Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate BWI76_RS26960 BWI76_RS26960 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Koxy:BWI76_RS26960 Length = 323 Score = 255 bits (652), Expect = 9e-73 Identities = 145/326 (44%), Positives = 196/326 (60%), Gaps = 7/326 (2%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLL--TDPID 58 MKP V + + +P+ ++E+HF + K+ P + + + V LL ++ +D Sbjct: 1 MKPSVILYKTLPDDLQQRLEQHFTVTQVKNLRP---ETVSQHAAAFAEAVGLLGSSEKVD 57 Query: 59 AEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARR 118 + E PKLR + +VGYDN DV R + + +TP VLTET AD AL+++ ARR Sbjct: 58 TALLEKMPKLRATSTISVGYDNFDVDALNARKVLLMHTPTVLTETVADTVMALVLSTARR 117 Query: 119 VVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYYD 177 VVE V+ G+W + P G DV+ +TLGIVGMGRIG A+A+RA GFGM ILY Sbjct: 118 VVEVANRVKAGEWTKSIGPDWF-GNDVHHKTLGIVGMGRIGMALAQRAHAGFGMPILYNA 176 Query: 178 SIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTS 237 + E+ Y L+ LL+E+DFV L +PLTEET+H+ G+ Q +MK +AI +N Sbjct: 177 RRQHPQAEERFNARYCDLDTLLQEADFVCLILPLTEETHHLFGKAQFAKMKSSAIFINAG 236 Query: 238 RGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSR 297 RG VVD+KAL AL+EG I AGLDVFEQEP+ D PLL + NVV PH SA+HETR Sbjct: 237 RGPVVDEKALIAALQEGEIYAAGLDVFEQEPLAKDSPLLSMPNVVALPHIGSATHETRYN 296 Query: 298 MAEMVAENLIAFKRGEIPPNLVNQEV 323 MA +NLI G + N VN +V Sbjct: 297 MAACAVDNLIDALNGSVEKNCVNPQV 322 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: 227 Number of extensions: 10 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: 323 Length adjustment: 28 Effective length of query: 304 Effective length of database: 295 Effective search space: 89680 Effective search space used: 89680 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 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