Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_018125230.1 B149_RS0111095 3-dehydroquinate dehydratase
Query= BRENDA::D4LCT8 (148 letters) >NCBI__GCF_000375485.1:WP_018125230.1 Length = 155 Score = 122 bits (306), Expect = 2e-33 Identities = 65/150 (43%), Positives = 95/150 (63%), Gaps = 5/150 (3%) Query: 2 RILVIHGPNLNLLGEREPGIYGKNDLAHVNGAI--LTRAKELGVECEVFQSNHEGEILVR 59 +ILV++GPNL +G+R+P +YG + + + L K +E E +QSN EG ++ R Sbjct: 5 KILVLNGPNLGHIGKRQPEVYGSETMEDLGKILDGLMGEKASEIELEYYQSNSEGALIDR 64 Query: 60 LHEARH-AFDGVVLNAGAYTHYSYAIRDAIAAIRIPCVEVHISNVHAR--EEFRHTSVIA 116 L +AR GV NAGAYTH S AI D +A I +PCVEVHISN+ AR + R S++ Sbjct: 65 LEKAREDKVSGVAFNAGAYTHTSLAIADCLAWIGVPCVEVHISNIWARTDQPLRQQSLMG 124 Query: 117 PACLGVVCGFGGDSYLLALEGLVRHCAGQK 146 +C+GV+ GFG SY +A++ L+ H + Q+ Sbjct: 125 ASCIGVIAGFGIMSYAMAVQALLDHISSQE 154 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: 91 Number of extensions: 5 Number of successful extensions: 3 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: 155 Length adjustment: 17 Effective length of query: 131 Effective length of database: 138 Effective search space: 18078 Effective search space used: 18078 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: 42 (20.8 bits)
This GapMind analysis is from Apr 10 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