Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate Synpcc7942_1493 Synpcc7942_1493 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__SynE:Synpcc7942_1493 Length = 279 Score = 168 bits (426), Expect = 1e-46 Identities = 93/255 (36%), Positives = 140/255 (54%), Gaps = 4/255 (1%) Query: 7 SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 +L +L V+ +L PE GCPWD+EQTP SL Y++EE +E+V A+R GN + + EE+GD+ Sbjct: 20 ALLQLVAVVAQLRDPEQGCPWDREQTPTSLIPYVLEEAYEVVHALRQGNPNAIAEELGDL 79 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAE 125 + + ++ ++ F L K+IRRHPHVF + + W++IK E Sbjct: 80 LLQVVLQAQIASESQQFDLATVADGITEKLIRRHPHVFGEAIAETPEAVQATWQAIKARE 139 Query: 126 KADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDVL 185 K + A+LPPL A +I +AA+ GF WP V + E E EL + L Sbjct: 140 KGEVAETLTHCLSRYAATLPPLTAALKISQRAAKAGFEWPNLAGVWDKFEEELAELKEAL 199 Query: 186 AGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDFP 245 D+ E ELGDL+FSLV + R + AL TN +F+ RF+++EA A G Sbjct: 200 DSGDRDHAEAELGDLLFSLVNIARWCQLDPVAALQGTNDRFVARFQKVEAAA---GQSLD 256 Query: 246 ALSLDDKDELWNEAK 260 +L ++ ++LW +AK Sbjct: 257 SLGIETLEKLWQQAK 271 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: 173 Number of extensions: 5 Number of successful extensions: 2 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: 279 Length adjustment: 25 Effective length of query: 242 Effective length of database: 254 Effective search space: 61468 Effective search space used: 61468 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