Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate GFF3772 Psest_3841 glycolate oxidase, subunit GlcD
Query= reanno::psRCH2:GFF3772 (499 letters) >FitnessBrowser__psRCH2:GFF3772 Length = 499 Score = 994 bits (2570), Expect = 0.0 Identities = 499/499 (100%), Positives = 499/499 (100%) Query: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV Sbjct: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 Query: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR Sbjct: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL Sbjct: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA Sbjct: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA Sbjct: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR Sbjct: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC Sbjct: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE Sbjct: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 Query: 481 FGRMHIHNGQLPFPELERF 499 FGRMHIHNGQLPFPELERF Sbjct: 481 FGRMHIHNGQLPFPELERF 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: 1046 Number of extensions: 23 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