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_085772065.1 B1812_RS13565 4a-hydroxytetrahydrobiopterin dehydratase
Query= curated2:O66462 (99 letters) >NCBI__GCF_002117405.1:WP_085772065.1 Length = 122 Score = 83.6 bits (205), Expect = 7e-22 Identities = 39/90 (43%), Positives = 58/90 (64%), Gaps = 1/90 (1%) Query: 3 RKLSEEEVKREL-ENLEGWEFCKDYIQKEFSTKNWKTTIFVVNAIASLAEAQWHHPDLEV 61 R SE E+ +L + L W + +I++ + T W T+ ++N I L+EA WHHPDL V Sbjct: 6 RVYSEAEIAEKLAKELPEWRYEGGWIRRTYKTHTWPGTLLLINTIGMLSEAAWHHPDLVV 65 Query: 62 SFKKVKVKLTTHEAGGITERDIKLAKSIDE 91 S+ V+VKL TH A GIT++D +LAK ++E Sbjct: 66 SYAFVEVKLATHSAKGITDKDFELAKKLEE 95 Lambda K H 0.315 0.130 0.377 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: 45 Number of extensions: 2 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: 99 Length of database: 122 Length adjustment: 12 Effective length of query: 87 Effective length of database: 110 Effective search space: 9570 Effective search space used: 9570 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