Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate PfGW456L13_3497 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= SwissProt::Q9C4M5 (331 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3497 Length = 321 Score = 176 bits (445), Expect = 9e-49 Identities = 104/272 (38%), Positives = 151/272 (55%), Gaps = 13/272 (4%) Query: 45 EVDALVTLVTDKVDKELLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDAT 104 ++DA++T + + + P LKII GY+++D++ A RGI VTN GV + Sbjct: 45 QIDAVLTRGPLGLYADEIAALPNLKIICVIGAGYEHVDLQAAANRGITVTNGAGVNASSV 104 Query: 105 ADLAFALLLAVARRIVEADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQA 164 AD A ALLLA+ R I DA VR GEW K + L GK LGI+G G +G A Sbjct: 105 ADHAMALLLALVRDIPRCDAAVRRGEWPK---------IMRPSLAGKRLGILGLGAVGMA 155 Query: 165 LAKRA-KGFGMKIIYYSRTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIG 223 +AKRA GF M + Y++R + + + + L + SDF+ + P T H+I Sbjct: 156 IAKRAANGFDMAVSYHNRQHRSDVPYTFCSTPTE---LARASDFLIVATPGGLGTRHLIN 212 Query: 224 EKELKLMKPNAILINTSRGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNV 283 + L + PN ++N +R +V+ T LI AL++ IAGA LDVF+ EP + L L NV Sbjct: 213 KAVLDTLGPNGFIVNIARASVIVTTDLISALEQRRIAGAALDVFDAEPKVPDALKTLSNV 272 Query: 284 VLAPHIGSATHEAREGMAELVAKNLIAFAKGE 315 +L PH+ + EA +G E+V KNL+AF G+ Sbjct: 273 ILTPHVAGLSPEATQGTVEMVGKNLVAFFSGQ 304 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: 225 Number of extensions: 11 Number of successful extensions: 3 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: 321 Length adjustment: 28 Effective length of query: 303 Effective length of database: 293 Effective search space: 88779 Effective search space used: 88779 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: 48 (23.1 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