Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_046008705.1 OLEAN_RS07465 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000967895.1:WP_046008705.1 Length = 307 Score = 132 bits (331), Expect = 1e-35 Identities = 95/287 (33%), Positives = 144/287 (50%), Gaps = 27/287 (9%) Query: 1 MTKDNASLARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVR 59 +T L L ++ RL PE GCPWD +QT +S+ + +EE E+ EAI S + V Sbjct: 5 VTDKKYDLKDLVYLMQRLRDPESGCPWDIKQTFDSIIPHTLEEAHEVAEAIESQDWPHVE 64 Query: 60 EEMGDVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVF-SDTTYADRD------ 112 EE+GD++F + F +L ++ F + K++RRHPHVF S +A RD Sbjct: 65 EELGDLLFQVIFYSQLGDEQTLFDFSSVIHVLVTKLVRRHPHVFPSGDLHAKRDLDSCPT 124 Query: 113 --EFLRNWESIKRAEKA-DAEG-----------EPQGVYDSLPASLPPLLKAYRIHSKAA 158 E W+ IK+ EKA AE E + +P SLP L +A +I + Sbjct: 125 DAEINAQWQIIKQQEKALKAEAGRLKLKKSEAFELVDYLNDIPTSLPELTRADKIQKMVS 184 Query: 159 RVGFTWPEDEDVERQVEAEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTA 218 GF W E + V +V E E+ + + D ++E+GDL+F+ V + R GI A Sbjct: 185 MRGFDWSEIQGVLDKVREELQEVEEEIEQADVQRLQHEVGDLLFASVNVARHLGINPEQA 244 Query: 219 LDMTNLKFLRRFRRM-EAL-ARERGLDF---PALSLDDKDELWNEAK 260 L N +F R+ + E+L A+ R L+ +S D+ ++ WNEAK Sbjct: 245 LGQANRRFSERYSLVAESLAAQNRSLELGNSNHVSSDEMEQAWNEAK 291 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: 206 Number of extensions: 15 Number of successful extensions: 3 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: 307 Length adjustment: 26 Effective length of query: 241 Effective length of database: 281 Effective search space: 67721 Effective search space used: 67721 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