Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate SMc01051 SMc01051 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Smeli:SMc01051 Length = 277 Score = 179 bits (453), Expect = 7e-50 Identities = 104/267 (38%), Positives = 146/267 (54%), Gaps = 11/267 (4%) Query: 8 LARLTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVM 66 + RL D++ L PE GCPWD QT E++ Y +EE +E+ +AI + D++ +E+GD++ Sbjct: 7 IQRLLDIMAALRDPETGCPWDIVQTFETIRPYTIEEAYEVADAIERHDMDDLCDELGDLL 66 Query: 67 FLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRAEK 126 + F R+ + GAF+ D + KMIRRHPHVF+ + + WE IK+AEK Sbjct: 67 LQVVFHARMAEEAGAFSFGDVVEAITRKMIRRHPHVFARSDADTAEAVKLQWEEIKQAEK 126 Query: 127 AD----------AEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEA 176 AD ++ E G S+ S P L++A ++ +AA+VGF W E E + +VE Sbjct: 127 ADRRQRRLQRGVSQEEHAGHLGSIQRSFPALVEALKLQERAAKVGFDWSEPEPILDKVEE 186 Query: 177 EWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEAL 236 E EL L D +ELGDLIF+LV +GR G AL TN KF RRF +E Sbjct: 187 EIGELRQALKDGDLGKVADELGDLIFALVNIGRHVGTDPEMALRGTNTKFRRRFGHIEKE 246 Query: 237 ARERGLDFPALSLDDKDELWNEAKAAE 263 G A SL+ +ELW AKA E Sbjct: 247 LEAGGETLDAASLERMEELWQAAKAIE 273 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: 225 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: 277 Length adjustment: 25 Effective length of query: 242 Effective length of database: 252 Effective search space: 60984 Effective search space used: 60984 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