Align 4a-hydroxytetrahydrobiopterin dehydratase (EC 4.2.1.96) (characterized)
to candidate CCNA_00245 CCNA_00245 pterin-4-alpha-carbinolamine dehydratase
Query= BRENDA::Q2Q449 (104 letters) >FitnessBrowser__Caulo:CCNA_00245 Length = 94 Score = 100 bits (250), Expect = 3e-27 Identities = 46/77 (59%), Positives = 59/77 (76%), Gaps = 1/77 (1%) Query: 24 WHLTDGHL-SIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTVDVELSTHDAA 82 W + H +I + F+F DFN+A+GFM+RVAL ADK+DHHP W+NVYN V+V L+THDA Sbjct: 18 WAIAPNHKDAIVKTFRFDDFNQAFGFMTRVALMADKLDHHPEWFNVYNRVEVLLTTHDAD 77 Query: 83 GLTEKDFALAKFMDDAA 99 G+T+ D LAKFMD AA Sbjct: 78 GVTDLDLTLAKFMDSAA 94 Lambda K H 0.321 0.132 0.410 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: 58 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: 104 Length of database: 94 Length adjustment: 10 Effective length of query: 94 Effective length of database: 84 Effective search space: 7896 Effective search space used: 7896 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 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