Align Pyrimidine/purine nucleoside phosphorylase; Adenosine phosphorylase; Cytidine phosphorylase; Guanosine phosphorylase; Inosine phosphorylase; Thymidine phosphorylase; Uridine phosphorylase; Xanthosine phosphorylase; EC 2.4.2.1; EC 2.4.2.2; EC 2.4.2.15; EC 2.4.2.4; EC 2.4.2.3 (characterized)
to candidate BWI76_RS06200 BWI76_RS06200 hypothetical protein
Query= SwissProt::P0C037 (94 letters) >FitnessBrowser__Koxy:BWI76_RS06200 Length = 94 Score = 169 bits (428), Expect = 7e-48 Identities = 81/94 (86%), Positives = 87/94 (92%) Query: 1 MLQSNEYFSGKVKSIGFSSSSTGRASVGVMVEGEYTFSTAEPEEMTVISGALNVLLPDAT 60 MLQSNEYF GKVKSIGF+SSSTGRASVGVM EGEYTF TA+PEEMTV+SGALNVLLP T Sbjct: 1 MLQSNEYFDGKVKSIGFTSSSTGRASVGVMAEGEYTFGTAQPEEMTVVSGALNVLLPGET 60 Query: 61 DWQVYEAGSVFNVPGHSEFHLQVAEPTSYLCRYL 94 +W+VY AG VFNVPG+SEFHLQVAEPTSYLCRYL Sbjct: 61 EWKVYAAGEVFNVPGNSEFHLQVAEPTSYLCRYL 94 Lambda K H 0.314 0.129 0.372 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: 88 Number of extensions: 1 Number of successful extensions: 1 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: 94 Length of database: 94 Length adjustment: 10 Effective length of query: 84 Effective length of database: 84 Effective search space: 7056 Effective search space used: 7056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (20.6 bits) S2: 39 (19.6 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