Align Probable 6-oxopurine nucleoside phosphorylase; EC 2.4.2.1; Purine nucleoside phosphorylase; PNP (uncharacterized)
to candidate PfGW456L13_4030 5'-methylthioadenosine phosphorylase (EC 2.4.2.28)
Query= curated2:O66839 (277 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4030 Length = 245 Score = 204 bits (520), Expect = 1e-57 Identities = 107/255 (41%), Positives = 148/255 (58%), Gaps = 16/255 (6%) Query: 4 IIGGSGLYNLPGIKVKEEVQVKTPFGEPSSPVVIAEVEGKKVAFLARHGRGHEYPPHLVP 63 IIGG+GL L G+ +++ + V TP+G PS+ V I E GK+V FLARHG H +PPH V Sbjct: 6 IIGGTGLTQLEGLSIRQSLAVDTPYGAPSADVQIGEYAGKEVLFLARHGHPHRFPPHQVN 65 Query: 64 YRANLWALREVGVKRVLGISAVGGINELLMPGDFVVIHDYLDFTKTRRSTYYEGKFSVKV 123 YRANLWAL++ G + +L ++AVGGI+ + G F V H +D+T R TY+ Sbjct: 66 YRANLWALKQAGAEAILAVNAVGGIHAAMGAGHFCVPHQLIDYTSGREHTYFADDLE--- 122 Query: 124 EGEDKVAKLLREGKVVHVDMSEAYCPEMRKVLIQILKEKNFRFHPKGVYACTEGPRFETP 183 V H+D S Y +R+ LI L + + GVYACT+GPR ET Sbjct: 123 -------------HVTHIDFSYPYSEPLRQQLIAALAAEGVGYSSHGVYACTQGPRLETV 169 Query: 184 SEIKMLKLLGADVVGMTGYPEVALARELTMCYASLCVVANPAAGIAGYRLTSNEVIQLMK 243 +EI L+ G D+VGMTG PE ALAREL + YA L +V NPAAG + +T E+ Q + Sbjct: 170 AEIARLERDGCDIVGMTGMPEAALARELELDYACLALVVNPAAGKSTAVITMAEIEQALH 229 Query: 244 RKEEEIKEVVLKFIK 258 ++K + + +K Sbjct: 230 DGMGKVKSTLARVLK 244 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: 216 Number of extensions: 9 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 Sep 17 2021. 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