Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate CA265_RS14355 CA265_RS14355 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Pedo557:CA265_RS14355 Length = 268 Score = 175 bits (444), Expect = 8e-49 Identities = 98/259 (37%), Positives = 143/259 (55%), Gaps = 13/259 (5%) Query: 7 SLARLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVM 66 + RL V+D L CPWDK+QT E+L +EE +EL +AI G+ DE+++E+GDVM Sbjct: 16 AFTRLLTVLDTLRTQ--CPWDKKQTMETLRHLTIEETYELSDAILEGDLDEIKKELGDVM 73 Query: 67 FLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEK 126 L F R+ ++ F + D + K++ RHPH++ D + ++ RNWE IK E Sbjct: 74 MHLVFYSRIASETNDFNITDVLNGVCDKLVNRHPHIYGDVEVQNEEDVKRNWEQIKLKE- 132 Query: 127 ADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLEL-LDVL 185 + V +P+SLP L+KA RI KA VGF W + V +VE E E + Sbjct: 133 -----GNKSVLAGVPSSLPALVKASRIQEKARGVGFDWEDKNQVWEKVEEELQEFKTEFN 187 Query: 186 AGDDKAAQ----ENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERG 241 D+KA E+E GD++FSL+ R I AL+ TN KF++RF+ +E A+E G Sbjct: 188 VSDNKAIDIEKAESEFGDVLFSLINYARFININPENALEKTNKKFIKRFQYLETKAKENG 247 Query: 242 LDFPALSLDDKDELWNEAK 260 ++L + D WNEAK Sbjct: 248 KALADMTLAEMDIYWNEAK 266 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: 196 Number of extensions: 13 Number of successful extensions: 3 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: 268 Length adjustment: 25 Effective length of query: 242 Effective length of database: 243 Effective search space: 58806 Effective search space used: 58806 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