Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate Ga0059261_0219 Ga0059261_0219 Lactate dehydrogenase and related dehydrogenases
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Korea:Ga0059261_0219 Length = 336 Score = 148 bits (374), Expect = 2e-40 Identities = 99/295 (33%), Positives = 151/295 (51%), Gaps = 21/295 (7%) Query: 46 CDALVSLLTDPIDAEVFEA--APKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTET 103 C A+ + D +DA V EA +R+VA G++N+D+ A + GI V P Sbjct: 45 CAAVCVFVNDCVDARVLEALAGSGVRLVALRCAGFNNVDLAAAERLGIDVVRVPAYSPHA 104 Query: 104 TADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVA 163 A+F L++A R + A VR+ + + ++G +++GR +G++G G+IGA VA Sbjct: 105 VAEFTIGLMLAVDRHIPRAWARVRDNNFALDG----LIGRNLHGRMVGVIGTGKIGALVA 160 Query: 164 RRAK-GFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEE 222 R + GFG +L D + + E+ +GV YVP LLE+++ V+LH PLT T H+I Sbjct: 161 RSLRAGFGCDVLASDVVTDPELER-VGVRYVPRATLLEQAEIVTLHCPLTPVTRHLIDAA 219 Query: 223 QLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQE----------PIPPD 272 + R + ++VNTSRG ++D AL LK I G LDV+EQE I D Sbjct: 220 AISRAREGLLIVNTSRGALIDTAALIDGLKSRKIGGVALDVYEQEADLFFEDLSNEIVGD 279 Query: 273 D---PLLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLVNQEVV 324 D LL NV++ H A + E + +AE ++ + G N V E V Sbjct: 280 DVFQRLLTFPNVLVTGHQAFLTEEALTAIAETTLASISDAEAGRELANRVGTERV 334 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: 232 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: 336 Length adjustment: 28 Effective length of query: 304 Effective length of database: 308 Effective search space: 93632 Effective search space used: 93632 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