Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate 6936852 Sama_1034 nucleoside triphosphate pyrophosphohydrolase (RefSeq)
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__SB2B:6936852 Length = 275 Score = 168 bits (426), Expect = 1e-46 Identities = 95/266 (35%), Positives = 146/266 (54%), Gaps = 5/266 (1%) Query: 5 NASLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMG 63 NA + L ++ +L P+ GCPWDK Q E++ + +EE +E+ + I + DE+ +E+G Sbjct: 12 NADINPLLAIMAKLRDPKHGCPWDKAQRFETIVPFTLEEAYEVADTIERMDLDELPDELG 71 Query: 64 DVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKR 123 D++F + F +L ++G F D+ + AK+ RHPHVF D + E NWE+IK Sbjct: 72 DLLFQVVFYCQLGKEQGLFDFDEVVKRICAKLTSRHPHVFGDIEVSSSKEVKDNWEAIKA 131 Query: 124 AEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLD 183 +E+ + V D +P LP L +A +I + ARVGF W E V +VE E E+L Sbjct: 132 SER--KAKDKHSVLDDVPVGLPALSRAAKIQKRVARVGFDWGELPPVVAKVEEEIAEVLA 189 Query: 184 VLAGD--DKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERG 241 + D D+ +E+GDL+F++V + R G++ AL N KF RRFR +E LA G Sbjct: 190 EVQVDSPDQERVASEMGDLLFAVVNMARHLGVEPEQALRRANQKFERRFRGVEELATLGG 249 Query: 242 LDFPALSLDDKDELWNEAKAAEAAAR 267 SL + D W++ K E + R Sbjct: 250 RQLTDYSLAELDGFWDQVKEQEKSPR 275 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: 182 Number of extensions: 8 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: 275 Length adjustment: 25 Effective length of query: 242 Effective length of database: 250 Effective search space: 60500 Effective search space used: 60500 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