Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate BWI76_RS22800 BWI76_RS22800 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Koxy:BWI76_RS22800 Length = 263 Score = 188 bits (477), Expect = 1e-52 Identities = 101/261 (38%), Positives = 150/261 (57%), Gaps = 5/261 (1%) Query: 6 ASLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGD 64 + + RL ++ RL PE GCPWDKEQT ++ Y +EE +E+++AI + D++R E+GD Sbjct: 2 SQIDRLLGIMQRLRDPENGCPWDKEQTFATIAPYTLEETYEVLDAIAREDFDDLRGELGD 61 Query: 65 VMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRA 124 ++F + F ++ ++G F +D A K+ RRHPH+F D + + E L WE IK A Sbjct: 62 LLFQVVFYAQMAQEEGRFDFNDICAAIGDKLERRHPHIFGDASAGNSSEVLARWEQIKSA 121 Query: 125 EKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDV 184 E+ AE D +P SLP L++A++I + + VGF W V +V E E++ Sbjct: 122 ER--AEKSQHSALDDIPHSLPALMRAHKIQKRCSAVGFDWTSLGPVLDKVHEEIDEVMHE 179 Query: 185 L--AGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGL 242 A D+A E E+GDL+F+ V L R G+KA AL NLKF RRFR +E + RGL Sbjct: 180 AQQAVVDEAKLEEEVGDLLFATVNLSRHLGVKAEVALQKANLKFERRFREVERIVAARGL 239 Query: 243 DFPALSLDDKDELWNEAKAAE 263 + + LD + +W E K E Sbjct: 240 EMTGVDLDTMELVWQEVKRQE 260 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: 211 Number of extensions: 14 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: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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