Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate WP_073036352.1 BUB04_RS01730 3-dehydroquinate synthase II
Query= SwissProt::Q58646 (361 letters) >NCBI__GCF_900129305.1:WP_073036352.1 Length = 331 Score = 253 bits (646), Expect = 5e-72 Identities = 145/361 (40%), Positives = 217/361 (60%), Gaps = 30/361 (8%) Query: 1 MKFGWVNVIGDNWEEKKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLDADIVL 60 MK WV + E K++VT A+E+ + VV+A P ++++ LG + VA+ D D + Sbjct: 1 MKEVWVRLK----EWNKEVVTAAVEAGVDVVMAPPGVAQQVRRLGRVVVAAE--DGDWI- 53 Query: 61 VNKNDNIEFLKEAKNLGKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRDWTIIPLE 120 +++ ET + S EDE+ S++ R G +++E DW IIPLE Sbjct: 54 -----------PGRDVHLET-----LRSPEDEKRISDLLRVG--KKVVVENTDWEIIPLE 95 Query: 121 NLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKE 180 NL+A ++V +V +A +LEKG GVL+ + + ++ ++ M Sbjct: 96 NLVAG----GGELVVAVEDESRMDLALGVLEKGVHGVLIPGDDPLTVSSWTRKVKSMGPV 151 Query: 181 KVALDVATVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATR 240 + ++ A + + +G GDRVCIDTCSLM G+G L+G+ + LFLVH+ET NPYVA R Sbjct: 152 EPLVE-AEIVGLRTVGLGDRVCIDTCSLMTDGQGALVGNSAGFLFLVHAETRRNPYVAPR 210 Query: 241 PFRVNAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIE 300 PFR+NAG VHAY+ P +T+YL EL AGD ++IVD G + EA+VGR+K+E+RPLV++E Sbjct: 211 PFRINAGAVHAYVKVPDGRTRYLCELGAGDPIVIVDAAGKSTEAVVGRIKVEKRPLVVVE 270 Query: 301 AEYKGDIIRTILQNAETIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIE 360 A +LQNAET+ L+ KGE +SV L+ G +VL+ P+ RHFGMA+ E+I+E Sbjct: 271 ARCDAGGGSILLQNAETVCLMTPKGEGVSVTSLEKGMRVLVSPQSRGRHFGMAVDESIVE 330 Query: 361 K 361 K Sbjct: 331 K 331 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: 378 Number of extensions: 18 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: 361 Length of database: 331 Length adjustment: 29 Effective length of query: 332 Effective length of database: 302 Effective search space: 100264 Effective search space used: 100264 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 Jul 25 2024. The underlying query database was built on Jul 25 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