Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate synthase; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate SMc01463 SMc01463 hypothetical protein
Query= curated2:Q8TUT6 (291 letters) >FitnessBrowser__Smeli:SMc01463 Length = 236 Score = 48.5 bits (114), Expect = 1e-10 Identities = 56/191 (29%), Positives = 78/191 (40%), Gaps = 45/191 (23%) Query: 100 GEPVSFRAVARAVSANADALITVDLHEPGTLKY-------FDVP-----AENVSAAEELG 147 G PV+F VAR + A+ + LI + PG ++ D P AE + A Sbjct: 49 GVPVAFE-VARTLGASLELLIVRKIGAPGHPEFGLGALVDSDEPQVVLNAEAMRIANPSE 107 Query: 148 KYLAERFEGEDLVVIGPDEGARELAREVASICGVEYDHLEKKRLSGDEVEIHPKELDVEG 207 KY+ E + L ELAR + GD+ I P G Sbjct: 108 KYVQAETERQRL----------ELARR-------------RVLYLGDQARISPS-----G 139 Query: 208 RTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALLTRNAATRLLASGFEDIIATD 267 R V++VDD I TGGT AA+ALR GA L A + +A L + ++ Sbjct: 140 RNVIIVDDGIATGGTAKAAAKALRQAGAAALMLAVP---VAPKSAIASLGDDVDRLVCLA 196 Query: 268 TVPNPFEKVSV 278 + P PF VS+ Sbjct: 197 S-PTPFHAVSI 206 Lambda K H 0.314 0.134 0.370 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: 149 Number of extensions: 3 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: 291 Length of database: 236 Length adjustment: 25 Effective length of query: 266 Effective length of database: 211 Effective search space: 56126 Effective search space used: 56126 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: 42 (22.0 bits) S2: 47 (22.7 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