Align phosphoribosyl-ATP diphosphatase (EC 3.6.1.31) (characterized)
to candidate WP_037579958.1 BS73_RS17085 MazG family protein
Query= metacyc::MONOMER-21148 (267 letters) >NCBI__GCF_000744815.1:WP_037579958.1 Length = 353 Score = 125 bits (313), Expect = 2e-33 Identities = 76/232 (32%), Positives = 113/232 (48%), Gaps = 23/232 (9%) Query: 6 ASLARLTDVIDRLLAPEGCPWDKEQTPESLCDYLVEECFELVEAIRSGNADEVREEMGDV 65 A L L V+DRL +P GCPWD +QT ESL YLVEE +ELVEAI G+ +REE+GDV Sbjct: 129 ARLLDLVSVMDRLRSPGGCPWDAQQTHESLVKYLVEESYELVEAIEEGDRPALREELGDV 188 Query: 66 MFLLAFLGRLYAD--KGAFTLDDAMANNAAKMIRRHPHVFSDTTYADRDEFLRNWESIKR 123 + + F R+ + + F +D+ K++ RHPHVF+D + W+ +K Sbjct: 189 LLQVLFHSRIAQEHPEDPFGIDEVAGGIVDKLVFRHPHVFADAGVPASEHLEATWDKLKA 248 Query: 124 AEKADAEGEPQGVYDSLPASLPPLLKAYRIHSKAARVGFTWPEDEDVERQVEAEWLELLD 183 AEK + + + D +P P L A ++ S+A + G P + + Q Sbjct: 249 AEK-----QRESLTDGVPLGQPSLALAAKLLSRARKAGLDLPLETEFTPQA--------- 294 Query: 184 VLAGDDKAAQENELGDLIFSLVELGRRKGIKANTALDMTNLKFLRRFRRMEA 235 E +LG+L+ +L + I AL L++ R R EA Sbjct: 295 -------PPAEEDLGELLLALAKTADAHSIDPEQALRAAALRYRARIREAEA 339 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: 237 Number of extensions: 10 Number of successful extensions: 2 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: 353 Length adjustment: 27 Effective length of query: 240 Effective length of database: 326 Effective search space: 78240 Effective search space used: 78240 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: 48 (23.1 bits)
This GapMind analysis is from Jul 26 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