Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_012676016.1 PERMA_RS06785 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000021565.1:WP_012676016.1 Length = 261 Score = 172 bits (435), Expect = 8e-48 Identities = 92/253 (36%), Positives = 152/253 (60%), Gaps = 12/253 (4%) Query: 11 LTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDVMFLLA 70 + D++ RL CPWD+EQT +S+ + L+EE +EL EAI S + + EE+GD++ + Sbjct: 16 VVDIVKRLRRE--CPWDREQTNQSIKNNLIEEAYELFEAIESDDDKAMVEELGDLLLQVV 73 Query: 71 FLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYA--DRDEFLRNWESIKRAEKAD 128 F ++ D+G+F ++D + N K+IRRHPHVF D Y+ + ++ L+ WE+IK EK Sbjct: 74 FHSQIKKDEGSFDINDVLENLKEKLIRRHPHVFGDVEYSQLEGEDHLKKWEAIKEKEK-- 131 Query: 129 AEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLDVLAGD 188 E + + + +P +P L++A ++ + A+VGF W EDV +V E EL + A Sbjct: 132 ---ERESILEGIPKRMPALMRAVKVQKRMAKVGFDWENPEDVWEKVMEELNELKN--AKT 186 Query: 189 DKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGLDFPALS 248 DK +E+E+GDL+ ++ L R GI AL + + + RF+ +E A+E+ + + Sbjct: 187 DK-EREHEIGDLLIAVTNLARVYGIDPEQALHHSIDRTVNRFQYIEKKAKEKNKELKEMK 245 Query: 249 LDDKDELWNEAKA 261 LDD ++LW EAK+ Sbjct: 246 LDDMEQLWQEAKS 258 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: 217 Number of extensions: 14 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: 261 Length adjustment: 25 Effective length of query: 242 Effective length of database: 236 Effective search space: 57112 Effective search space used: 57112 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 10 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