Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate 8501013 DvMF_1750 3-dehydroquinate synthase (RefSeq)
Query= SwissProt::Q58646 (361 letters) >FitnessBrowser__Miya:8501013 Length = 323 Score = 233 bits (595), Expect = 4e-66 Identities = 138/310 (44%), Positives = 194/310 (62%), Gaps = 14/310 (4%) Query: 54 LDADIVLVNKNDNIEFLKEAKNLGKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRD 113 +D IV + D++ L + L E I + +K DEE A+ AR + ++LE R Sbjct: 24 VDGIIVPRAQVDSVATLARCRVLADEDVATIALSAKADEEEAA--ARLARGETVVLE-RG 80 Query: 114 WTIIPLENLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKL 173 W IIP+ENL+A + + V + EA++A ILE+G V++ P E EL + Sbjct: 81 WEIIPVENLLA----QSDDVAVEVADLSEARLAAGILERGVATVVVLP---EGAGELKSI 133 Query: 174 IEEMNKEKVALDVA--TVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSET 231 + ++ + +D+A VT VE +G G RVC+DT S+++ G+GML+G+ S FLVH+ET Sbjct: 134 VADLKLSQGCMDLAPAVVTAVENVGLGHRVCVDTMSMLRRGQGMLVGNSSAFTFLVHAET 193 Query: 232 VENPYVATRPFRVNAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKI 291 N YVA RPFR+NAG VHAY PG++T YL EL+AGD+VLIV DG+T A VGR+K+ Sbjct: 194 EHNEYVAARPFRINAGAVHAYAQMPGDRTTYLEELRAGDEVLIVSADGSTTVATVGRLKM 253 Query: 292 ERRPLVLIEAEYKGDIIRTI-LQNAETIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHF 350 E RP++L+ A+ GD+ + LQNAETIRL G P+SVV LK GD++L + + RHF Sbjct: 254 EARPMLLVRAKV-GDVEGAVFLQNAETIRLTRPDGTPVSVVSLKEGDQILCRTDCAGRHF 312 Query: 351 GMAIKETIIE 360 GM IKE I E Sbjct: 313 GMRIKEDIKE 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: 321 Number of extensions: 15 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