Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate RR42_RS09465 RR42_RS09465 bifunctional glyoxylate/hydroxypyruvate reductase B
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Cup4G11:RR42_RS09465 Length = 325 Score = 215 bits (548), Expect = 1e-60 Identities = 128/316 (40%), Positives = 180/316 (56%), Gaps = 3/316 (0%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 M+ V V R IP L++IE ++ + PP + + + L+ AE Sbjct: 1 MRKNVLVFRPIPPDLLARIEAEHDVIVADPRQPPQRPAFRAALANAHGLIGSSVKLGAAE 60 Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 + EA +L +++ +VG DN D+ +RGI + +TPGVLTETTAD FAL+MAA+RR+V Sbjct: 61 LAEAG-RLEVISSISVGVDNYDLACLRRRGITLCHTPGVLTETTADTVFALIMAASRRLV 119 Query: 121 EADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAK-GFGMRILYYDSI 179 E +VREG+W A + G+DV+G+TL I+G GRIG AVARRA GFGM +LY + Sbjct: 120 ELAAHVREGRW-AANIGESLFGWDVHGKTLAILGFGRIGQAVARRAALGFGMEVLYVNET 178 Query: 180 RREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSRG 239 E + L+ L +D V++ +PLT+ T ++G+ + MK AI VN +RG Sbjct: 179 AAEPPDLVGRATRTELDDALRRADIVAVTLPLTKSTRGLMGQREFALMKPGAIFVNGARG 238 Query: 240 KVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASHETRSRMA 299 ++V + AL AL G + AGLDVF EP+P D PL V PH SA+HETR MA Sbjct: 239 QIVQEDALLAALDSGHLRAAGLDVFATEPLPQDSPLRCHARVTALPHIGSATHETRRAMA 298 Query: 300 EMVAENLIAFKRGEIP 315 E+ NL+ G P Sbjct: 299 ELATRNLLDALAGRPP 314 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: 266 Number of extensions: 12 Number of successful extensions: 5 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: 325 Length adjustment: 28 Effective length of query: 304 Effective length of database: 297 Effective search space: 90288 Effective search space used: 90288 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 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