Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate WP_008537918.1 HMPREF9454_RS03270 2-hydroxyacid dehydrogenase
Query= SwissProt::P53839 (350 letters) >NCBI__GCF_000245775.1:WP_008537918.1 Length = 315 Score = 118 bits (295), Expect = 2e-31 Identities = 77/234 (32%), Positives = 116/234 (49%), Gaps = 18/234 (7%) Query: 92 GYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGALRNF---GIGNRRLIEGNWPE 148 G D +D++ + +I V+N + A ++ + + + R G+ + N Sbjct: 82 GVDHVDMDYCHEHNILVSNCSGYANEAVSELVIGMCISLYRKLAECGMATKNHETSNGLR 141 Query: 149 AGPACGSPFGYDPEGKTVGILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEY 208 C FG I+G G IG + + K FG E + Y R +P E E+ Sbjct: 142 GLELCRKKFG---------IIGAGAIGLKVAKLAKAFGCEVYCY--RRHIPENSEF--EF 188 Query: 209 VGFEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALR 268 V + LK DI+S+++PL T +INAE I MK +++NTARG VID QA+ DAL Sbjct: 189 VDMDTILKECDIISLHMPLTKETTSMINAEKIALMKKNAILINTARGKVIDTQALADALN 248 Query: 269 SGKIRSAGLDVFEYEPKISKE--LLSMSQVLGLPHMGTHSVETRKKMEELVVEN 320 GKI A +DVF+ EP I E LL+ V+ PH+G + E +K + +EN Sbjct: 249 KGKIAGASVDVFDTEPPIGAENPLLTAKNVVLSPHIGFDTQEAMQKRAIIALEN 302 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: 268 Number of extensions: 15 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: 315 Length adjustment: 28 Effective length of query: 322 Effective length of database: 287 Effective search space: 92414 Effective search space used: 92414 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 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