Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_012675113.1 SULAZ_RS00600 nucleoside triphosphate pyrophosphohydrolase
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000021545.1:WP_012675113.1 Length = 254 Score = 174 bits (442), Expect = 1e-48 Identities = 88/258 (34%), Positives = 151/258 (58%), Gaps = 12/258 (4%) Query: 3 KDNASLARLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEM 62 K+ + +L D+++RL CPWD++QT +S+ + L+EE +EL+EAI + +++ EE+ Sbjct: 5 KEGENFQKLVDIVERLRRE--CPWDRQQTNQSIKNNLIEEAYELLEAIEENDNEKMIEEL 62 Query: 63 GDVMFLLAFLGRLYADKGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIK 122 GDV+ + F ++ D+ +F ++ + N K+IRRHPHVF DT +E L W IK Sbjct: 63 GDVLLQVVFHSQIKKDENSFDINTVIENLIEKLIRRHPHVFGDTQVKTEEEVLDQWHKIK 122 Query: 123 RAEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELL 182 + EK + + D +P +P L +A ++ ++AA+VGF W + V ++VE E EL Sbjct: 123 QKEK-------KSILDGIPKRMPALTRAVKVQNRAAKVGFEWENIDQVWKKVEEELQELK 175 Query: 183 DVLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEALARERGL 242 + ++K +E+GDL+ ++ L R I AL ++ + ++RF +E A++ G Sbjct: 176 EAKTQEEKV---HEIGDLLIAITNLARFMKIDPEEALHLSVDRMIKRFNYIEEKAKQMGK 232 Query: 243 DFPALSLDDKDELWNEAK 260 +SL + D+LWNEAK Sbjct: 233 SLDDMSLQEMDDLWNEAK 250 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: 196 Number of extensions: 11 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: 254 Length adjustment: 24 Effective length of query: 243 Effective length of database: 230 Effective search space: 55890 Effective search space used: 55890 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