Align Glycolate oxidase subunit GlcE; Glycolate dehydrogenase subunit GlcE; EC 1.1.99.14 (characterized)
to candidate N515DRAFT_1999 N515DRAFT_1999 D-lactate dehydrogenase
Query= SwissProt::P52073 (350 letters) >FitnessBrowser__Dyella79:N515DRAFT_1999 Length = 456 Score = 85.1 bits (209), Expect = 3e-21 Identities = 72/226 (31%), Positives = 105/226 (46%), Gaps = 29/226 (12%) Query: 22 KTPLVIQGSNSKAFLGRPVTGQTLDV---------RCHRGIVNYDPTELVITARVGTPLV 72 + PLV +G G TG T+ V R +R I+ DP + G Sbjct: 64 RVPLVARGR------GTNTTGATVPVDGGVVASFERMNR-ILRIDPDNRLAVVEPGVLNG 116 Query: 73 TIEAALESAGQMLPCEPPHYGEEATW---GGMVACGLAGPRRPWSGSVRDFVLGTRIITG 129 ++ AL+ G P +P + W GG +AC AGPR GS R+ LG R + G Sbjct: 117 DLQQALKPHGFFWPPDPT----SSPWCSIGGNLACNSAGPRTVKYGSPRENTLGLRAVAG 172 Query: 130 AGKHLRFGGEVMKNVAGYDLSRLMVGSYGCLGVLTEISMKVLPRPRASLSLR---REISL 186 G R G K GYDL+RL++GS G L ++TE ++K+ P+P +LR R++S Sbjct: 173 TGVGFRCGTYTSKGSTGYDLTRLLIGSEGTLALITEATLKLTPKPSGLRTLRATYRDVS- 231 Query: 187 QEAMSEIAEWQLQPLPISGLCYFDN-ALWIRLEGGEGSVKAARELL 231 A +A QP+ L + D+ AL + + G SV A +L Sbjct: 232 -AAARAVARIMAQPVTPCALEFIDDVALKLARDHGGDSVPVAGAML 276 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: 339 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: 350 Length of database: 456 Length adjustment: 31 Effective length of query: 319 Effective length of database: 425 Effective search space: 135575 Effective search space used: 135575 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