Align 3-dehydroquinate dehydratase; 3-dehydroquinase; EC 4.2.1.10; Type I DHQase; Type I dehydroquinase; DHQ1 (uncharacterized)
to candidate WP_093393471.1 BM091_RS03435 type I 3-dehydroquinate dehydratase
Query= curated2:A0LLU8 (234 letters) >NCBI__GCF_900114975.1:WP_093393471.1 Length = 255 Score = 130 bits (328), Expect = 2e-35 Identities = 78/223 (34%), Positives = 115/223 (51%), Gaps = 1/223 (0%) Query: 8 ICGCLMRESTEDTARFLEYPGIGLVEWRLDALHGIHTRNGLDEALAGLSLPGRHPVIATV 67 +CG L S + ++ +P + LVE RLD R GL GL R PVI Sbjct: 8 LCGILEHVSFDVLGSYMRHPDVDLVECRLDLWETKVGRAGLYVLFDGLLEAQRWPVIIAC 67 Query: 68 RPERFRGGFRGTEEARIRALERTVRAGAEWIDLEDDLPEDVLSPFRDSAARVVISHH-DF 126 RP R G F G ++ R+ L R V +GAEW++L D PE+ F + ARV+ ++ Sbjct: 68 RPRRDGGFFEGNDKERVSVLLRAVESGAEWVELGYDEPEEFFHLFSEKRARVIRTYRVQP 127 Query: 127 DGTPASDPLKHRVEHLATLGAHVLKIATYARTVEDNLRVLELIPFARKQFGAETIAFCMG 186 D + ++ LK R +A GA VL+I + D L++IP +++ G IA+ +G Sbjct: 128 DESIDTNLLKDRCREIAQKGADVLRIIGHVEHPADCCIFLKIIPEMQEELGKGVIAYGLG 187 Query: 187 PTGRWSRLACLLMGSPWTYVRFPELPASAPGQFTVAQMQTLLE 229 GRWSR+ACL +GSPWTYV F + +F + +L+ Sbjct: 188 NKGRWSRIACLFLGSPWTYVHFSPIDMKERHKFDAHTARMILK 230 Lambda K H 0.323 0.139 0.430 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: 190 Number of extensions: 8 Number of successful extensions: 2 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: 234 Length of database: 255 Length adjustment: 24 Effective length of query: 210 Effective length of database: 231 Effective search space: 48510 Effective search space used: 48510 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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