Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_086509103.1 BZY95_RS06210 D-glycerate dehydrogenase
Query= curated2:B1L765 (332 letters) >NCBI__GCF_002151265.1:WP_086509103.1 Length = 328 Score = 245 bits (626), Expect = 1e-69 Identities = 144/324 (44%), Positives = 193/324 (59%), Gaps = 7/324 (2%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALV--SLLTDPID 58 M R+ + L ++ + F +D ++ + + LV SL+ P Sbjct: 1 MTKRIVAYTRLKPIHLDQLRQRFHVDYFEALKSTDDPGFRQALGQAHGLVGSSLVIAP-- 58 Query: 59 AEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARR 118 E+ + AP+L VA +VGYDN V+ T+RGI + NTP VLTETTAD F L+MA ARR Sbjct: 59 -ELIDLAPQLEAVATISVGYDNYPVEALTRRGILLCNTPDVLTETTADTGFLLIMATARR 117 Query: 119 VVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARR-AKGFGMRILYYD 177 +E V+ G W + G DV+G+TLG+VG GRIGA VARR A GFGMR+LY Sbjct: 118 AIELADLVKRGDWTASIGEPHF-GTDVHGKTLGMVGFGRIGAGVARRGALGFGMRVLYAC 176 Query: 178 SIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTS 237 S + E+ELG L++LL ++DFV + VPLT ET H+IG + MK +AI VN + Sbjct: 177 SSPKPALEQELGAVRCELDELLSQADFVCVTVPLTAETTHLIGRREFGLMKPSAIFVNIA 236 Query: 238 RGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSR 297 RGKVVD+ AL AL+ G I AGLDVFEQEP+ P+ PL + NVV PH SA+HETR Sbjct: 237 RGKVVDEAALIAALETGEIHAAGLDVFEQEPLSPESPLPHMANVVALPHVGSATHETRDA 296 Query: 298 MAEMVAENLIAFKRGEIPPNLVNQ 321 MA+ +N+ G+ P +LVN+ Sbjct: 297 MAQRAVDNITLALEGKRPLSLVNE 320 Lambda K H 0.319 0.137 0.398 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: 271 Number of extensions: 12 Number of successful extensions: 3 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: 332 Length of database: 328 Length adjustment: 28 Effective length of query: 304 Effective length of database: 300 Effective search space: 91200 Effective search space used: 91200 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: 49 (23.5 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