Align purine-nucleoside phosphorylase (EC 2.4.2.1) (characterized)
to candidate WP_067643618.1 I596_RS02340 S-methyl-5'-thioinosine phosphorylase
Query= BRENDA::Q8U2I1 (265 letters) >NCBI__GCF_001632775.1:WP_067643618.1 Length = 249 Score = 197 bits (500), Expect = 2e-55 Identities = 103/215 (47%), Positives = 141/215 (65%), Gaps = 8/215 (3%) Query: 4 IAIVGGSGVYDFPA-ENKREETVKTPYGEV--KITVGVVGDEEVAFLARHGKGHSIPPHK 60 +A++GG+G+Y FP E+ + V T +G +I +G VG++ +AFLARHG+GHS+ PH+ Sbjct: 7 LAVIGGTGLYRFPGLEDAEKHVVNTRFGTPSDRIVIGRVGNKRIAFLARHGEGHSVAPHR 66 Query: 61 INYRANIWALYELGVERIIATSAVGSMNPEMKPGDFVILDQIIDFTVSRPRTFYDGEESP 120 +NYRAN+WAL+ LG R++A +AVG + +M P V+ DQIID+T R +F D E + Sbjct: 67 VNYRANVWALHHLGARRVVAVNAVGGIREDMGPRAVVVPDQIIDYTHGRLSSFCDVEGAE 126 Query: 121 HERKFVAHVDFTEPYCPEIRKALITAARNLGLPYHPRGTYVCTEGPRFETAAEIRAYRIL 180 V HVDF+ PY +R L+ AAR G+ G Y T+GPR ET AEI R Sbjct: 127 -----VRHVDFSHPYSAGLRAELLVAARKAGVAVVNGGCYGATQGPRLETVAEIARLRRD 181 Query: 181 GGDVVGMTQCPEAILARELEMCYATVAIVTNYAAG 215 G D+VGMT PEA LARELE+ YA +A+V N+AAG Sbjct: 182 GCDLVGMTGMPEAALARELELDYACLALVANWAAG 216 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: 237 Number of extensions: 11 Number of successful extensions: 3 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: 249 Length adjustment: 24 Effective length of query: 241 Effective length of database: 225 Effective search space: 54225 Effective search space used: 54225 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 24 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