Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_066920254.1 ACG33_RS08180 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_001579945.1:WP_066920254.1 Length = 273 Score = 160 bits (405), Expect = 3e-44 Identities = 97/268 (36%), Positives = 144/268 (53%), Gaps = 14/268 (5%) Query: 7 SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 S+ RL +++ L P+ GCPWD EQ S+ Y +EE +E+V+AI + +REE+GD+ Sbjct: 2 SIERLLNIMALLRDPQRGCPWDLEQDFRSVAPYTIEEAYEVVDAIERNDLQGLREELGDL 61 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAE 125 +F + F ++ ++G F ++ +A KM RRHPHVF + + WE IK+ E Sbjct: 62 LFQIVFHAQIAQEQGIFGFEEVVAGICEKMQRRHPHVFGNERIDTVAQQNLAWEQIKQRE 121 Query: 126 KADAEG-EPQGVYD-----------SLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQ 173 +A G GV D +P +LP L +A ++ +AA+ GF WP+ + Sbjct: 122 RAPRGGHSASGVADGSGSDAASLLSDVPLALPSLTRAAKLGRRAAQAGFQWPDVAGALDK 181 Query: 174 VEAEWLELLDVLA-GDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRR 232 ++ E E+ LA G D A E+GD++F LV + R I T+L TN KF RRFR Sbjct: 182 LDEEIAEMRAELARGADPEAIAAEIGDVLFCLVNVCRYLQIDPETSLRGTNAKFERRFRH 241 Query: 233 MEALARERGLDFPALSLDDKDELWNEAK 260 +E RERG SL++ D LW E K Sbjct: 242 VERRLRERGRSLQDASLEEMDALWEEGK 269 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: 175 Number of extensions: 9 Number of successful extensions: 5 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: 273 Length adjustment: 25 Effective length of query: 242 Effective length of database: 248 Effective search space: 60016 Effective search space used: 60016 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 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