Align 3-dehydroquinate synthase; DHQ synthase; 3-dehydroquinate synthase II; EC 1.4.1.24 (characterized)
to candidate WP_013705646.1 DESAC_RS03230 3-dehydroquinate synthase II
Query= SwissProt::Q58646 (361 letters) >NCBI__GCF_000195295.1:WP_013705646.1 Length = 331 Score = 290 bits (743), Expect = 3e-83 Identities = 170/361 (47%), Positives = 226/361 (62%), Gaps = 30/361 (8%) Query: 1 MKFGWVNVIGDNWEEKKKIVTTALESSIPVVVAEPEDIEKIKELGNIKVASHSLDADIVL 60 MK WV V D W++K+ VTTALE V P ++K LG I V + D Sbjct: 1 MKQVWVKV--DPWDKKR--VTTALEGGADAVWTPPGYAAEVKTLGKIPVIAPDGD----- 51 Query: 61 VNKNDNIEFLKEAKNLGKETAIYIPIESKEDEEFASEVARFGFVDNIILEGRDWTIIPLE 120 L ++L + T S+ D+E +++A +++ DWTIIPLE Sbjct: 52 ---------LAPGQDLFEVTL------SRADDE--ADIAAKAKTHPVVVHCADWTIIPLE 94 Query: 121 NLIADLFHRDVKIVASVNSVDEAKVAYEILEKGTDGVLLNPKNLEDIKELSKLIEEMNKE 180 NL+A + +V+EA+ ILE+G DG+++ +L ++K+L +L++E++ Sbjct: 95 NLVAQC---PANLFVEAATVEEARTFLGILERGVDGLVITAADLGEVKQLLRLVKEISPP 151 Query: 181 KVALDVATVTKVEPIGSGDRVCIDTCSLMKIGEGMLIGSYSRALFLVHSETVENPYVATR 240 V L ATV V +G GDRVC+DTC+ M G+GMLIG+ S ALFLVH+E++ENPYVA R Sbjct: 152 -VELTPATVASVHLLGMGDRVCVDTCTQMGRGQGMLIGNSSAALFLVHAESLENPYVAAR 210 Query: 241 PFRVNAGPVHAYILCPGNKTKYLSELKAGDKVLIVDKDGNTREAIVGRVKIERRPLVLIE 300 PFRVNAGPVHAYI PG KT+YLSELKAGD+VL+VD G T A VGRVKIE+RPL+LI Sbjct: 211 PFRVNAGPVHAYIRVPGGKTRYLSELKAGDEVLVVDYSGRTLPATVGRVKIEKRPLMLIT 270 Query: 301 AEYKGDIIRTILQNAETIRLVNEKGEPISVVDLKPGDKVLIKPEEYARHFGMAIKETIIE 360 A ++G TI+QNAETIRL GE +SVV L PGD+VL+ EE RHFG + ETI+E Sbjct: 271 ATHEGRECSTIVQNAETIRLTRPDGEAVSVVQLSPGDQVLVALEEAGRHFGYKVTETILE 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: 375 Number of extensions: 16 Number of successful extensions: 4 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 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