRL AG+ G LGV+TE+S+KV+PKP +L E Sbjct: 123 IRLLNGKGEHLRFGGQVMKNVAGYDVSRLQAGALGTLGVITEISMKVMPKPAASLTLVQE 182 Query: 185 IDLERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPG--YW 242 + ++ + + +P PI+AA ++LRL G + V A E+ GE ++ G +W Sbjct: 183 MGMDEVVHYMNSRAAEPKPITAACWVDGKVYLRLAGAKSGVEATAEKWSGEVMEEGDHFW 242 Query: 243 NDLREQRLAFFA-DPRPLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIA 301 +++ FFA + PLWR S+ + L G+ +DWAG+QRW + + + A Sbjct: 243 RQVQDMHHEFFAGNDVPLWRFSVGSTAATPKLEGNWFIDWAGSQRWFRGAGELKDLEPAA 302 Query: 302 IEVGGHATCFTAGATTNP---FQPLAAPLLRYHRQLKAALDPQGIFNPGRMYS 351 GG + F G T QP A L R++K A DP IFNPGR+YS Sbjct: 303 RAAGGQVSLFRGGDRTGEVMHHQPEA--LKGIQRRIKNAFDPDNIFNPGRLYS 353 Lambda K H 0.319 0.137 0.417 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: 455 Number of extensions: 35 Number of successful extensions: 4 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: 353 Length of database: 355 Length adjustment: 29 Effective length of query: 324 Effective length of database: 326 Effective search space: 105624 Effective search space used: 105624 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 (21.7 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