Align 4a-hydroxytetrahydrobiopterin dehydratase (EC 4.2.1.96) (characterized)
to candidate Synpcc7942_1636 Synpcc7942_1636 pterin-4-alpha-carbinolamine dehydratase
Query= BRENDA::Q2Q449 (104 letters) >FitnessBrowser__SynE:Synpcc7942_1636 Length = 135 Score = 58.5 bits (140), Expect = 3e-14 Identities = 36/81 (44%), Positives = 50/81 (61%), Gaps = 6/81 (7%) Query: 13 RLLQLHKTVPQWHLTDGHLSIKRKFQFSDFNEAWGFMSRVALYADKVDHHPNWYNVYNTV 72 RLL+L P W L DG SI +F+ F EA F++R+ A+ HHP+ YN V Sbjct: 56 RLLRL----PAWRL-DGQ-SIVCDRRFAGFPEAIAFLNRLVEPAEAAGHHPDLEVSYNRV 109 Query: 73 DVELSTHDAAGLTEKDFALAK 93 + L+THDA GLT++DF+LA+ Sbjct: 110 IIRLTTHDAGGLTDQDFSLAE 130 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: 30 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: 104 Length of database: 135 Length adjustment: 13 Effective length of query: 91 Effective length of database: 122 Effective search space: 11102 Effective search space used: 11102 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: 41 (21.9 bits) S2: 41 (20.4 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