Align 3-dehydroquinate synthase; DHQ synthase; EC 1.4.1.24; 3-dehydroquinate synthase II (uncharacterized)
to candidate WP_064504629.1 HM1_RS08045 3-dehydroquinate synthase
Query= curated2:Q8TVI1 (402 letters) >NCBI__GCF_000019165.1:WP_064504629.1 Length = 380 Score = 209 bits (532), Expect = 1e-58 Identities = 124/306 (40%), Positives = 178/306 (58%), Gaps = 6/306 (1%) Query: 96 DISESIDAALIEKARDRGFEVAEYVEILDKPYERFAAEIAKNVGPDYVIAIGRDWKIIPL 155 DI S AL++ AR++GF + ++ + + V DY + IPL Sbjct: 80 DIVLSSVPALLDAAREKGFSTCISL-FIEGGQDDLEEASRRAVSHDYAVVDFDLPTNIPL 138 Query: 156 ENLIAELQGEKTQLIAGARDAEEARIAFETLEVGSDGVLLDAERIDPSEIKKTAEIAERA 215 E +IA LQ KT L+ + E +AF LE GSDGVLL + D +EI + R Sbjct: 139 ELIIARLQKSKTVLLKAEKSVEAMEVAFGVLEQGSDGVLLSTD--DMNEIIELKAFLSRR 196 Query: 216 AAERFELVAVEVKEVKPIGKGDRVCVDTCSLMSEGEGMLVGSTSRGMFLIHSESLENPYV 275 AE +L + V EV IG G R C+DT +M+ EGM++GSTS G + SE+ PY+ Sbjct: 197 GAEPLQLHPLTVTEVSHIGMGLRSCIDTTDIMTRDEGMIIGSTSSGGIFVCSETHYLPYM 256 Query: 276 EPRPFRVNAGPVHAYIRVPGGKTKYLAELRPGDEVLIVDTEGRTRAAVVGRLKIERRPLM 335 RPFRVNAG VH+Y+ PG T YL +LR G VL V+T+G+TR +VGR+K E RPL+ Sbjct: 257 NLRPFRVNAGAVHSYVWRPGNATDYLTDLRAGTAVLCVNTKGKTRPVIVGRVKTEVRPLL 316 Query: 336 LIRAEYEGVEIQTIVQNAETIHLVREDGEPVSVVDLKPGDKVLAYVETEEGKGRHFGMEV 395 LI+ +G+++ IVQ+ I ++ +GEP + ++PGD++LAYV GRH G++V Sbjct: 317 LIKGVADGIDLNVIVQDDWHIRVMGANGEPRNATTVQPGDQLLAYV---CAPGRHVGIKV 373 Query: 396 EETIVE 401 +E I+E Sbjct: 374 DEKIIE 379 Lambda K H 0.314 0.136 0.383 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: 415 Number of extensions: 25 Number of successful extensions: 3 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: 402 Length of database: 380 Length adjustment: 31 Effective length of query: 371 Effective length of database: 349 Effective search space: 129479 Effective search space used: 129479 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 (21.9 bits) S2: 50 (23.9 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