Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_012504809.1 PAES_RS01075 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000020625.1:WP_012504809.1 Length = 273 Score = 160 bits (405), Expect = 3e-44 Identities = 87/239 (36%), Positives = 129/239 (53%), Gaps = 8/239 (3%) Query: 24 CPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVMFLLAFLGRLYADKGAFT 83 CPWD++QTP+SL L+EE +ELV AI G+ E+++E+GD+ ++F + + FT Sbjct: 42 CPWDRKQTPQSLAHLLLEESYELVHAIDEGDQQELKKELGDLFLHISFQVLMAEEAKTFT 101 Query: 84 LDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEKADAEGEPQGVYDSLPAS 143 + K+I RHPHVF DTT + + L+NWES+K EK + + D +P + Sbjct: 102 YAEVFDALCDKLINRHPHVFGDTTAENEQDVLKNWESLKLLEK-----NRRSLLDGVPKA 156 Query: 144 LPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDVLAGDDKAAQENELGDLIFS 203 + LL+AYR+ K A VGF W DE V ++ E EL + A QE E GDL+F+ Sbjct: 157 MSELLRAYRVQKKVAGVGFDWQSDEGVLDKLTEEIAELKN---AKTSAEQEEEFGDLLFT 213 Query: 204 LVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDFPALSLDDKDELWNEAKAA 262 +V R AL KF+ +F +E + + + S ++ D LWN AK A Sbjct: 214 IVNYSRFISTNPEDALRKATNKFMSQFMHVEKMVQASEKSWREFSPEELDALWNSAKKA 272 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: 178 Number of extensions: 6 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: 273 Length adjustment: 25 Effective length of query: 242 Effective length of database: 248 Effective search space: 60016 Effective search space used: 60016 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