Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate 206855 DVU1412 D-isomer specific 2-hydroxyacid dehydrogenase family protein
Query= curated2:B1L765 (332 letters) >MicrobesOnline__882:206855 Length = 326 Score = 180 bits (456), Expect = 5e-50 Identities = 111/289 (38%), Positives = 158/289 (54%), Gaps = 6/289 (2%) Query: 34 PSKKVIIERVKDCDALVSLLTDPIDAEVFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYV 93 PS K IIER +++ P+D +A P LR V+ A GYD +DV A GI V Sbjct: 34 PSDK-IIERAAGAHVVLTNKV-PLDMSALQALPGLRFVSVLATGYDKVDVAAAGVLGIPV 91 Query: 94 TNTPGVLTETTADFAFALLMAAARRVVEADRYVREGKWKVA--WHPMMMLGYDVYGRTLG 151 +N PG T++ A FALL+ RR D +R G W + W ++ G+T+G Sbjct: 92 SNVPGYGTDSVAQHVFALLLELCRRTALHDHRIRAGAWTQSPDWCFWDSTQEELTGKTMG 151 Query: 152 IVGMGRIGAAVARRAKGFGMRILYYDSIRREDFEKELGVEYVPLEKLLEESDFVSLHVPL 211 IVG G G V R A GM ++ Y R D + E+V L++L +D VSLH PL Sbjct: 152 IVGFGNTGRRVGRIANALGMNVIAYAPRSRFDPDYR-PFEHVGLDELFTSADVVSLHCPL 210 Query: 212 TEETYHMIGEEQLRRMKRTAILVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPP 271 T ET ++ +L M+ + L+NT+RG ++D++A+ +AL G +AGAGLDV QEP Sbjct: 211 TPETEGLVDARRLASMRPGSYLINTARGPLLDERAVAEALDSGRLAGAGLDVLSQEPPAA 270 Query: 272 DDPLLKLENVVLAPHAASASHETRSRMAEMVAENLIAFKRGEIPPNLVN 320 D+PLL +N ++ PH A AS R + + A N+ +F G P N+VN Sbjct: 271 DNPLLSAKNCLITPHLAWASRTARRTLMDSTAANIRSFIEG-TPVNVVN 318 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: 248 Number of extensions: 11 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: 326 Length adjustment: 28 Effective length of query: 304 Effective length of database: 298 Effective search space: 90592 Effective search space used: 90592 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 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