Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 15502 b1380 D-lactate dehydrogenase (NCBI)
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Keio:15502 Length = 329 Score = 167 bits (424), Expect = 3e-46 Identities = 105/332 (31%), Positives = 170/332 (51%), Gaps = 21/332 (6%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 MK V+ T++ ++ L ++ E F +L + ++K + C+A+ + D Sbjct: 1 MKLAVYSTKQYDKKYLQQVNESFGFELEFFDFLLTEKTA-KTANGCEAVCIFVNDDGSRP 59 Query: 61 VFEAAPK--LRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARR 118 V E K ++ +A G++N+D+ A + G+ V P E A+ A ++M RR Sbjct: 60 VLEELKKHGVKYIALRCAGFNNVDLDAAKELGLKVVRVPAYDPEAVAEHAIGMMMTLNRR 119 Query: 119 VVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVARRAKGFGMRILYYDS 178 + A + R+ + + + G+ +YG+T G++G G+IG A+ R KGFGMR+L +D Sbjct: 120 IHRAYQRTRDANFSLEG----LTGFTMYGKTAGVIGTGKIGVAMLRILKGFGMRLLAFDP 175 Query: 179 IRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAILVNTSR 238 ELGVEYV L L ESD +SLH PLT E YH++ E +MK ++VNTSR Sbjct: 176 YPSAA-ALELGVEYVDLPTLFSESDVISLHCPLTPENYHLLNEAAFEQMKNGVMIVNTSR 234 Query: 239 GKVVDQKALYKALKEGWIAGAGLDVFEQE----------PIPPDDPLLKL---ENVVLAP 285 G ++D +A +ALK I G+DV+E E + DD +L NV+ Sbjct: 235 GALIDSQAAIEALKNQKIGSLGMDVYENERDLFFEDKSNDVIQDDVFRRLSACHNVLFTG 294 Query: 286 HAASASHETRSRMAEMVAENLIAFKRGEIPPN 317 H A + E + +++ +NL ++GE PN Sbjct: 295 HQAFLTAEALTSISQTTLQNLSNLEKGETCPN 326 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: 230 Number of extensions: 9 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: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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