Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_040574358.1 H035_RS0106710 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000421465.1:WP_040574358.1 Length = 263 Score = 184 bits (466), Expect = 2e-51 Identities = 106/258 (41%), Positives = 144/258 (55%), Gaps = 2/258 (0%) Query: 7 SLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 S+ RL ++ RL PE GCPWD++QT ESL Y +EE +E+ +AI +E+ E+GD+ Sbjct: 3 SIDRLLTLMARLRDPETGCPWDRKQTFESLIPYTLEEAYEVADAIEREAWEELEGELGDL 62 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAE 125 + + F R+ ++G F D + K+ RRHPHVF+ YA R WE IKRAE Sbjct: 63 LLQVVFYARIAEEQGWFDFDRVVEGICDKLERRHPHVFAGVEYASEKARKRAWEEIKRAE 122 Query: 126 KADAEG-EPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDV 184 + + E V +PA+LP LL+ +I ++AAR GF WPE V +VE E EL + Sbjct: 123 RRNQPAPEDDSVLADIPATLPGLLQTEKIQTQAARHGFDWPEVPPVFEKVEEELDELREA 182 Query: 185 LAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDF 244 A D A + E+GDL+F V L R + TAL +N KF RRFR ME E G Sbjct: 183 YASGDAAHIQEEVGDLLFVAVNLARHLNVHPETALRESNRKFGRRFRYMEKRLAEDGKTL 242 Query: 245 PALSLDDKDELWNEAKAA 262 L D D LW+EAK + Sbjct: 243 AETPLADLDSLWDEAKGS 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: 204 Number of extensions: 11 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