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 209396 DVU0460 predicted phospho-2-dehydro-3-deoxyheptonate aldolase
Query= SwissProt::Q6LZE3 (272 letters) >MicrobesOnline__882:209396 Length = 266 Score = 317 bits (813), Expect = 1e-91 Identities = 147/259 (56%), Positives = 200/259 (77%) Query: 9 NVGKLIRLERIFDKKSEKTVIIPMDHGVSSGPLDGIKDMRITTNAVADGGANAVLGHKGL 68 ++GK IR+ER+F++ + ++VI+P+DHGVS GP+DG+ DMR T N VA+GGA+AVL HKGL Sbjct: 2 HIGKKIRMERLFNRTTGRSVIVPLDHGVSVGPIDGLVDMRDTVNQVAEGGADAVLMHKGL 61 Query: 69 VRHGHRGYGRDIGLIIHMSAGTSISPDPNKKVIVTTVEDAMRMGADAVSLHVNVGAESDF 128 VR GHR GRD+GLI+H+SA TS+SP PN K + TVEDA++ GAD VS+HVN+G E++ Sbjct: 62 VRCGHREGGRDVGLIVHLSASTSLSPLPNAKTLTATVEDAIKHGADGVSVHVNLGDETER 121 Query: 129 EMYRDLGLISETCEHWGMPLIAMMYPRGPKIKDEKDPEVVAHAARLGAELGADIIKTNYT 188 +M DLG ++ WG+PL+AMMY RGP+I+D+ DP+VVAH AR+G ELGAD++K YT Sbjct: 122 DMLADLGRVATIANDWGVPLLAMMYARGPRIRDQYDPQVVAHCARVGVELGADVVKVPYT 181 Query: 189 GDPDTFKEVVKGCPAPIVIAGGPKTNTDEEFLQMVKDAMHAGGKGVASGRNVFQHKDVKG 248 GD DTF VV+ C P+VIAGGPK ++ +FLQMV DA+ AGG G++ GRN+FQH Sbjct: 182 GDMDTFAHVVQSCCVPVVIAGGPKLDSTRDFLQMVHDAVRAGGSGLSVGRNIFQHARPSQ 241 Query: 249 ITSAICKIVHEDVEVEEAL 267 + A+ +VHED +VE+A+ Sbjct: 242 LVKAVRGLVHEDWDVEQAI 260 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: 323 Number of extensions: 14 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: 272 Length of database: 266 Length adjustment: 25 Effective length of query: 247 Effective length of database: 241 Effective search space: 59527 Effective search space used: 59527 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 09 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