Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_011159587.1 TX73_RS20665 3-dehydroquinate synthase
Query= curated2:Q980I9 (354 letters) >NCBI__GCF_000195775.1:WP_011159587.1 Length = 372 Score = 162 bits (411), Expect = 1e-44 Identities = 102/289 (35%), Positives = 155/289 (53%), Gaps = 9/289 (3%) Query: 57 IPINDGESTKELSSVISLVEKLFEKNFDRGDYIIGVGGGTVTDVAGFLASIYLRGLNLIN 116 I I+ E+ K L L+ +L + DR +++ +GGG + DV F ASI++RGL Sbjct: 53 IRIDALEANKSLEYAPHLISELRKAGADRSTHLVAIGGGIIQDVVTFAASIFMRGLPWTY 112 Query: 117 VPTTFLGMVDAAIGGKNGVNFNNIKNLIGTFYQPSMIISDLEFLETLPIEELKKGLAEVI 176 +PTT L MVD+ IGGK+ +N KNL+G FY P ++ D+ F+ TL E + GL E Sbjct: 113 MPTTLLSMVDSCIGGKSSINAAGYKNLVGNFYPPKKVLVDVSFISTLDAEMIAGGLFEAA 172 Query: 177 KYGLTLDKELY-DYLSLNKEKILNKDKQALEDIIFRSTLDKLSIVKEDERETKGIRIVLN 235 K + + + DYL+ + + D+QA+ ++I S L K ++ DE + K R++LN Sbjct: 173 KICYASNYQAFLDYLACS-PGLKMTDEQAV-NVIRHSLLTKKWFIEIDEFDQKE-RLLLN 229 Query: 236 FGHTIGHAIEAGSSFNVPHGYAISVGMVCEAKMAEELGYAEEGVVEDVLWLLQ-----IY 290 FGHT GHA+EA + F + HG + +GM+ A+ A+ + + V L++ I Sbjct: 230 FGHTFGHALEAATDFGISHGVGVGLGMLVAAQYAKRETELTDAGKDHVAHLIEHVKDMIG 289 Query: 291 GLPYDISQIDAPVDLKLALNAINMDKKHRKDVILIPFPTRIGSWKKVEV 339 + Q A VDL LA+ DKKH+ D I P R G+ V V Sbjct: 290 PRAERVLQSPAHVDLDLAMEKFEFDKKHKSDSYRIVIPNREGALALVSV 338 Lambda K H 0.318 0.139 0.394 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: 276 Number of extensions: 11 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: 354 Length of database: 372 Length adjustment: 29 Effective length of query: 325 Effective length of database: 343 Effective search space: 111475 Effective search space used: 111475 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: 41 (21.7 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