Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_011319662.1 AVA_RS14755 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000204075.1:WP_011319662.1 Length = 268 Score = 187 bits (474), Expect = 3e-52 Identities = 99/260 (38%), Positives = 153/260 (58%), Gaps = 7/260 (2%) Query: 6 ASLARLTDVIDRLLAPEG-CPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGD 64 A+L L +V+ +L +P+G CPWD QTP++L Y++EE +E+V+AI+SG+ + + EE+GD Sbjct: 7 AALQELIEVVAKLRSPDGGCPWDLAQTPQTLTPYVIEEAYEVVDAIKSGDQEAIAEELGD 66 Query: 65 VMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKRA 124 ++ + ++ ++ G F+L D K+IRRHPHVF D + DE +NWE IK A Sbjct: 67 LLLQVVLQAQIASEYGQFSLQDVAQGITQKLIRRHPHVFGDVSVNSVDEVRQNWEQIKAA 126 Query: 125 EKADAEGEPQGVYDSLP---ASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLEL 181 EK + E Q + L +LPPL A +I KAA VGF W + V + E E Sbjct: 127 EKGEPSAESQKLSTKLSRYGRTLPPLTAAMKISRKAAAVGFEWENIDGVWAKFHEELQEF 186 Query: 182 LDVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERG 241 LA + Q+ ELGDL+F++++L R + + L TN +F++R ++MEA+ Sbjct: 187 QQALAEETPERQQAELGDLLFAVIQLARWHNLDPSEGLQGTNQRFVQRLQKMEAVVDRPL 246 Query: 242 LDFPALSLDDKDELWNEAKA 261 D+ SLD+ + LW +AKA Sbjct: 247 SDY---SLDELETLWQQAKA 263 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: 177 Number of extensions: 7 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: 268 Length adjustment: 25 Effective length of query: 242 Effective length of database: 243 Effective search space: 58806 Effective search space used: 58806 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 Jul 25 2024. The underlying query database was built on Jul 25 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