Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate 16865 b2781 nucleoside triphosphate pyrophosphohydrolase (NCBI)
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Keio:16865 Length = 263 Score = 182 bits (462), Expect = 6e-51 Identities = 97/259 (37%), Positives = 148/259 (57%), Gaps = 9/259 (3%) Query: 10 RLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVMFL 68 RL ++ RL PE GCPWDKEQT ++ Y +EE +E+++AI + D++R E+GD++F Sbjct: 6 RLLTIMQRLRDPENGCPWDKEQTFATIAPYTLEETYEVLDAIAREDFDDLRGELGDLLFQ 65 Query: 69 LAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEKAD 128 + F ++ ++G F +D A + K+ RRHPHVF+D++ + E L WE IK E+ Sbjct: 66 VVFYAQMAQEEGRFDFNDICAAISDKLERRHPHVFADSSAENSSEVLARWEQIKTEER-- 123 Query: 129 AEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTW----PEDEDVERQVEAEWLELLDV 184 A+ D +P SLP L++A +I + A VGF W P + V +++ E Sbjct: 124 AQKAQHSALDDIPRSLPALMRAQKIQKRCANVGFDWTTLGPVVDKVYEEIDEVMYEARQA 183 Query: 185 LAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDF 244 + D+A E E+GDL+F+ V L R G KA AL N KF RRFR +E + RGL+ Sbjct: 184 VV--DQAKLEEEMGDLLFATVNLARHLGTKAEIALQKANEKFERRFREVERIVAARGLEM 241 Query: 245 PALSLDDKDELWNEAKAAE 263 + L+ +E+W + K E Sbjct: 242 TGVDLETMEEVWQQVKRQE 260 Lambda K H 0.318 0.134 0.393 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: 192 Number of extensions: 10 Number of successful extensions: 4 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: 267 Length of database: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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 (21.7 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