Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_026595833.1 A3OQ_RS0114265 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000385335.1:WP_026595833.1 Length = 278 Score = 176 bits (446), Expect = 5e-49 Identities = 100/271 (36%), Positives = 146/271 (53%), Gaps = 8/271 (2%) Query: 5 NASLARLTDVIDRLLAP-EGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMG 63 ++ +ARL +++ L P GCPWD EQT E++ + +EE +E+V+A++ G+ ++R+E+G Sbjct: 4 SSDIARLIEIVAALRTPGSGCPWDLEQTFETIVPFTLEEAYEVVDAVQRGDLQDLRDELG 63 Query: 64 DVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKR 123 D++ + F R+ ++ AF + AKMIRRHPHVF + D R W IK Sbjct: 64 DLLLQVVFHARMAEEQKAFDFGGVVEAITAKMIRRHPHVFGEAKDLTPDATKRLWAEIKA 123 Query: 124 AEKADAEGE-------PQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEA 176 AEKA E P GV + +LP L +A ++ KA+RVGF W + + V ++ Sbjct: 124 AEKAAKAAERGGEAQAPAGVLADVAVTLPALTRAVKLQEKASRVGFDWKDAKVVVAKIRE 183 Query: 177 EWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEAL 236 E E+ L G D A E+GDL F++ L R G + L N KF RRF +E Sbjct: 184 ETDEVEAALDGGDADAIAEEIGDLFFAVANLARHHGRDPESILRAANAKFERRFGFIEET 243 Query: 237 ARERGLDFPALSLDDKDELWNEAKAAEAAAR 267 RG F A SL + LW EAK AE A+ Sbjct: 244 LARRGQAFAATSLAKMEALWTEAKKAEEKAQ 274 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: 204 Number of extensions: 18 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: 278 Length adjustment: 25 Effective length of query: 242 Effective length of database: 253 Effective search space: 61226 Effective search space used: 61226 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