Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_008538761.1 HMPREF9454_RS06920 phosphoglycerate dehydrogenase
Query= curated2:A1RYE4 (339 letters) >NCBI__GCF_000245775.1:WP_008538761.1 Length = 528 Score = 213 bits (541), Expect = 1e-59 Identities = 122/336 (36%), Positives = 197/336 (58%), Gaps = 16/336 (4%) Query: 5 KVYVTRIIPEPGLSMLKECCDVVVHESKDWPPSREELLRNIRDKDALLCLLTDKIDAEVM 64 K+ V + G+ +L++ V KD P+ EELL I D D L+ K+ EV+ Sbjct: 2 KILVADGVSPKGIEILQKAGFETV--IKDKLPA-EELLEIIPDFDGLIVRSASKVTKEVI 58 Query: 65 DAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVEA 124 + A LK++ VG D+IDI AT GI V ++PG T A E T+G+++A+ R I A Sbjct: 59 ERAKKLKIVGRAGVGTDNIDINAATSHGIMVINSPGGNTIAATEHTMGMMMAMARNIAVA 118 Query: 125 DKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYYDI---- 180 ++ ++ G+W++ TG EL+GKT+G++GLGRIG A R +FD+ ++ YD Sbjct: 119 NETMQHGEWNRKK----YTGVELRGKTLGVIGLGRIGSGVATRALAFDMNVIGYDPYVNE 174 Query: 181 ERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTA 240 ER + ++ LD L+++SD +++H+PLT +T ++N++ + KMK LIN A Sbjct: 175 ERAHSL-----GIKVVSLDELIKQSDFITVHMPLTPKTKGMLNKDNIAKMKNGVRLINCA 229 Query: 241 RGPVVDTEALVKALKEGWIAGAALDVFEQEPLPPNHPLTKFDNVVLAPHIASATIEARQR 300 RG +++ + L A+K G +AGAA+DVFE EP+ PNHPL V L PH+ ++T+EA+ Sbjct: 230 RGGIINEQDLADAVKSGHVAGAAIDVFESEPIDPNHPLIGLPGVTLTPHLGASTVEAQVG 289 Query: 301 MAELAARNLIAVLKGEMPPALVNKEVLKVRPLEKVK 336 ++ A+ ++A L GE VN + + ++ +K Sbjct: 290 VSVDVAQGIVAALNGEPVSTAVNMAPVSPQTMKFIK 325 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: 384 Number of extensions: 15 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: 339 Length of database: 528 Length adjustment: 32 Effective length of query: 307 Effective length of database: 496 Effective search space: 152272 Effective search space used: 152272 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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