Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate GFF1604 Psest_1641 MazG family protein
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__psRCH2:GFF1604 Length = 276 Score = 172 bits (436), Expect = 7e-48 Identities = 100/267 (37%), Positives = 144/267 (53%), Gaps = 11/267 (4%) Query: 8 LARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVM 66 L L ++ RL P+ GCPWD +Q S+ + +EE +E+ +AI SG+ D + E+GD++ Sbjct: 4 LPDLLHLMARLRDPQHGCPWDLQQNYASIVPHTLEEAYEVADAIESGDFDHLPGELGDLL 63 Query: 67 FLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLR--------NW 118 F + + +L ++G F + K+IRRHPHVF D E R W Sbjct: 64 FQVVYYSQLAREEGRFEFATVVDAITRKLIRRHPHVFPDGDLYGSPELPRLDEAAIKQRW 123 Query: 119 ESIKRAEKADAEGEPQ--GVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEA 176 E IK E+A+ P+ + D +P++LP L +A ++ +AA+VGF WPE V +V Sbjct: 124 EEIKAEERAEKAAAPEQLSLLDDVPSALPALSRAAKLQKRAAQVGFDWPEALPVVDKVRE 183 Query: 177 EWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEAL 236 E E+L+ ++ DD A ELGDL+F +V L R + AL N KF RRFR +E Sbjct: 184 ELGEVLEAMSEDDPQAIAEELGDLLFVVVNLARHLKVDPENALRAANGKFERRFRFIEQA 243 Query: 237 ARERGLDFPALSLDDKDELWNEAKAAE 263 RE G LD+ D LW EAK AE Sbjct: 244 LREAGRPIEHCDLDELDALWGEAKKAE 270 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: 223 Number of extensions: 16 Number of successful extensions: 6 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: 276 Length adjustment: 25 Effective length of query: 242 Effective length of database: 251 Effective search space: 60742 Effective search space used: 60742 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