Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_078210872.1 BXU11_RS02295 hydroxyacid dehydrogenase
Query= curated2:A1RYE4 (339 letters) >NCBI__GCF_002017945.1:WP_078210872.1 Length = 315 Score = 167 bits (423), Expect = 3e-46 Identities = 106/301 (35%), Positives = 165/301 (54%), Gaps = 30/301 (9%) Query: 29 HESKDWPPSREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLKVISTYSVGFDHIDIPEA 88 H D+ S+E + I+D ++ KID +D A NL+ I+ G + ID A Sbjct: 25 HNEADFTSSKEAVEDKIKDYHGIVIRSRFKIDKNFIDKATNLRFIARVGAGLESIDCEYA 84 Query: 89 TKRGIYVTHTPGVLTDAVAEFTVGLILAVTRRIVEADKIIRTGQWDKPWNPYFLTGPELK 148 + I + P +AV+E ++G+IL++ ++ +AD IR GQW++ N G EL Sbjct: 85 LSKNIALIAAPEGNRNAVSEHSLGMILSLFNKLNQADAEIRKGQWNRESN----RGHELD 140 Query: 149 GKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVIPNMEFTD-----LDTLLE 203 GKT+G++G G +G A AK+L FDV++L YDI +PN+ T+ L+ L + Sbjct: 141 GKTVGIIGYGNMGKAFAKKLRGFDVEVLCYDI---------LPNVGDTNAKQVTLEELQQ 191 Query: 204 KSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARGPVVDTEALVKALKEGWIAGAA 263 K+D++S+H+P T ET ++N + + + +LINT+RG V T LV+AL+ G I GA Sbjct: 192 KADVLSLHIPWTPETDKMVNADFIASFSNSFWLINTSRGKNVVTADLVQALESGKILGAG 251 Query: 264 LDVFEQEPL-------PPNHP-----LTKFDNVVLAPHIASATIEARQRMAELAARNLIA 311 LDV E E L N P L K V+L+PHIA T E+ +R+A++ + A Sbjct: 252 LDVLEYEKLSFETLFQDKNTPEAFDYLLKSPKVLLSPHIAGWTFESHERLAQVIVDKIKA 311 Query: 312 V 312 + Sbjct: 312 L 312 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: 260 Number of extensions: 10 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: 339 Length of database: 315 Length adjustment: 28 Effective length of query: 311 Effective length of database: 287 Effective search space: 89257 Effective search space used: 89257 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: 48 (23.1 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