Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate GFF813 HP15_792 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >FitnessBrowser__Marino:GFF813 Length = 285 Score = 139 bits (350), Expect = 7e-38 Identities = 90/275 (32%), Positives = 135/275 (49%), Gaps = 25/275 (9%) Query: 11 LTDVIDRLLAPE-GCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVMFLL 69 L ++ RL PE GCPWD Q+ ++ + +EE +E+ +AI + +++E+GD++F + Sbjct: 8 LKTLMARLRDPETGCPWDTRQSYRTIVPHTLEEAYEVADAIEREDYPHLKDELGDLLFQV 67 Query: 70 AFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTY---------ADRDEFLRNWES 120 F +L + G F D + + K++RRHPHVF + T D +WE Sbjct: 68 IFYTQLGREDGHFDFDGVVDHLVRKLVRRHPHVFPEGTLESSIDPDNRPDEAWIKESWER 127 Query: 121 IKRAEK----ADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPE--------DE 168 IK E+ A P D + +LP + +A ++ +AAR GF WP E Sbjct: 128 IKAEERAMKPAPEASAPVSRLDGIARTLPAMARAEKLQKRAARHGFDWPNVGPVFDKLHE 187 Query: 169 DVERQVEAEWLELLDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLR 228 +++ EA W E AGD A E+ELGDL+F V L R + AL+ TN KF Sbjct: 188 EIDELKEA-W-EAAQTGAGDPDAV-EDELGDLLFVCVNLARFMKVNPEQALNRTNHKFDA 244 Query: 229 RFRRMEALARERGLDFPALSLDDKDELWNEAKAAE 263 RFR +E + G D SL+ D +W K E Sbjct: 245 RFRAIERVLEREGRDMDEESLEALDAVWQAVKGVE 279 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: 214 Number of extensions: 18 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: 285 Length adjustment: 25 Effective length of query: 242 Effective length of database: 260 Effective search space: 62920 Effective search space used: 62920 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