Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011158428.1 TX73_RS14685 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::Q9WYH8 (338 letters) >NCBI__GCF_000195775.1:WP_011158428.1 Length = 287 Score = 126 bits (316), Expect = 8e-34 Identities = 91/277 (32%), Positives = 141/277 (50%), Gaps = 26/277 (9%) Query: 81 TVIDLGDVKIGNGY-FTIIAGPCSVEGREMLMETAHFLSELGVKVLRGGAYKP------R 133 T + G+VK GN ++IAGPC +E R +E A L E+ ++ G YK R Sbjct: 9 TSVVAGNVKFGNALPLSVIAGPCQLESRAHALEVASALKEIATRLGIGLVYKTSFDKANR 68 Query: 134 TSPYSFQGLG-EKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFR 192 TS S +GLG + L E D G+ V+T+ + + AE DI+QI A + Sbjct: 69 TSAASARGLGLDAALPIFAEIRDHLGLPVLTDVHENEQCARAAEAVDILQIPAFLCRQTD 128 Query: 193 LLSKAGSYNKPVLLKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTL-- 250 LL A + + V +K+G + I ++GN+K+++ ERG+ NTL Sbjct: 129 LLLAAAATGRIVNVKKGQFLAPWDMGNVVSKITHAGNSKVLVTERGV----SFGYNTLVS 184 Query: 251 DISAVPIIRKESHLPILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEV 299 D+ A+PI+ K + P++ D +HS GG R+ V L+RAA+AVG G+ +E Sbjct: 185 DMRALPIMAKTTGAPVIFDATHSVQQPGGKGTSSGGEREYVPVLARAAVAVGVAGVFIET 244 Query: 300 HPEPEKALSDGKQSLDFELFKELVQEMKKLADALGVK 336 HP+P+ A SDG + F+ L++ + + DAL K Sbjct: 245 HPDPDHAPSDGPNMVPLREFEALIKTLMEF-DALAKK 280 Lambda K H 0.318 0.138 0.388 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: 206 Number of extensions: 13 Number of successful extensions: 5 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: 338 Length of database: 287 Length adjustment: 27 Effective length of query: 311 Effective length of database: 260 Effective search space: 80860 Effective search space used: 80860 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