Align Glyoxylate reductase; EC 1.1.1.26 (uncharacterized)
to candidate WP_092482325.1 BM299_RS04760 hydroxyacid dehydrogenase
Query= curated2:B1L765 (332 letters) >NCBI__GCF_900115975.1:WP_092482325.1 Length = 330 Score = 219 bits (557), Expect = 1e-61 Identities = 129/334 (38%), Positives = 205/334 (61%), Gaps = 12/334 (3%) Query: 1 MKPRVFVTREIPERGLSKIEEHFELDLWKDEAPPSKKVIIERVKDCDALVSLLTDPIDAE 60 M +V +T I E G++ I E EL++ D P ++ +I+ + D DAL+ + + + + Sbjct: 1 MTKKVLLTEAIHEEGMNIIREAAELEIAAD---PGEETVIKAIADADALI-VRSSKVTSA 56 Query: 61 VFEAAPKLRIVAQYAVGYDNIDVKEATKRGIYVTNTPGVLTETTADFAFALLMAAARRVV 120 + EA KL+++ ++ +G DNID+K A + G+ V NTP + A+ A ++ +R+ Sbjct: 57 IIEAGKKLKVIGRHGMGLDNIDLKAADQYGVAVVNTPDANVLSVAEHVLATMLYLCKRLK 116 Query: 121 EADRYVREGKW-KVAWHPMMM--LGY---DVYGRTLGIVGMGRIGAAVARRA-KGFGMRI 173 E D +R G++ + P ++ LGY ++YG+TLG+VG+G+I +A KGF M++ Sbjct: 117 EVDNALRTGEFDRPGSLPGLVTKLGYTTQELYGKTLGLVGVGKIARRIAEICTKGFDMQV 176 Query: 174 LYYDSIRREDFEKELGVEYV-PLEKLLEESDFVSLHVPLTEETYHMIGEEQLRRMKRTAI 232 YD+ D ++ GVE LE++ E++DF+S+HVPLT T +IG++QL MK TA Sbjct: 177 CGYDAYLAPDVIQQAGVEPCGSLEEVFEKADFISVHVPLTPGTRGLIGKKQLDLMKPTAF 236 Query: 233 LVNTSRGKVVDQKALYKALKEGWIAGAGLDVFEQEPIPPDDPLLKLENVVLAPHAASASH 292 L+N++RG VV++ LY+ALKE IAGA +DVF QEP + PL L+NVV+ PH A+ + Sbjct: 237 LINSARGGVVNEDDLYQALKEKSIAGAAVDVFAQEPPGKNHPLFTLDNVVVTPHIAAMTD 296 Query: 293 ETRSRMAEMVAENLIAFKRGEIPPNLVNQEVVKV 326 RMA VAE +++ RGE P LVN + K+ Sbjct: 297 GALVRMARDVAEGVVSVLRGERPKYLVNPRIWKI 330 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: 291 Number of extensions: 11 Number of successful extensions: 6 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: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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 Apr 09 2024. 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