Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate 3607751 Dshi_1160 MazG family protein (RefSeq)
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Dino:3607751 Length = 279 Score = 176 bits (446), Expect = 5e-49 Identities = 100/256 (39%), Positives = 147/256 (57%), Gaps = 4/256 (1%) Query: 8 LARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVM 66 L RL +++ RL PE GCPWD EQT E++ Y +EE +E+ +AI G+ +++ E+GD++ Sbjct: 23 LPRLLEIMRRLRDPETGCPWDVEQTFETIAPYTIEEAYEVSDAIDRGDWADLKSELGDLL 82 Query: 67 FLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYA-DRDEFLRNWESIKRAE 125 + ++ A++G F D A KM+ RHPHVF D + A ++ R+WE+ K E Sbjct: 83 LQTVYQTQIGAERGLFDFHDVANGIAQKMLDRHPHVFGDESNAKSAEQQTRDWEAQKARE 142 Query: 126 KADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDVL 185 +A A+ E +GV D + LP L++A ++ +AARVGF W + + V ++ E EL D Sbjct: 143 RA-AKAE-KGVLDGVALGLPALMRALKLQKRAARVGFDWDDADQVLAKLAEESAELADAR 200 Query: 186 AGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDFP 245 D A E GDL+F +V LGR G+ AL N KF RRF +EA G + Sbjct: 201 DAGDAAKLHEEFGDLLFVVVNLGRHLGLDPEHALRDANAKFTRRFAHIEAELARAGRNPE 260 Query: 246 ALSLDDKDELWNEAKA 261 A SLD+ + LW AKA Sbjct: 261 AASLDEMEALWQAAKA 276 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: 226 Number of extensions: 14 Number of successful extensions: 5 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: 279 Length adjustment: 25 Effective length of query: 242 Effective length of database: 254 Effective search space: 61468 Effective search space used: 61468 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