Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate BWI76_RS26540 BWI76_RS26540 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= curated2:B1L765 (332 letters) >FitnessBrowser__Koxy:BWI76_RS26540 Length = 317 Score = 182 bits (461), Expect = 1e-50 Identities = 101/261 (38%), Positives = 155/261 (59%), Gaps = 7/261 (2%) Query: 39 IIERVKDCDALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPG 98 II + DCD ++ L+ D VFEAA KL++VA++ GYD +D++ A + G+ V N P Sbjct: 37 IIRDIGDCDGIIVRLSKMSD-RVFEAAKKLKVVARHGAGYDTVDLESAKRHGVVVLNAPI 95 Query: 99 VLTETTADFAFALLMAAARRVVEADRYVREGKWKVAWHPMMMLGYDVYGRTLGIVGMGRI 158 + + A+ A ++ +R + E + W + ++ G+TLG++G+G I Sbjct: 96 ANSMSVAELAIFYMLHCSRNFKLVQEKMLEDYY---WAKLRTPKVELDGKTLGLIGVGNI 152 Query: 159 GAAVARRA-KGFGMRILYYDSIRREDFEKELGVEYVP-LEKLLEESDFVSLHVPLTEETY 216 G+ VA +A GF M+++ YD + + E GVE +++ ESDFVSLH P T ET Sbjct: 153 GSRVAIKALHGFNMKVIAYDPYKTQQQIPE-GVELTDDFDRIFTESDFVSLHCPTTAETT 211 Query: 217 HMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLL 276 +GE+Q MK +A +NT+RGK+VD+KALY AL IAGAG+DV ++EP +DP+ Sbjct: 212 DFVGEKQFSMMKPSAYFINTARGKLVDEKALYHALSTHAIAGAGVDVLKKEPFDANDPIF 271 Query: 277 KLENVVLAPHAASASHETRSR 297 L N+V+APH +A+ E R Sbjct: 272 SLSNIVIAPHIGAATIEATDR 292 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: 261 Number of extensions: 9 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: 317 Length adjustment: 28 Effective length of query: 304 Effective length of database: 289 Effective search space: 87856 Effective search space used: 87856 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 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