Align Pyrimidine/purine nucleoside phosphorylase; EC 2.4.2.2; Adenosine phosphorylase; Cytidine phosphorylase; Guanosine phosphorylase; EC 2.4.2.15; Inosine phosphorylase; Thymidine phosphorylase; EC 2.4.2.4; Uridine phosphorylase; EC 2.4.2.3; Xanthosine phosphorylase (uncharacterized)
to candidate WP_019866684.1 METMI_RS0112740 DUF1255 domain-containing protein
Query= curated2:Q30NQ5 (103 letters) >NCBI__GCF_000384075.1:WP_019866684.1 Length = 103 Score = 147 bits (370), Expect = 4e-41 Identities = 64/102 (62%), Positives = 85/102 (83%) Query: 1 MTKFENVTVVKKANIYDGGKVTSRTVEFADGTRKTLGIMMPGEYTFNTAEAEIMEMMSGE 60 M++F NVTVVKKAN+Y GG V+SRT+ FADG+ KTLG M+PGEYTFNTA AE+ME++ G+ Sbjct: 1 MSEFNNVTVVKKANVYFGGNVSSRTLRFADGSSKTLGFMLPGEYTFNTAAAEVMEILDGD 60 Query: 61 LDIRLPNEDWKTLNTPESFNVPANSSFDLKIRTVTDYCCSYI 102 L++ LP +W+T+ E+FNVPAN+ F +KIRT TDYCCS++ Sbjct: 61 LEVLLPGAEWQTVKGGEAFNVPANAQFTVKIRTATDYCCSFL 102 Lambda K H 0.316 0.131 0.381 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: 84 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: 103 Length of database: 103 Length adjustment: 11 Effective length of query: 92 Effective length of database: 92 Effective search space: 8464 Effective search space used: 8464 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.1 bits) S2: 40 (20.0 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