Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate GFF2835 PS417_14475 2-hydroxyacid dehydrogenase
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__WCS417:GFF2835 Length = 317 Score = 164 bits (416), Expect = 2e-45 Identities = 99/258 (38%), Positives = 141/258 (54%), Gaps = 10/258 (3%) Query: 59 DCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAAR 118 D LL P+L+++ + ID+ A LGI V T A E TWALI+A+ R Sbjct: 63 DKALLQGLPKLKLLVTGGMRNAAIDLPAARALGITVCGTDSY-KHAAPELTWALIMASTR 121 Query: 119 RVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRII 178 ++ + +R G W + LG +L GKTLG+LG+G IG +VA+ + FGMR+I Sbjct: 122 NLLAEANALRAGHW---------QVGLGGDLYGKTLGVLGLGSIGQKVAKFAQVFGMRVI 172 Query: 179 YHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILV 238 S + E E G + S + L ++DIL++HL L+D +R L+ L MK +A LV Sbjct: 173 AWSENLTPERAAESGVTWVSKQALFEQADILTVHLVLSDRSRGLVDAEALGWMKPSARLV 232 Query: 239 NTGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFKNVVLAPHAASATRET 298 NT RG IVD ALV+AL G +A AALDV+ EEPL +HP NV+ PH + + Sbjct: 233 NTARGPIVDESALVRALESGRLAGAALDVYTEEPLPVDHPFRRLPNVLATPHVGYVSEQN 292 Query: 299 RLRMAMMAAENLVAFAQG 316 + E++ A+A G Sbjct: 293 YRQFYAQMIEDIQAWANG 310 Lambda K H 0.322 0.136 0.406 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: 239 Number of extensions: 11 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: 335 Length of database: 317 Length adjustment: 28 Effective length of query: 307 Effective length of database: 289 Effective search space: 88723 Effective search space used: 88723 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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