Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 353847 BT4321 2-dehydro-3-deoxyphosphooctonate aldolase (NCBI ptt file)
Query= BRENDA::Q9WYH8 (338 letters) >FitnessBrowser__Btheta:353847 Length = 266 Score = 114 bits (285), Expect = 3e-30 Identities = 80/259 (30%), Positives = 133/259 (51%), Gaps = 21/259 (8%) Query: 93 GYFTIIAGPCSVEGREMLMETAHFL----SELGVKVLRGGAYKP--RTSPYSFQGLG-EK 145 G F ++AGPC +EG EM M A + +L + + G+Y+ R+ SF G+G EK Sbjct: 10 GNFFLLAGPCVIEGEEMAMRIAERVVGVTEKLQIPYVFKGSYRKANRSRLDSFTGIGDEK 69 Query: 146 GLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGSYNKPVL 205 L+ L++ D +G+ VT+ D+ AEY DI+QI A + LL A K + Sbjct: 70 ALKVLKKVHDTFGVPTVTDIHSADEAEMAAEYVDILQIPAFLCRQTDLLVAAAKTGKTIN 129 Query: 206 LKRGFMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDISAVPIIRKESHLP 265 +K+G + +A+ + +GN ++L ERG TF +D +P ++ + P Sbjct: 130 IKKGQFLSPLAMQFAADKVVEAGNKNVMLTERG-TTFGYQDL-VVDYRGIPEMQTFGY-P 186 Query: 266 ILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHPEPEKALSDGKQSL 314 +++D +HS GG L+ +++A IAVGA GI +E H P A SDG L Sbjct: 187 VILDVTHSLQQPNQTSGVTGGMPQLIETVAKAGIAVGADGIFIETHENPAVAKSDGANML 246 Query: 315 DFELFKELVQEMKKLADAL 333 +L + L+ ++ ++ +A+ Sbjct: 247 KLDLLEGLLTKLVRIREAI 265 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: 178 Number of extensions: 9 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: 338 Length of database: 266 Length adjustment: 27 Effective length of query: 311 Effective length of database: 239 Effective search space: 74329 Effective search space used: 74329 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 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