Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate Pf1N1B4_3509 Nucleoside triphosphate pyrophosphohydrolase MazG (EC 3.6.1.8)
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3509 Length = 277 Score = 172 bits (435), Expect = 9e-48 Identities = 95/268 (35%), Positives = 151/268 (56%), Gaps = 11/268 (4%) Query: 7 SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 SL L +++RL P+ GCPWD +QT ++ + +EE +E+ +AI G+ D ++ E+GD+ Sbjct: 3 SLEDLLHLMNRLRDPQYGCPWDIKQTYATIVPHTLEEAYEVADAIERGDFDHLQGELGDL 62 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFS--------DTTYADRDEFLRN 117 +F + + +L ++G F D + + K+IRRHPHVF D + ++ + Sbjct: 63 LFQVVYYSQLAREEGRFEFDGVVDSITRKLIRRHPHVFPTGDLYAPLDIPRLNEEQVKQR 122 Query: 118 WESIKRAEKADAEGEPQ--GVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVE 175 WE IK E+A+ PQ + D +PA+LP L ++ ++ +A +VGF W + V +V Sbjct: 123 WEEIKAEERAEKSSAPQQLSLLDDVPAALPALSRSAKLQKRAGQVGFDWSDALPVLDKVR 182 Query: 176 AEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEA 235 E E+L +A +D AA +E+GDL+FS+V L R + TAL N KF RRFR +E Sbjct: 183 EELDEVLQAMADNDSAAIADEVGDLLFSVVNLARHLKVDPETALRSANSKFERRFRFIEQ 242 Query: 236 LARERGLDFPALSLDDKDELWNEAKAAE 263 R+ +L++ D LW EAK E Sbjct: 243 ALRDTHRPIEDCTLEELDALWGEAKRQE 270 Score = 35.4 bits (80), Expect = 1e-06 Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 5/96 (5%) Query: 177 EWLELLDVLAGDDKAAQENELGDLIFSLV---ELGRRKG-IKANTALDMTNLKFLRRFRR 232 E E+ D + D + ELGDL+F +V +L R +G + + +D K +RR Sbjct: 39 EAYEVADAIERGDFDHLQGELGDLLFQVVYYSQLAREEGRFEFDGVVDSITRKLIRRHPH 98 Query: 233 MEALARERG-LDFPALSLDDKDELWNEAKAAEAAAR 267 + LD P L+ + + W E KA E A + Sbjct: 99 VFPTGDLYAPLDIPRLNEEQVKQRWEEIKAEERAEK 134 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: 208 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 267 Length of database: 277 Length adjustment: 25 Effective length of query: 242 Effective length of database: 252 Effective search space: 60984 Effective search space used: 60984 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