Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate 8499605 DvMF_0373 3-dehydroquinate dehydratase (RefSeq)
Query= BRENDA::D4LCT8 (148 letters) >FitnessBrowser__Miya:8499605 Length = 159 Score = 126 bits (317), Expect = 1e-34 Identities = 75/144 (52%), Positives = 91/144 (63%), Gaps = 4/144 (2%) Query: 2 RILVIHGPNLNLLGEREPGIYGKNDLAHVNGAI--LTRAKELGVECEVFQSNHEGEILVR 59 RILV++GPNL LG R+P IYG + V G + + A VE E FQSN EG ++ R Sbjct: 5 RILVLNGPNLGALGVRQPDIYGSVGMDAVPGLVGQVLGAGASDVELEFFQSNGEGALIDR 64 Query: 60 LHEARH-AFDGVVLNAGAYTHYSYAIRDAIAAIRIPCVEVHISNVHAREE-FRHTSVIAP 117 L +AR DGVVLNAGAYTH S A+ D +A I +PCVEVH+SNV AR E R S I Sbjct: 65 LEQARRDGVDGVVLNAGAYTHTSLALADCLAWIGLPCVEVHLSNVLARSEPLRQKSYIGR 124 Query: 118 ACLGVVCGFGGDSYLLALEGLVRH 141 +GVV GFG SY LA++ L H Sbjct: 125 HVIGVVAGFGITSYALAVQALALH 148 Lambda K H 0.324 0.141 0.429 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: 99 Number of extensions: 11 Number of successful extensions: 4 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: 148 Length of database: 159 Length adjustment: 17 Effective length of query: 131 Effective length of database: 142 Effective search space: 18602 Effective search space used: 18602 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 43 (21.2 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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