Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate WP_028998005.1 H537_RS0111215 D-glycerate dehydrogenase
Query= SwissProt::Q9C4M5 (331 letters) >NCBI__GCF_000430725.1:WP_028998005.1 Length = 328 Score = 262 bits (669), Expect = 1e-74 Identities = 148/328 (45%), Positives = 208/328 (63%), Gaps = 8/328 (2%) Query: 2 KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVR-EVDALVTLVTDKVDKE 60 KP V + R++ ++ + + +E+E + L +++ + A VTL ++++D Sbjct: 4 KPAVLVARKVFPEVVQRLAQHFEVEDNPADRIYTPDELRARLQGKAGAFVTL-SERIDAA 62 Query: 61 LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120 LL+ P+L+ + AVGY+NID+ + RG+ V+NTP VLT+ TAD FAL++A ARRI Sbjct: 63 LLDANPQLRAVCNMAVGYNNIDVGACSARGVLVSNTPDVLTETTADFGFALMMATARRIT 122 Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKR-AKGFGMKIIYY 179 E++ F+R G W + W MF G L G TLGI+G GRIGQ +A+R A GFGM++IY+ Sbjct: 123 ESERFLREGRWDR----WAYDMFAGSDLHGATLGILGMGRIGQGIARRGALGFGMQVIYH 178 Query: 180 SRTRKP-EAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILIN 238 +R+R P + E I A YVD +TLL+E+D + + VP + +T+H IG EL MKP A L N Sbjct: 179 NRSRLPADQEAPINARYVDKQTLLREADHLVVVVPYSPQTHHAIGAAELAQMKPTATLSN 238 Query: 239 TSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEARE 298 +RG VVD AL +AL +G IA AGLDVFE EP + +L L+NVVL PHI SA+ R Sbjct: 239 IARGGVVDDAALAQALAQGHIAAAGLDVFEGEPQVHPQLLALRNVVLTPHIASASVATRR 298 Query: 299 GMAELVAKNLIAFAKGEIPPNLVNKDVL 326 MA+L A NLIA G + P VN VL Sbjct: 299 AMADLAADNLIAALTGGVSPTPVNPQVL 326 Lambda K H 0.317 0.137 0.392 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: 250 Number of extensions: 16 Number of successful extensions: 4 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: 331 Length of database: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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