Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate N515DRAFT_1746 N515DRAFT_1746 ATP diphosphatase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Dyella79:N515DRAFT_1746 Length = 270 Score = 168 bits (425), Expect = 1e-46 Identities = 94/260 (36%), Positives = 144/260 (55%), Gaps = 3/260 (1%) Query: 7 SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 SL L ++ RL P+ GCPWD +Q ++ Y +EE +E+ +AI + ++R+E+GD+ Sbjct: 8 SLDDLLAIMARLRDPQRGCPWDVQQDFATIAPYTIEEAYEVADAIDRKDWHDLRDELGDL 67 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAE 125 + + F ++ ++G F D + KMIRRHPHVF D +Y D + WE+IK E Sbjct: 68 LLQVVFHAQMAQEQGLFDFADVAHAISDKMIRRHPHVFGDVSYDDVEAQKEAWEAIKAEE 127 Query: 126 K-ADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLEL-LD 183 + A E + LP +A ++ +AA+VGF WP+++ V ++ E E+ + Sbjct: 128 RAAKGESHDDSALAGVSRGLPEWKRALKLQQRAAKVGFDWPDEQPVLDKLAEEIEEVRAE 187 Query: 184 VLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLD 243 AG DKA ++E+GD+ F LV L R + + AL N KF RRFR MEALARE G+ Sbjct: 188 FAAGADKARLQDEIGDVAFVLVNLARHADVDFSQALRHANEKFERRFRGMEALAREEGVP 247 Query: 244 FPALSLDDKDELWNEAKAAE 263 L+ ++ LW K E Sbjct: 248 LAERGLEAQEALWQRVKGGE 267 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: 239 Number of extensions: 14 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: 270 Length adjustment: 25 Effective length of query: 242 Effective length of database: 245 Effective search space: 59290 Effective search space used: 59290 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