Align D-lactate oxidase and glycolate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate AO356_01090 AO356_01090 glycolate oxidase subunit GlcD
Query= reanno::psRCH2:GFF3772 (499 letters) >lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01090 AO356_01090 glycolate oxidase subunit GlcD Length = 499 Score = 872 bits (2254), Expect = 0.0 Identities = 425/499 (85%), Positives = 463/499 (92%) Query: 1 MNILYDERVDGALPKVDKAALLAELQAQLPDLDILHRSEDLKPYECDGLSAYRTTPLLVV 60 MNILYDE +DG LPKVDK LL QAQ+PDLDILH+ +DLKPYECDGLSAYRTTPLLVV Sbjct: 1 MNILYDEHLDGPLPKVDKQTLLQAFQAQIPDLDILHQEQDLKPYECDGLSAYRTTPLLVV 60 Query: 61 LPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDPAGR 120 LP R+EQV+ LLKLCH++ VPVVARGAGTGLSGGALPL G+LLVMARFN+IL +DP R Sbjct: 61 LPRRVEQVQALLKLCHEQNVPVVARGAGTGLSGGALPLASGVLLVMARFNQILHIDPDAR 120 Query: 121 FARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 AR+QPGVRNLAISQAAAP+ LYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL Sbjct: 121 TARLQPGVRNLAISQAAAPFGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVHNLL 180 Query: 181 KVDILTVEGERMTLGSDALDSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKVLLAA 240 K++ILTVEGER+TLGS++LDSPG DLLALFTGSEG+LG++TEVTVKLLP+PQVAKVLLA+ Sbjct: 181 KLEILTVEGERLTLGSESLDSPGLDLLALFTGSEGLLGVITEVTVKLLPRPQVAKVLLAS 240 Query: 241 FDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 FDSV+KAGRAV DIIAAGIIPGGLEMMDNL+IRAAEDFIHAGYPVDAEAILLCELDGVEA Sbjct: 241 FDSVDKAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGYPVDAEAILLCELDGVEA 300 Query: 301 DVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMDGTIPR 360 DVHDDC RV +VL+ AGATEVR A+DEAER+RFWAGRKNAFPAVGR++PDYYCMDGTIPR Sbjct: 301 DVHDDCERVRQVLEQAGATEVRQARDEAERLRFWAGRKNAFPAVGRLAPDYYCMDGTIPR 360 Query: 361 RELPGVLKGISDLSEQFGLRVANVFHAGDGNMHPLILFDANQPGELERAEDLGGKILELC 420 R LP VL+ I+ L ++GLRVANVFHAGDGNMHPLILFDANQPGELERAE LGGKILELC Sbjct: 361 RALPEVLQRIASLGAEYGLRVANVFHAGDGNMHPLILFDANQPGELERAETLGGKILELC 420 Query: 421 VKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIPTLHRCAE 480 V+VGGSITGEHGVGREKINQMC+QFN+DEL LFHAVKAAFDP GLLNPGKNIPTL RCAE Sbjct: 421 VQVGGSITGEHGVGREKINQMCTQFNSDELNLFHAVKAAFDPQGLLNPGKNIPTLQRCAE 480 Query: 481 FGRMHIHNGQLPFPELERF 499 FG MHIH GQLPFPELERF Sbjct: 481 FGAMHIHGGQLPFPELERF 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: 945 Number of extensions: 20 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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