Align Putative pterin-4-alpha-carbinolamine dehydratase; PHS; EC 4.2.1.96; 4-alpha-hydroxy-tetrahydropterin dehydratase; Pterin carbinolamine dehydratase; PCD (uncharacterized)
to candidate WP_058931872.1 AU252_RS17880 4a-hydroxytetrahydrobiopterin dehydratase
Query= curated2:A9WI69 (93 letters) >NCBI__GCF_001484605.1:WP_058931872.1 Length = 108 Score = 71.2 bits (173), Expect = 3e-18 Identities = 37/86 (43%), Positives = 49/86 (56%), Gaps = 1/86 (1%) Query: 4 LSEAEIAEQLAQRPDWSLENNEIVRTFRLANFPAAIAFVTHVAFLAEAAGHHPDIDIRYN 63 L+ I LA PDW +V ++ AA+ + V +AE HHPD+D RYN Sbjct: 8 LTRERIEAVLAALPDWQYRLGGLVAVYKTPTAAAALELIAAVGRVAEEQNHHPDLDWRYN 67 Query: 64 RVRLALTTHDAGG-LTEKDFALAAAI 88 RV L T+HDAGG +TE+D A AAA+ Sbjct: 68 RVHLRYTSHDAGGEVTERDAAAAAAV 93 Lambda K H 0.322 0.135 0.392 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: 48 Number of extensions: 3 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: 93 Length of database: 108 Length adjustment: 11 Effective length of query: 82 Effective length of database: 97 Effective search space: 7954 Effective search space used: 7954 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: 39 (21.0 bits) S2: 39 (19.6 bits)
This GapMind analysis is from Apr 09 2024. 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