Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_012565380.1 RC1_RS00625 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000016185.1:WP_012565380.1 Length = 269 Score = 176 bits (446), Expect = 5e-49 Identities = 99/263 (37%), Positives = 148/263 (56%), Gaps = 6/263 (2%) Query: 7 SLARLTDVIDRLLAPEG-CPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 S+ RL D++ +L PEG CPWD EQ S+ + +EE +E+ +AI G+ +++E+GD+ Sbjct: 4 SMKRLVDLMAKLRDPEGGCPWDLEQDFRSIAPHTIEEAYEVADAIEKGDMAALKDELGDL 63 Query: 66 MFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIK--- 122 +F + F R+ ++G + D A+ AKM+RRHPHVF +T + + WE +K Sbjct: 64 LFQVVFYARMAEERGDWDFDAVAAHITAKMVRRHPHVFGETVVDTAADQTQRWEDLKARE 123 Query: 123 RAEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELL 182 RAEKA AEG D + LP L +A ++ +AARVGF W E++ ++E E EL Sbjct: 124 RAEKAAAEGRRPSALDGVIGGLPALTRAVKLQKRAARVGFDWTRAEEILDKIEEEIGELR 183 Query: 183 DVL--AGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARER 240 L A +E GDL+F+LV L RR + +AL TN KF RRFR +E + Sbjct: 184 HELRAATPHPDRIRDETGDLLFALVNLARRLEVDPESALRGTNAKFERRFRHIEDRLAAQ 243 Query: 241 GLDFPALSLDDKDELWNEAKAAE 263 G +L++ + LW +AK E Sbjct: 244 GRTPGDATLEEMEALWQQAKRLE 266 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: 215 Number of extensions: 15 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: 269 Length adjustment: 25 Effective length of query: 242 Effective length of database: 244 Effective search space: 59048 Effective search space used: 59048 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