Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate WP_086511792.1 BZY95_RS20765 glycolate oxidase subunit GlcD
Query= reanno::psRCH2:GFF3772 (499 letters) >NCBI__GCF_002151265.1:WP_086511792.1 Length = 501 Score = 761 bits (1964), Expect = 0.0 Identities = 371/481 (77%), Positives = 422/481 (87%) Query: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 MNILYDER+DG P++D+A + L +P + +LHR ED++P+ECDGLS YRT PLLV Sbjct: 1 MNILYDERLDGPAPEMDRAGIRDALLKAIPGMTLLHREEDMRPFECDGLSVYRTLPLLVA 60 Query: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 LP+ ++QV+ LL CH+ GVPVV RGAGTGLS GALPL G+LLVM+RF++ILE+DP R Sbjct: 61 LPDSLDQVQRLLVECHRLGVPVVTRGAGTGLSAGALPLTHGVLLVMSRFSRILEIDPEAR 120 Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 ARV+PGVRNLAIS+AA+PY LYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHN++ Sbjct: 121 IARVEPGVRNLAISEAASPYGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNVI 180 Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 KV++LT+EGERMTLGSDALD+PGFDLLALF GSEGMLG+VTE+TVKLLPKP+VAKVL+A+ Sbjct: 181 KVEVLTIEGERMTLGSDALDAPGFDLLALFNGSEGMLGVVTEITVKLLPKPEVAKVLMAS 240 Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 FD VEKAG AVG IIAAGIIPGGLEMMD L+I AAEDFI AGYPVDAEAILLCELDGVEA Sbjct: 241 FDDVEKAGNAVGAIIAAGIIPGGLEMMDKLAIIAAEDFIGAGYPVDAEAILLCELDGVEA 300 Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 DV DDC V +VL+ AGAT +R A+D+AER RFWAGRKNAFPAVGR+SPDYYCMDGTIPR Sbjct: 301 DVDDDCETVRQVLEKAGATGIRQARDDAERARFWAGRKNAFPAVGRMSPDYYCMDGTIPR 360 Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 REL VLKGISDLSE++GL+VANVFHAGDGNMHPLILFDAN+ GEL AE LGG+ILELC Sbjct: 361 RELARVLKGISDLSERYGLKVANVFHAGDGNMHPLILFDANREGELAVAEALGGEILELC 420 Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 V+VGG+ITGEHGVGREKINQMC+QF DEL F A KAAFDP LLNPGKNIPT RC+E Sbjct: 421 VEVGGTITGEHGVGREKINQMCAQFRPDELATFRAAKAAFDPHDLLNPGKNIPTPARCSE 480 Query: 481 F 481 F Sbjct: 481 F 481 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: 889 Number of extensions: 22 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: 501 Length adjustment: 34 Effective length of query: 465 Effective length of database: 467 Effective search space: 217155 Effective search space used: 217155 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 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