Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate WP_028999516.1 H537_RS0121640 2-hydroxyacid dehydrogenase
Query= SwissProt::P53839 (350 letters) >NCBI__GCF_000430725.1:WP_028999516.1 Length = 325 Score = 137 bits (345), Expect = 4e-37 Identities = 86/256 (33%), Positives = 138/256 (53%), Gaps = 18/256 (7%) Query: 72 DEELALALPSSVVAVCHTGAGYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGAL 131 D + ALP V + G G D+ID+ ++R IQV P ++ + ADT + L++ A Sbjct: 66 DAAMMAALPGLQV-ISSFGVGLDRIDLAAARERGIQVGYTPHVLDDCVADTAMGLVIDAA 124 Query: 132 RNFGIGNRRLIEGNWPEAGPACGSPFGY--DPEGKTVGILGLGRIGRCILERLKPFGFEN 189 R +R + G WP G PF G +GI+G+GRIG+ I R + F E Sbjct: 125 RGLSAADRYVRAGRWP------GGPFATMRKVSGARMGIVGMGRIGQQIAARAEGFRME- 177 Query: 190 FIYHNRH---QLPSEEEHGCEYVGFEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDG 246 YH R +LP E + + +D + + +P T H+++A ++ + Sbjct: 178 VRYHARQPVSRLPQAHEPSLHALA-----RWADFLVLALPGGAATRHIVDAAVLDALGPE 232 Query: 247 VVIVNTARGAVIDEQAMTDALRSGKIRSAGLDVFEYEPKISKELLSMSQVLGLPHMGTHS 306 +VN ARG+V+DE A+ +AL G+I AGLDV++ EP++ + LL + V+ LPH+G+++ Sbjct: 233 GFLVNIARGSVVDEDALVEALAEGRIAGAGLDVYQNEPRVPERLLQLDNVVLLPHVGSNT 292 Query: 307 VETRKKMEELVVENAK 322 ETR M +LVV+N + Sbjct: 293 RETRAAMADLVVDNLR 308 Lambda K H 0.317 0.136 0.396 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: 244 Number of extensions: 6 Number of successful extensions: 2 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: 350 Length of database: 325 Length adjustment: 28 Effective length of query: 322 Effective length of database: 297 Effective search space: 95634 Effective search space used: 95634 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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