Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate BPHYT_RS11290 BPHYT_RS11290 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= curated2:B1L765 (332 letters) >FitnessBrowser__BFirm:BPHYT_RS11290 Length = 321 Score = 268 bits (685), Expect = 1e-76 Identities = 149/325 (45%), Positives = 208/325 (64%), Gaps = 12/325 (3%) Query: 4 RVFVTREIPERGLSKIEEH---FELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 ++ + +PE L+ +++H ++D + +A + +KD D + I Sbjct: 3 KIVAWKSLPEDVLAYLQQHAQVVQVDATQHDA------FVAALKDADGGIGSSVK-ITPA 55 Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 + E A +L+ ++ +VG+D DV + T+RGI + NTP VLTE+TAD F+L++A+ARRVV Sbjct: 56 MLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVFSLILASARRVV 115 Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYYDSI 179 E +V+ G W+ + P + G DV G+TLGIVG+GRIG AVARRA GF M++LY + Sbjct: 116 ELAEWVKAGHWQHSIGPALF-GVDVQGKTLGIVGLGRIGGAVARRAALGFNMKVLYTNRS 174 Query: 180 RREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRG 239 E+ G V L +LL +DFV L VPLT ET H+IG +L+ MK++AIL+N SRG Sbjct: 175 ANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKSMKKSAILINASRG 234 Query: 240 KVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMA 299 VD+KAL +AL+ G I GAGLDVFE EP+P D PLLKL NVV PH SA+HETR MA Sbjct: 235 ATVDEKALIEALQNGTIHGAGLDVFETEPLPSDSPLLKLANVVALPHIGSATHETRHAMA 294 Query: 300 EMVAENLIAFKRGEIPPNLVNQEVV 324 AENL+A G + N+VN+EV+ Sbjct: 295 RNAAENLVAALDGTLTSNIVNREVL 319 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: 248 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: 321 Length adjustment: 28 Effective length of query: 304 Effective length of database: 293 Effective search space: 89072 Effective search space used: 89072 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