Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_057509293.1 ABB28_RS14455 2-hydroxyacid dehydrogenase
Query= curated2:B1L765 (332 letters) >NCBI__GCF_001431535.1:WP_057509293.1 Length = 334 Score = 152 bits (384), Expect = 1e-41 Identities = 106/289 (36%), Positives = 147/289 (50%), Gaps = 21/289 (7%) Query: 46 CDALVSLLTDPIDAEVFEAAPKL--RIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTET 103 CDA+ + D +DA V +A + R V G++N+D+ A + G +V P E Sbjct: 49 CDAVCVFVNDRLDAPVLQALHGMGVRAVLLRCAGFNNVDLAAAERLGFFVARVPAYSPEA 108 Query: 104 TADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRIGAAVA 163 A+ AL+M R+ A VREG + + +LG ++G+T GIVG G+IG A A Sbjct: 109 VAEHTLALIMTLNRQTHRAFNRVREGNFMLEG----LLGRTLHGKTAGIVGTGKIGLATA 164 Query: 164 RRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPLTEETYHMIGEEQ 223 R G G +L +D DF LG E+V L+ LL SD VSLH PLT +T H+I ++ Sbjct: 165 RILHGMGCTVLGHDPYPSPDFAG-LG-EFVSLQDLLARSDIVSLHCPLTIQTRHLINDDS 222 Query: 224 LRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQE----------PIPPDD 273 L MK A+LVNTSRG +VD A+ +ALK + +DV+EQE I DD Sbjct: 223 LALMKPGAMLVNTSRGGLVDTDAVIRALKSRQLGHLAIDVYEQESALFFQDRSGQIIDDD 282 Query: 274 ---PLLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLV 319 L+ NV++ H + E +AE NL F G PN V Sbjct: 283 VFQRLMTFPNVLVTGHQGFFTTEALQEIAETTLGNLGHFAAGTECPNEV 331 Lambda K H 0.319 0.137 0.398 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: 228 Number of extensions: 14 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: 332 Length of database: 334 Length adjustment: 28 Effective length of query: 304 Effective length of database: 306 Effective search space: 93024 Effective search space used: 93024 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: 49 (23.5 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