Align D-lactate oxidase and glycolate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate WP_022948030.1 H035_RS0105670 glycolate oxidase subunit GlcE
Query= reanno::psRCH2:GFF3771 (353 letters) >NCBI__GCF_000421465.1:WP_022948030.1 Length = 351 Score = 357 bits (917), Expect = e-103 Identities = 190/351 (54%), Positives = 246/351 (70%), Gaps = 5/351 (1%) Query: 7 DASAQLLDQVNQALAANTPLRIQGSGSKSFLGLQADGVLLDTREHRGIVSYDPTELVVTV 66 D +++L + + A+A+ PL I G GSK+F G ++ G L HRG+V Y P+ELV+T Sbjct: 2 DRTSELKETIEAAIASRRPLCIVGGGSKNFYGRRSQGDPLSIAGHRGVVEYAPSELVITA 61 Query: 67 RAGTPLTELETALDEAGQMLPCEPPHFGEGATVGGMIAAGLSGPRRPWSGSVRDFVLGSR 126 RAGTPL +LE AL GQMLP EPP FG ATVGG IAAGLSGPRRP++G+VRDFVLG + Sbjct: 62 RAGTPLADLEQALAAEGQMLPFEPPRFGP-ATVGGAIAAGLSGPRRPFTGAVRDFVLGVK 120 Query: 127 VITGQGKHLRFGGEVMKNVAGYDLSRLMAGSFGCLGVLTEVSLKVLPKPRLCTSLRLEID 186 ++TG+G+ L FGG+VMKNVAG+DLSRL+AGS G LGV+ EVSLKVLP+P + +L E+ Sbjct: 121 LLTGRGEVLSFGGQVMKNVAGFDLSRLLAGSLGTLGVILEVSLKVLPRPAVELTLSREVA 180 Query: 187 LERALLKLAEWGQQPIPISAASHDGQALHLRLEGGEGSVGAARERIGGEDLDPG--YWND 244 ++RAL +A+W Q +P+SA +++ L++RL G E +V +A +R+GGE L G +W Sbjct: 181 IDRALDTMADWMGQSLPLSALAYEEPLLYVRLSGTERAVASAADRLGGERLAEGERFWES 240 Query: 245 LREQRLAFFADPR-PLWRLSLPNNTPALGLPGDQLVDWAGAQRWLKSDADAVTIRGIAIE 303 LREQ+ FF + LWRLSLP PA LPG L+DWAGAQRWL+S DA I A + Sbjct: 241 LREQQRPFFTEGNADLWRLSLPPAAPAPDLPGRMLLDWAGAQRWLRSLEDAQKIFRAAAD 300 Query: 304 VGGHATCF-TAGATTNPFQPLAAPLLRYHRQLKAALDPQGIFNPGRMYSEV 353 +GGHAT F + GA FQPL L + HR LK A DP I NPGRMY+E+ Sbjct: 301 LGGHATLFRSRGARHEVFQPLPESLAKLHRALKEAFDPHRILNPGRMYAEL 351 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: 426 Number of extensions: 18 Number of successful extensions: 5 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: 351 Length adjustment: 29 Effective length of query: 324 Effective length of database: 322 Effective search space: 104328 Effective search space used: 104328 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 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