Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate WP_041277980.1 DP_RS12420 aldolase
Query= BRENDA::Q57843 (273 letters) >NCBI__GCF_000025945.1:WP_041277980.1 Length = 306 Score = 73.9 bits (180), Expect = 4e-18 Identities = 51/162 (31%), Positives = 78/162 (48%), Gaps = 8/162 (4%) Query: 115 AVSIHVNVGSDEDWEAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARL 174 AV V +GS+ + E I G+ + +YPRGK + +E+DP L+A A Sbjct: 140 AVGYTVYLGSEYEPEMLHQAAQIISHAHQHGLISVLWVYPRGKAVADEKDPHLIAGATGA 199 Query: 175 GAELGADIVKTSYTGDIDS-----FRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAME- 228 A LG+D VK +Y D F++ V VV G ++ E FL+ + D + Sbjct: 200 AACLGSDFVKVNYPKKEDCASKEIFKEAVMAAGRTKVVCAGGSSDDVEGFLERLYDQIHV 259 Query: 229 AGAAGVAVGRNIFQH--DDVVGITRAVCKIVHENADVEEALK 268 +GA+G A GRNI Q + + + A+ I + V EA+K Sbjct: 260 SGASGNATGRNIHQKALKEAIRMCNAIYAITVDGKTVNEAMK 301 Lambda K H 0.318 0.138 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: 201 Number of extensions: 9 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: 273 Length of database: 306 Length adjustment: 26 Effective length of query: 247 Effective length of database: 280 Effective search space: 69160 Effective search space used: 69160 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: 48 (23.1 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