Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate GFF1962 PGA1_c19950 protein MazG
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Phaeo:GFF1962 Length = 278 Score = 186 bits (472), Expect = 5e-52 Identities = 102/265 (38%), Positives = 148/265 (55%), Gaps = 4/265 (1%) Query: 4 DNASLARLTDVIDRLLAPEG-CPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEM 62 + A + RL +++ RL P+G CPWD EQ S+ Y +EE +E+ +AI DE++ E+ Sbjct: 10 ETAGIERLLEIMRRLRDPKGGCPWDIEQNFASIAPYTIEEAYEVADAIEREAWDELKGEL 69 Query: 63 GDVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYA-DRDEFLRNWESI 121 GD++F F ++ A+ G FT D + + KM+ RHPHVF D + D+ +WE+I Sbjct: 70 GDLLFQSVFHAQMAAEAGHFTFQDVVTTMSNKMVSRHPHVFGDESREKSADQQTADWEAI 129 Query: 122 KRAEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLEL 181 K AE+AD +G D + LP LL+AY++ +AARVGF WP ++V ++ E EL Sbjct: 130 KAAERADKA--QRGTLDGVAVGLPALLRAYKLQKRAARVGFDWPSADNVIDKIAEESAEL 187 Query: 182 LDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERG 241 ++ +A E E GDL+F + LGR GI+ AL N KF RRF +EA RG Sbjct: 188 VEARDSLSQAEVEEEFGDLMFVMANLGRHLGIEPEAALRAANAKFTRRFEGVEAKLSARG 247 Query: 242 LDFPALSLDDKDELWNEAKAAEAAA 266 L + D LW+E K AA Sbjct: 248 KRPEDSDLTEMDALWDEVKVESRAA 272 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: 222 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: 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