Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase; ADH synthase; ADHS; ADTH synthase; EC 2.2.1.10 (characterized)
to candidate WP_048065481.1 MA_RS13900 aldolase
Query= SwissProt::Q6LZE3 (272 letters) >NCBI__GCF_000007345.1:WP_048065481.1 Length = 305 Score = 84.0 bits (206), Expect = 4e-21 Identities = 50/161 (31%), Positives = 82/161 (50%), Gaps = 8/161 (4%) Query: 116 VSLHVNVGAESDFEMYRDLGLISETCEHWGMPLIAMMYPRGPKIKDEKDPEVVAHAARLG 175 V + +G+ES+ EM + GM + +YPRG +KDEKDP ++A A G Sbjct: 137 VGYTIYLGSESEAEMLLQAAQVVYDAHQHGMVSVLWIYPRGTAVKDEKDPHLIAGATGAG 196 Query: 176 AELGADIIKTNY-----TGDPDTFKEVVKGCPAPIVIAGGPKTNTDEEFLQMVKDAMH-A 229 A LG D ++ NY + FKE +K V+ G ++ ++FL+ + D +H + Sbjct: 197 ACLGTDFVQVNYPEKEGANSAEIFKEAIKAAGRTKVVCAGGASDEVDDFLRKLHDQLHIS 256 Query: 230 GGKGVASGRNVFQH--KDVKGITSAICKIVHEDVEVEEALK 268 G G A+ RN+ Q + + +AI + ED +E++LK Sbjct: 257 GAMGSATRRNIHQKPLDEAIRMCNAIYAMTIEDATIEKSLK 297 Lambda K H 0.317 0.137 0.398 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: 218 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 272 Length of database: 305 Length adjustment: 26 Effective length of query: 246 Effective length of database: 279 Effective search space: 68634 Effective search space used: 68634 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 (21.6 bits) S2: 47 (22.7 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