Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate Echvi_0181 Echvi_0181 Phosphoglycerate dehydrogenase and related dehydrogenases
Query= curated2:A1RYE4 (339 letters) >FitnessBrowser__Cola:Echvi_0181 Length = 311 Score = 162 bits (411), Expect = 8e-45 Identities = 101/276 (36%), Positives = 150/276 (54%), Gaps = 15/276 (5%) Query: 37 SREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLKVISTYSVGFDHIDIPEATKRGIYVT 96 +REE+ I D + L+ +D +++ A LK I G D ID+ K+GI + Sbjct: 31 TREEIEAIIADYEGLIIRSKTPMDKPLLEKAKKLKFIGRAGAGLDKIDLDFIQKQGIKLF 90 Query: 97 HTPGVLTDAVAEFTVGLILAVTRRIVEADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVG 156 H P DAV E V ++L + + +AD +R G WD+ N G EL+GKT+G+ G Sbjct: 91 HAPEGNRDAVGEHAVAMLLMLFNNLKKADSEVRQGVWDREGN----RGEELQGKTVGIFG 146 Query: 157 LGRIGVATAKRLSSFDVKILYYDIERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTK 216 G +G A A+RLS F VK++ YD + + F D L +++D++SIHVPLT+ Sbjct: 147 YGNMGKAFARRLSGFGVKVVAYDKYLDKYSDEYAAQVTF---DQLQQQADVLSIHVPLTE 203 Query: 217 ETYHLINEERLRKMKKTAYLINTARGPVVDTEALVKALKEGWIAGAALDVFEQEPLPPNH 276 ET + EE L K YLINTARG V+ E L AL++G + GA LDV E E L + Sbjct: 204 ETRNFFTEEVLAGFSKPFYLINTARGEVISMETLNAALEKGILKGALLDVLENEKLHTLN 263 Query: 277 PLTKF--------DNVVLAPHIASATIEARQRMAEL 304 + K D+V+ +PHIA T ++ +++ E+ Sbjct: 264 DVQKTAFEKLSVRDDVLFSPHIAGWTFQSYKKINEV 299 Lambda K H 0.319 0.137 0.404 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: 214 Number of extensions: 7 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: 339 Length of database: 311 Length adjustment: 28 Effective length of query: 311 Effective length of database: 283 Effective search space: 88013 Effective search space used: 88013 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