Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate 209397 DVU0461 predicted 3-dehydroquinate synthase
Query= SwissProt::Q58646 (361 letters) >MicrobesOnline__882:209397 Length = 323 Score = 236 bits (601), Expect = 8e-67 Identities = 137/344 (39%), Positives = 205/344 (59%), Gaps = 34/344 (9%) Query: 17 KKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLDADIVLVNKNDNIEFLKEAKNL 76 K+ VT ALES + ++ + + ++ L KV L Sbjct: 13 KEAVTLALESGVDGIIVPEKHVAPVQALARCKV--------------------------L 46 Query: 77 GKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRDWTIIPLENLIADLFHRDVKIVAS 136 + + + +K DEE A+ +R ++++L R W IIP+ENL+A R ++ Sbjct: 47 CDDAVCTLELTAKADEEEAA--SRLAAGEDVVL-ARGWEIIPVENLLA----RSDRVTVE 99 Query: 137 VNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKEKVALDVATVTKVEPIG 196 V S+DEA++A ILE+G V++ P+ + ++K + + ++ +++ ++ L A VT V P+G Sbjct: 100 VASLDEARLAAGILERGVSTVVVLPQAVTELKAIVQELK-LSQGRIDLAPAVVTAVRPVG 158 Query: 197 SGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATRPFRVNAGPVHAYILCP 256 G RVC+DT SL++ G+GML+G+ S FLV++ET N YVA RPFR+NAG VHAY + P Sbjct: 159 LGHRVCVDTMSLLRTGQGMLVGNSSAFTFLVNAETEHNEYVAARPFRINAGAVHAYAVMP 218 Query: 257 GNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIEAEYKGDIIRTILQNAE 316 G++T YL EL++G +VLIV DG T A VGR+K+E RP++L+EA + LQNAE Sbjct: 219 GDRTTYLEELRSGSEVLIVGADGATTIATVGRLKVEVRPMLLVEARVGDTVGAVFLQNAE 278 Query: 317 TIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIE 360 TIRLV G P+SVV L+ GD+VL + + RHFGM I E I E Sbjct: 279 TIRLVRADGTPVSVVALREGDEVLCRTDVAGRHFGMRITEDIRE 322 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: 300 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 361 Length of database: 323 Length adjustment: 29 Effective length of query: 332 Effective length of database: 294 Effective search space: 97608 Effective search space used: 97608 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 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