Align Probable 6-oxopurine nucleoside phosphorylase; EC 2.4.2.1; Purine nucleoside phosphorylase; PNP (uncharacterized)
to candidate WP_041098386.1 SUTH_RS08025 S-methyl-5'-thioinosine phosphorylase
Query= curated2:O66839 (277 letters) >NCBI__GCF_000828635.1:WP_041098386.1 Length = 245 Score = 194 bits (493), Expect = 2e-54 Identities = 105/232 (45%), Positives = 138/232 (59%), Gaps = 16/232 (6%) Query: 1 MLGIIGGSGLYNLPGIKVKEEVQVKTPFGEPSSPVVIAEVEGKKVAFLARHGRGHEYPPH 60 MLGIIGGSGL L + V V+TP+GEPS P+ + G V F+ARHG GH PPH Sbjct: 1 MLGIIGGSGLTQLANLDVSHREVVRTPYGEPSGPLTFGRINGHDVVFIARHGYGHTIPPH 60 Query: 61 LVPYRANLWALREVGVKRVLGISAVGGINELLMPGDFVVIHDYLDFTKTRRSTYYEGKFS 120 LV YRAN+ AL GV +++ +++VGGI L PG VV H +D+T R T+ G Sbjct: 61 LVNYRANIHALETSGVTQIVSVASVGGIRGDLGPGALVVPHQIIDYTWGREMTFQSG--- 117 Query: 121 VKVEGEDKVAKLLREGKVVHVDMSEAYCPEMRKVLIQILKEKNFRFHPKGVYACTEGPRF 180 +G V+HVD ++ Y E+R++L+ + + VYA T+GPR Sbjct: 118 -------------GDGPVIHVDFTDPYDAEVRQLLLDVSRRIGEPVIDGAVYATTQGPRL 164 Query: 181 ETPSEIKMLKLLGADVVGMTGYPEVALARELTMCYASLCVVANPAAGIAGYR 232 ET +EI ++ GAD+VGMTG PE LAREL + YA+LCVVAN AAG A R Sbjct: 165 ETAAEINRMEDDGADIVGMTGMPEAGLARELELPYAALCVVANWAAGRADSR 216 Lambda K H 0.319 0.139 0.406 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: 7 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: 277 Length of database: 245 Length adjustment: 24 Effective length of query: 253 Effective length of database: 221 Effective search space: 55913 Effective search space used: 55913 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Sep 17 2021.
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