Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate Dsui_2698 Dsui_2698 purine nucleoside phosphorylase
Query= BRENDA::Q8U2I1 (265 letters) >FitnessBrowser__PS:Dsui_2698 Length = 250 Score = 188 bits (477), Expect = 1e-52 Identities = 97/215 (45%), Positives = 134/215 (62%), Gaps = 8/215 (3%) Query: 4 IAIVGGSGVYDFP-AENKREETVKTPYGEVK--ITVGVVGDEEVAFLARHGKGHSIPPHK 60 +AI+GGSG+ + E V+TPYGE +T G + + F+ARHG GH+IPPH+ Sbjct: 2 LAIIGGSGLTQLANLDISHREIVRTPYGEPSGPVTFGNICGQPAMFVARHGYGHTIPPHE 61 Query: 61 INYRANIWALYELGVERIIATSAVGSMNPEMKPGDFVILDQIIDFTVSRPRTFYDGEESP 120 +NYRAN+WAL+ I++ ++VG + ++ PGD V+ QIID+T R TF++G+ Sbjct: 62 VNYRANLWALWSKKATAIVSVASVGGIRGDLAPGDIVVPHQIIDYTWGRRSTFHEGDGCT 121 Query: 121 HERKFVAHVDFTEPYCPEIRKALITAARNLGLPYHPRGTYVCTEGPRFETAAEIRAYRIL 180 V HVDFT PY +R ++TAA +G G Y T+GPR ETAAEI Sbjct: 122 -----VTHVDFTHPYDELLRNQILTAASMIGEEVRMGGVYAATQGPRLETAAEINRMERD 176 Query: 181 GGDVVGMTQCPEAILARELEMCYATVAIVTNYAAG 215 G D+VGMT PEA+LAREL++ YA + +V NYAAG Sbjct: 177 GADLVGMTGMPEAVLARELDLPYAAINVVANYAAG 211 Lambda K H 0.320 0.138 0.412 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: 242 Number of extensions: 13 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: 265 Length of database: 250 Length adjustment: 24 Effective length of query: 241 Effective length of database: 226 Effective search space: 54466 Effective search space used: 54466 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 (21.8 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