Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_012408009.1 NPUN_RS06450 3-dehydroquinate synthase
Query= curated2:A1WZA9 (354 letters) >NCBI__GCF_000020025.1:WP_012408009.1 Length = 394 Score = 167 bits (424), Expect = 3e-46 Identities = 115/332 (34%), Positives = 171/332 (51%), Gaps = 21/332 (6%) Query: 21 VLDQGVLAEHLVADRALLVSNETVAPLYAERLAVPGAEVQSVTLHDGERYKTLQTCEQVY 80 V+D G+L + L+ + Y E LA+ + + + GE K +T + Sbjct: 56 VIDAGILKYQPELVKQLVAYTK----FYGEVLAIAA---EPMIISGGEAAKNDRTLVEQI 108 Query: 81 DALIE-GRFDRSATVIALGGGVVGDMAGFCAATYQRGVGYIQVPTTLLAQVDSSVGGKTG 139 LIE R + V+A+GGG V D+ G+ AAT RG+ I+VPTT+LAQ DS VG K G Sbjct: 109 QQLIETAGLCRHSYVLAIGGGAVLDLVGYAAATAHRGIRLIRVPTTVLAQNDSGVGVKNG 168 Query: 140 VNHPRGKNMIGAFHQPRAVVADTGVLATLPEREYNAGLAEVVKYGLIRDPAFFDWLEAHV 199 +N KN +G F P AV+ D+ L TL +R++ +G+AE VK LI+D FFD++ +H Sbjct: 169 INAFGKKNFLGTFAPPYAVINDSAFLTTLDDRDWRSGIAEAVKVALIKDANFFDFIHSHS 228 Query: 200 DALRRRDPEALAHAVAESCRNKAEVVA--ADEREAGERALLNLGHTFGHAIETYTDYCTW 257 AL RRD +A+ + + E +A D E G L+ GH H +E T+Y Sbjct: 229 KALGRRDMDAMQQVIYRCAQLHLEHIANSGDPFEMGSSRPLDFGHWAAHKLEHLTNY-RL 287 Query: 258 LHGEAVAAGMVMAARMSVRLGWLQRNGLERTIALLEAFGLPTRPPAI---------PEAR 308 HGEAVA G+ + + S G L + +R + L A G P + P+ Sbjct: 288 RHGEAVAIGIALDSTYSYLAGLLDCSEWQRILNTLSALGFTLYVPELAQKLSQQEHPDCL 347 Query: 309 FRELMSVDKKNRGGQLRLVLLRSVGDAVVTGE 340 FR L +++ GG+L L LL+++G A+ E Sbjct: 348 FRGLTEF-REHLGGELTLTLLKNIGKAIEVHE 378 Lambda K H 0.320 0.136 0.401 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: 283 Number of extensions: 16 Number of successful extensions: 2 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: 354 Length of database: 394 Length adjustment: 30 Effective length of query: 324 Effective length of database: 364 Effective search space: 117936 Effective search space used: 117936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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