Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate Pf1N1B4_1220 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60)
Query= BRENDA::D4GST8 (299 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1220 Length = 291 Score = 53.5 bits (127), Expect = 6e-12 Identities = 48/159 (30%), Positives = 70/159 (44%), Gaps = 18/159 (11%) Query: 1 MQLGVIGLGRMGRIVVDRVLDAGHEVVAFDLSAEAVAAAADAGAEPADSVA------DLV 54 M+LG IGLG MG +V +L AGH V ++ S+ + A AGA+P DS A L+ Sbjct: 1 MELGFIGLGTMGVPMVLNLLKAGHRVKVWNRSSAPLDELARAGAQPVDSPALAAQAEVLI 60 Query: 55 DRLGDDKRIWLMVPAGDAVDATLDDLDPHLDGDDVVV----DGGNSHFEESVRRAEACSA 110 LGDD I + G +D L H++ V V + H E V A Sbjct: 61 SMLGDDVAIRSVFIDGKGLDG-LAAGSVHVNMSTVSVALAKEFAALHTERDVAYVSAPVL 119 Query: 111 AYLDCGTSGGPAGAELGFSLMVGGPQWAYDELTPVFDAV 149 +D +G +++ GP A + P+FD + Sbjct: 120 GRVDVAAAG-------NLNILASGPAQALARVQPLFDVL 151 Lambda K H 0.317 0.137 0.413 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: 166 Number of extensions: 5 Number of successful extensions: 1 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: 299 Length of database: 291 Length adjustment: 26 Effective length of query: 273 Effective length of database: 265 Effective search space: 72345 Effective search space used: 72345 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