Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate WP_027177587.1 G496_RS0100770 3-dehydroquinate synthase II family protein
Query= SwissProt::Q58646 (361 letters) >NCBI__GCF_000429985.1:WP_027177587.1 Length = 327 Score = 253 bits (647), Expect = 4e-72 Identities = 149/350 (42%), Positives = 220/350 (62%), Gaps = 40/350 (11%) Query: 16 KKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLDADIVLVN-KNDNIEFLKEAK 74 +K +VT ALES + V+ E E+ + ++ LG +KV + D IV +N K+D E +K A Sbjct: 12 EKNLVTLALESGVDAVLVEQENKKAVEALGRVKVVTPD-DMPIVAINEKSDEDEAVKFAA 70 Query: 75 NLGKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRDWTIIPLENLIADLFHRDVKIV 134 + GKET + + W IIP+EN++A + DV + Sbjct: 71 S-GKETIL----------------------------AKGWEIIPVENILAQV---DV-LA 97 Query: 135 ASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKEKVALDVATVTKVEP 194 V S+D+A++A ILE+G D +++ P+ ++K++ ++ +++ K+ L A V ++P Sbjct: 98 LEVESLDKARLAAGILERGADTLVVVPEGAAELKQIVAELK-LSQGKIELQKAVVKSIDP 156 Query: 195 IGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATRPFRVNAGPVHAYIL 254 +G G RVC+DT SL+K G+GML+G+ S FLVH+ET NPYVA RPFR+NAG VHAY + Sbjct: 157 VGLGHRVCVDTISLLKKGQGMLVGNSSAFTFLVHAETESNPYVAARPFRINAGAVHAYAV 216 Query: 255 CPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIEA---EYKGDII-RT 310 PG+KT YL EL +G +VLIV DG T A+VGR K+E RP++LI A +G + + Sbjct: 217 MPGDKTCYLEELSSGREVLIVGADGETSIAVVGRSKVEVRPMLLITAVVETAEGAVEGKV 276 Query: 311 ILQNAETIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIE 360 LQNAETIR+V+ GEP+SVV++KPGD++L + ++ RHFGM IKE I E Sbjct: 277 FLQNAETIRVVSSTGEPVSVVNVKPGDEILCRLDDAGRHFGMRIKEEITE 326 Lambda K H 0.315 0.136 0.380 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: 337 Number of extensions: 17 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 361 Length of database: 327 Length adjustment: 29 Effective length of query: 332 Effective length of database: 298 Effective search space: 98936 Effective search space used: 98936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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