Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate Echvi_3161 Echvi_3161 Lactate dehydrogenase and related dehydrogenases
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__Cola:Echvi_3161 Length = 331 Score = 139 bits (350), Expect = 1e-37 Identities = 95/300 (31%), Positives = 151/300 (50%), Gaps = 24/300 (8%) Query: 40 LLSKAREADALYTLLTDRIDCDLLSQAPRLRI--VAQMAVGFDNIDVECATRLGIYVTNT 97 LL++ +A AL++ D ++L +L I +A + GF+++D+E A L I V Sbjct: 39 LLAEGSKAIALFS--NDDASSEVLDILHKLGIKFIALRSAGFNHVDLEKAAELNIKVARV 96 Query: 98 PGVLTEATAEFTWALILAAARRVVEADHFVRWGEWWRLRTGWHPMMMLGVELRGKTLGIL 157 P A AE T ALILA RR+++A + VR + + G +L GKT+G++ Sbjct: 97 PAYSPYAIAEHTMALILALNRRLIKAHNRVR-------EQNFSLNGLTGFDLNGKTVGVI 149 Query: 158 GMGRIGSRVAEIGKAFGMRIIYHSRSRKREIEKELGAEYRSLEDLLRESDILSIHLPLTD 217 G G+IGS + +I FG I+ +++ + G Y L + +DI+S+H+PL Sbjct: 150 GTGKIGSVLVKILHGFGCNILAQDIEESKDLIDKYGLIYSDCATLCKHADIISLHVPLKA 209 Query: 218 ETRHLIGESELKLMKKTAILVNTGRGAIVDTGALVKALREGWIAAAALDVFEEEP--LNP 275 T+HLI + + LMK +L+NT RG +VDT A+++ L+ I LDV+EEE Sbjct: 210 STKHLINKEHIALMKSGVMLINTSRGGLVDTKAVIEGLKTKKIGYLGLDVYEEEEGLFFE 269 Query: 276 NHP-----------LTAFKNVVLAPHAASATRETRLRMAMMAAENLVAFAQGKVPPNLVN 324 +H L F NV++ H A T+ +A NL F + K N ++ Sbjct: 270 DHSDDILQDDVIARLMTFNNVLITSHQAFLTKTALTNIAETTIYNLDCFEKQKPSGNEIS 329 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: 223 Number of extensions: 10 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: 331 Length adjustment: 28 Effective length of query: 307 Effective length of database: 303 Effective search space: 93021 Effective search space used: 93021 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: 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