Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate Echvi_1176 Echvi_1176 MazG family protein
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Cola:Echvi_1176 Length = 266 Score = 178 bits (451), Expect = 1e-49 Identities = 99/256 (38%), Positives = 147/256 (57%), Gaps = 12/256 (4%) Query: 10 RLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVMFLL 69 RL ++D L E CPWD++QT ESL +EE FEL +AI + +EV++E+GD++ + Sbjct: 16 RLLTIMDELR--EQCPWDRKQTIESLRHLTIEETFELSDAILDADLEEVKKELGDILLHI 73 Query: 70 AFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEKADA 129 F ++ +KGAF + + + K+IRRHPH++ DT D + +NWE IK EK + Sbjct: 74 VFYAKIGEEKGAFDIATVIESLCEKLIRRHPHIYGDTEANDDEAVKQNWEKIKLQEKGN- 132 Query: 130 EGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVE---AEWLELLDVLA 186 + V +P SLP L+KA RI KA VGF W + V +VE E+ E DV A Sbjct: 133 ----KSVLGGVPRSLPALIKAMRIQEKARGVGFDWEDKAQVWEKVEEEMQEFKEAFDVTA 188 Query: 187 GD--DKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDF 244 + D+ E GD++FSL+ R I AL+ TN KF+ RF+ +E A++ G + Sbjct: 189 PEDIDRERATGEFGDVLFSLINYARFVDINPEEALEKTNRKFIYRFQYLEEAAKKAGKNL 248 Query: 245 PALSLDDKDELWNEAK 260 ++L++ D WNEAK Sbjct: 249 GDMTLNEMDIFWNEAK 264 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: 217 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: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 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