Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_086510268.1 BZY95_RS12560 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_002151265.1:WP_086510268.1 Length = 298 Score = 157 bits (398), Expect = 2e-43 Identities = 95/281 (33%), Positives = 148/281 (52%), Gaps = 17/281 (6%) Query: 1 MTKDNASLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVR 59 M+++ + L ++ L PE GCPWD +Q +S+ + +EE +E+ +AI E+ Sbjct: 1 MSENRHGIDDLLTLMAVLRDPEQGCPWDLKQDWDSIVPHTLEEAYEVADAIERRAWGELP 60 Query: 60 EEMGDVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRD------- 112 E+GD++F +A+ + +++G F D + AKM+RRHPHVF D T A R Sbjct: 61 GELGDLLFQVAYYSQFASEEGRFDFHDVVHTLTAKMVRRHPHVFPDGTLASRRPPGVSAE 120 Query: 113 -----EFLRNWESIK---RAEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTW 164 + WES+K R E+A+A+ V D +P +LP L +A ++ +AARVGF W Sbjct: 121 QVETRQVNSRWESLKAEERVERAEADAGVS-VLDDVPRTLPALSRAAKLSKRAARVGFDW 179 Query: 165 PEDEDVERQVEAEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNL 224 P+ V ++ E E+ LA ++ E+GDL+F++ L R L TN Sbjct: 180 PDATGVIAKIREELDEVEQALAEGNRRHAAEEVGDLLFAVTNLARTLKADPEQCLRDTNA 239 Query: 225 KFLRRFRRMEALARERGLDFPALSLDDKDELWNEAKAAEAA 265 KF RRFR +E ERG+ + LD + W EAK E++ Sbjct: 240 KFERRFRHVERALAERGMTTRDVDLDTMERHWQEAKRLESS 280 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: 222 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: 298 Length adjustment: 26 Effective length of query: 241 Effective length of database: 272 Effective search space: 65552 Effective search space used: 65552 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 10 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