Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Pf1N1B4_4688 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)
Query= BRENDA::H9JRZ9 (432 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4688 Length = 317 Score = 128 bits (322), Expect = 2e-34 Identities = 77/242 (31%), Positives = 134/242 (55%), Gaps = 5/242 (2%) Query: 156 VVRSATQVTKEVLDAGVKLKVVGRAGAGVDNIDVDSAGKKGVGVINAPGANALSACELTC 215 V+R T+ +++L LK++ G +D+ +A G+ V +A ELT Sbjct: 55 VMRERTRFDEDLLRRLPTLKLLVTGGMRNAALDLKAAAALGIQVCGTDSYKH-AAPELTW 113 Query: 216 TLMLVLARHVVPASTALKAGRWDRALYTGSELAGKTLAILGLGRVGREVATRMYAFGMNI 275 L++ R++V + AL+AG+W + L G +L GKTLAILGLG +G+ VA FGM + Sbjct: 114 ALIMAATRNLVAEANALRAGQWQQGL--GGDLQGKTLAILGLGSIGQRVARFGQVFGMRV 171 Query: 276 IGFDPFVSADQCAQFHCTKMELEDIWPLADYITLHTPLIESTRNFINADVLKQCKKGVKI 335 I + ++A++ A+ T + ++++ AD +++H L E +R ++A L K + Sbjct: 172 IAWSENLTAERAAEVDVTYVSKQELFEQADVLSVHLVLSERSRGLVDAQALDWMKPTAWL 231 Query: 336 INVGRGGLIQETDFLQALKSGKVGGAALDVFEQEPPTDPVTLEIIQQPAVIATPHLGAST 395 +N RG ++ E+ ++AL+ ++ GAALDVFE EP + V+ATPH+G + Sbjct: 232 VNTARGPIVDESALIKALQKKRLAGAALDVFEHEPLPRHHPFRTLDN--VLATPHVGYVS 289 Query: 396 KE 397 ++ Sbjct: 290 RQ 291 Lambda K H 0.320 0.135 0.387 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: 256 Number of extensions: 12 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: 432 Length of database: 317 Length adjustment: 30 Effective length of query: 402 Effective length of database: 287 Effective search space: 115374 Effective search space used: 115374 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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