Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_085544045.1 B9Y55_RS03840 hydroxyacid dehydrogenase
Query= curated2:A1RYE4 (339 letters) >NCBI__GCF_900177735.1:WP_085544045.1 Length = 316 Score = 173 bits (438), Expect = 6e-48 Identities = 99/259 (38%), Positives = 149/259 (57%), Gaps = 8/259 (3%) Query: 59 IDAEVMDAAPNLKVISTYSVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEFTVGLILAVT 118 + +V+ + LK+IS G+DH+D+ + I V++ G TD+V E +GL LAV Sbjct: 59 LGGQVISSCDRLKMISVAFTGYDHVDMESCLSKRITVSNCAGYSTDSVVELALGLSLAVV 118 Query: 119 RRIVEADKIIRTGQWDKPWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYY 178 R+IV D +R G+ L G +L GKT+G+VG G IGV A + ++ Y Sbjct: 119 RKIVPCDGAVRAGKTKDG-----LIGNQLAGKTVGIVGTGAIGVKVAAVFKALGCNVVAY 173 Query: 179 DIERRWDVETVIPNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLIN 238 +R +V ++ + + L L+ D++S+H+P ET LI+ + + MK++++LIN Sbjct: 174 SRSQRDEVLSM--GIPYLSLKDLMSSCDLISLHLPCNGETAGLIDRDMISSMKRSSFLIN 231 Query: 239 TARGPVVDTEALVKALKEGWIAGAALDVFEQE-PLPPNHPLTKFDNVVLAPHIASATIEA 297 TARGP+VD +AL ALK G IAGA +DVF+ E PL +PL N VL PH+A AT EA Sbjct: 232 TARGPIVDNKALADALKSGSIAGAGIDVFDMEPPLLEGYPLLDAPNCVLTPHVAFATPEA 291 Query: 298 RQRMAELAARNLIAVLKGE 316 Q A +A N+ + G+ Sbjct: 292 LQSRAVIAIDNVRLWMDGK 310 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: 224 Number of extensions: 7 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: 316 Length adjustment: 28 Effective length of query: 311 Effective length of database: 288 Effective search space: 89568 Effective search space used: 89568 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