Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 200152 SO0968 D-lactate dehydrogenase (NCBI ptt file)
Query= curated2:Q9YAW4 (335 letters) >FitnessBrowser__MR1:200152 Length = 329 Score = 121 bits (303), Expect = 3e-32 Identities = 79/261 (30%), Positives = 126/261 (48%), Gaps = 21/261 (8%) Query: 70 RIVAQMAVGFDNIDVECATRLGIYVTNTPGVLTEATAEFTWALILAAARRVVEADHFVRW 129 +I+A GF+N+D+ A RLG+ V N P E+ AE T AL+L R++ +A R Sbjct: 70 KIIAMRCAGFNNVDLVAAKRLGMQVVNVPAYSPESVAEHTVALMLTLNRKIHKAYQRTR- 128 Query: 130 GEWWRLRTGWHPMMMLGVELRGKTLGILGMGRIGSRVAEIGKAFGMRIIYHSRSRKREIE 189 + ++G + GKT+G++G G+IG ++ FG ++I +E Sbjct: 129 ------DANFSLEGLVGFNMFGKTVGVIGTGKIGVATIKVLLGFGCKVIAFDPYPNPAVE 182 Query: 190 KELGAEYRSLEDLLRESDILSIHLPLTDETRHLIGESELKLMKKTAILVNTGRGAIVDTG 249 L EY+ L+ + SDI+S+H PLT + HL+ + MK +++NT RG +++ Sbjct: 183 A-LDVEYQDLDTIYATSDIISLHCPLTPDNHHLLNKDSFAKMKPGVMVINTSRGGLLNAF 241 Query: 250 ALVKALREGWIAAAALDVFEEEPL-------------NPNHPLTAFKNVVLAPHAASATR 296 ++AL+ G I A LDV+E E + L+A NV+ H A T Sbjct: 242 DAMEALKLGQIGALGLDVYENEKELFFEDKSNQIIQDDVFRRLSACHNVIFTGHQAFLTE 301 Query: 297 ETRLRMAMMAAENLVAFAQGK 317 E +A N+ A GK Sbjct: 302 EALGAIANTTLSNVQAVLAGK 322 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: 243 Number of extensions: 11 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: 335 Length of database: 329 Length adjustment: 28 Effective length of query: 307 Effective length of database: 301 Effective search space: 92407 Effective search space used: 92407 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