Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 5210768 Shew_3196 D-3-phosphoglycerate dehydrogenase (RefSeq)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__PV4:5210768 Length = 409 Score = 159 bits (401), Expect = 1e-43 Identities = 100/289 (34%), Positives = 151/289 (52%), Gaps = 14/289 (4%) Query: 39 LLEKVREVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPG 98 LL +++ + ++ K +L+ A KL I + +G + +D+ A K GI V N P Sbjct: 47 LLASIKDAHFVGIRSRTQLTKAVLDKAEKLVSIGCFCIGTNQVDLAAAEKLGIPVFNAPF 106 Query: 99 VLTDATADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGF 158 T + A+L ++ + R I + +A G W KS G + +GKTLG++G+ Sbjct: 107 SNTRSVAELVLGEIIMLLRGIPQRNALAHRGGWLKSANG-------SFEARGKTLGVIGY 159 Query: 159 GRIGQALAKRAKGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKET 218 G IG L A+ GM++I++ K + E LL +D +SLHVP T +T Sbjct: 160 GHIGTQLGILAETLGMRVIFFDIEDKLPLGN--AQQIHSLEQLLSLADVVSLHVPETPQT 217 Query: 219 YHMIGEKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELF 278 +MIG KEL M+ +ILIN SRG VVD +AL +A++ I GA +DVF EP N++ F Sbjct: 218 KNMIGSKELAAMRQGSILINASRGTVVDIDALAEAIRGDHIVGAAIDVFPVEPKSNDDEF 277 Query: 279 -----KLKNVVLAPHIGSATHEAREGMAELVAKNLIAFAKGEIPPNLVN 322 L NV+L PH+G +T EA+E + VA L ++ VN Sbjct: 278 VSPLRGLDNVLLTPHVGGSTQEAQENIGIEVAGKLAKYSDNGSTMTAVN 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: 296 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 409 Length adjustment: 30 Effective length of query: 301 Effective length of database: 379 Effective search space: 114079 Effective search space used: 114079 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 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