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 YP_001327713.1 Smed_2045 phosphoribosyltransferase
Query= curated2:Q8TUT6 (291 letters) >NCBI__GCF_000017145.1:YP_001327713.1 Length = 223 Score = 49.7 bits (117), Expect = 6e-11 Identities = 60/197 (30%), Positives = 81/197 (41%), Gaps = 33/197 (16%) Query: 92 RQDRRFEP--------GEPVSFRAVARAVSANADALITVDLHEPGTLKYFDVPAENVSAA 143 R++R EP G PV+F VA+ ++A D LI + PG +Y + Sbjct: 23 RKERFSEPLVMALPRGGVPVAFE-VAKILAAPLDLLIVRKIGAPGHPEYGIGALVDSDGP 81 Query: 144 EELGKYLAERF--EGEDLVVIGPDEGARELAREVASICGVEYDHLEKKRLSGDEVEIHPK 201 + + A R E V + ELAR A G D++ P+ Sbjct: 82 QVVLNAEAMRSVNPSESYVEAETERQRHELARRRALYLG-------------DQMRRSPR 128 Query: 202 ELDVEGRTVVLVDDMIDTGGTMVEAARALRDQGAGTLYAACTHALLTRNAATRLLASGFE 261 GR V++VDD I TGGT AARALR GA L A A + A+ R F Sbjct: 129 -----GRNVIIVDDGIATGGTAKAAARALRQAGAAALMLAVPVAPASAVASLRDEVDRFV 183 Query: 262 DIIATDTVPNPFEKVSV 278 + T PN F VS+ Sbjct: 184 CL----TTPNRFHAVSI 196 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: 154 Number of extensions: 6 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: 223 Length adjustment: 24 Effective length of query: 267 Effective length of database: 199 Effective search space: 53133 Effective search space used: 53133 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 10 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