Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_106713529.1 CU102_RS23600 2-hydroxyacid dehydrogenase
Query= curated2:B1L765 (332 letters) >NCBI__GCF_003010955.1:WP_106713529.1 Length = 315 Score = 165 bits (417), Expect = 2e-45 Identities = 94/252 (37%), Positives = 147/252 (58%), Gaps = 5/252 (1%) Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 + EA P L I++ Y VGYD +D+ ++GI VTNTP VLT AD A+++ +R V+ Sbjct: 61 MIEACPNLEIISVYGVGYDAVDLSACQEKGIRVTNTPDVLTNDVADLGVAMMLCQSRGVI 120 Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDSIR 180 A+ +V++G W + + V+GR GI+G+GRIG VA+R KGF M I Y D + Sbjct: 121 GAEGWVKDGSWSA--KGLYPVKRRVWGRRAGILGLGRIGFEVAKRLKGFDMEISYSD-VG 177 Query: 181 REDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRGK 240 + + + + P+E L + DF+ + + + ET H++G + + + +L+N SR Sbjct: 178 AKSYAEGMRFVADPVE-LARDVDFLFVTLAASAETRHIVGPDVIAALGPQGMLINISRAS 236 Query: 241 VVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMAE 300 +D++AL AL+ G + A LDVFE EP + L L+NV+L PH AS + ETR M + Sbjct: 237 NIDEEALLDALESGALGSAALDVFEGEP-KLNPRFLALDNVLLQPHHASGTIETRKAMGK 295 Query: 301 MVAENLIAFKRG 312 ++ +NL A G Sbjct: 296 LMRDNLAAHFSG 307 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: 229 Number of extensions: 13 Number of successful extensions: 4 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: 315 Length adjustment: 28 Effective length of query: 304 Effective length of database: 287 Effective search space: 87248 Effective search space used: 87248 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: 48 (23.1 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