Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_011800960.1 PNAP_RS07785 3-dehydroquinate dehydratase
Query= BRENDA::Q88IJ6 (145 letters) >NCBI__GCF_000015505.1:WP_011800960.1 Length = 148 Score = 224 bits (572), Expect = 3e-64 Identities = 107/139 (76%), Positives = 119/139 (85%) Query: 5 VLMLHGINHNMFGKRDPRQYGTATLADIDQALQALGEELGAQVESFQSNFEGAMCERIHQ 64 +LMLHGINHNMFGKRDPRQYGT TL +I+ +L ALG+ELG VE FQ+N EG MCERIHQ Sbjct: 3 ILMLHGINHNMFGKRDPRQYGTITLDEINASLAALGKELGTDVECFQTNSEGEMCERIHQ 62 Query: 65 AYEDRVDAVLINAGAWTHYSYGIRDALAIIEVPVVEVHMSNIHAREPFRHHSVFAEVVRG 124 Y D VDAVLINAGAWTHYSYGIRDALAI+ P+VE+HMSNIHARE FRH SVF E+VRG Sbjct: 63 GYTDGVDAVLINAGAWTHYSYGIRDALAILTCPIVELHMSNIHAREAFRHVSVFGEIVRG 122 Query: 125 QICGFGVETYLLALRAAMS 143 QICGFGV++YLL LRA S Sbjct: 123 QICGFGVDSYLLGLRAGHS 141 Lambda K H 0.324 0.136 0.404 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: 128 Number of extensions: 6 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: 145 Length of database: 148 Length adjustment: 16 Effective length of query: 129 Effective length of database: 132 Effective search space: 17028 Effective search space used: 17028 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: 40 (21.6 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