Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 7023349 Shewana3_0583 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__ANA3:7023349 Length = 310 Score = 95.1 bits (235), Expect = 2e-24 Identities = 81/283 (28%), Positives = 125/283 (44%), Gaps = 18/283 (6%) Query: 44 AREADALYTLLTDRIDCDLLSQAPRLRIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTE 103 A A+A L ++ L+ A +L+ + G D + + R +TN G+ Sbjct: 35 ANIAEANIWLAEPKLAAPLVPHAKQLKWLQSSFAGIDAL-MGPRARKDYQLTNIKGIFGP 93 Query: 104 ATAEFTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIG 163 +E+ + +LA R H ++ + + + W L+G L +LG G I Sbjct: 94 LMSEYLFGYLLAHVR-----GH--QFYQAQQRQKSWQVQSATRGSLQGMRLLLLGTGSIA 146 Query: 164 SRVAEIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTDETRHLI 223 VA+ K FGM I +RS + +L L L +SD+++ LP T ETR L+ Sbjct: 147 QHVAKTAKHFGMHITGINRSGREVDGFDLIQPLSQLGQCLSQSDVVTNLLPSTPETRLLL 206 Query: 224 GESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFEEEPLNPNHPLTAFK 283 L +K AILVN GRG ++D AL L A LDVF +EPL +HP+ Sbjct: 207 NADMLATLKADAILVNVGRGDVLDLDALNTQLIARPEQHAVLDVFTQEPLPASHPIWERP 266 Query: 284 NVVLAPHAASATR----------ETRLRMAMMAAENLVAFAQG 316 N ++ PH ++ + R +A +N V F QG Sbjct: 267 NAIITPHISAPSHPEQIVRIFSDNYRRYIAAEPLQNQVDFIQG 309 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: 230 Number of extensions: 9 Number of successful extensions: 2 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: 310 Length adjustment: 28 Effective length of query: 307 Effective length of database: 282 Effective search space: 86574 Effective search space used: 86574 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 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