Align Glycolate oxidase subunit GlcE; Glycolate dehydrogenase subunit GlcE; EC 1.1.99.14 (characterized)
to candidate 8502165 DvMF_2875 FAD linked oxidase domain protein (RefSeq)
Query= SwissProt::P52073 (350 letters) >FitnessBrowser__Miya:8502165 Length = 474 Score = 77.8 bits (190), Expect = 5e-19 Identities = 48/137 (35%), Positives = 71/137 (51%), Gaps = 1/137 (0%) Query: 53 IVNYDPTELVITARVGTPLVTIEAALESAGQMLPCEPPHYGEEATWGGMVACGLAGPRRP 112 I++ + V G ++ A+E+ G P +P + +T GG VA G R Sbjct: 102 ILDIADDDFVAEVEPGVVTSDLQRAVEARGLFYPPDPASI-DISTIGGNVATCAGGMRAL 160 Query: 113 WSGSVRDFVLGTRIITGAGKHLRFGGEVMKNVAGYDLSRLMVGSYGCLGVLTEISMKVLP 172 G R++VLG + G+ L GG KNV G DL+RL VGS G LG++T I++K+LP Sbjct: 161 KYGVTREYVLGLTAVLPGGRVLHTGGRCHKNVVGLDLTRLFVGSEGTLGIVTRITLKLLP 220 Query: 173 RPRASLSLRREISLQEA 189 P+A+ +L EA Sbjct: 221 LPQATATLLAGFGSMEA 237 Score = 26.6 bits (57), Expect = 0.001 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%) Query: 318 APLSAPLFRYHQQLKQQLDPCGVFNPGRMY 347 +PL L R Q+K DP G+ NP + Y Sbjct: 448 SPLETELMR---QVKHAFDPLGIMNPDKAY 474 Lambda K H 0.320 0.138 0.430 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: 398 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 350 Length of database: 474 Length adjustment: 31 Effective length of query: 319 Effective length of database: 443 Effective search space: 141317 Effective search space used: 141317 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: 50 (23.9 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