Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate HSERO_RS13915 HSERO_RS13915 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::Q9WYH8 (338 letters) >FitnessBrowser__HerbieS:HSERO_RS13915 Length = 284 Score = 106 bits (265), Expect = 6e-28 Identities = 81/265 (30%), Positives = 133/265 (50%), Gaps = 30/265 (11%) Query: 87 DVKIGNGYFTIIAGPCSVEGREMLMETAHFL----SELGVKVLRGGAYKP--RTSPYSFQ 140 DV + + +F +IAG C +E +M ++TA L +ELG+ + ++ R+S SF+ Sbjct: 7 DVGLDHPFF-LIAGTCVIESEQMALDTAGTLKEITAELGIPFIYKSSFDKANRSSGSSFR 65 Query: 141 GLG-EKGLEYLREAADKYGMYVVTEALGEDDLPKVAEYADIIQIGARNAQNFRLLSKAGS 199 GLG EKGLE L + + G+ V+T+ D++ VA D++Q A + + Sbjct: 66 GLGMEKGLEILAKVKKEIGVPVLTDIHEIDEIKPVAAVVDVLQTPAFLCRQTDFIRACAQ 125 Query: 200 YNKPVLLKRG-------FMNTIEEFLLSAEYIANSGNTKIILCERGIRTFEKATRNTLDI 252 KPV +K+G +N I++ +A+ A + + CERG+ N + Sbjct: 126 SGKPVNIKKGQFLAPHDMVNVIDKARAAAKE-AGLPTDQFMACERGVSF---GYNNLVSD 181 Query: 253 SAVPIIRKESHLPILVDPSHS-----------GGRRDLVIPLSRAAIAVGAHGIIVEVHP 301 I +E+ P++ D +HS GG+R+ V L+RAAIAVG G+ +E HP Sbjct: 182 MRSLAIMRETGAPVVFDATHSVQLPGGQGTSSGGQREFVPVLARAAIAVGISGVFMETHP 241 Query: 302 EPEKALSDGKQSLDFELFKELVQEM 326 P +A SDG ++ K+L+ M Sbjct: 242 NPAEAKSDGPNAVPLARMKDLLGTM 266 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: 196 Number of extensions: 11 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: 284 Length adjustment: 27 Effective length of query: 311 Effective length of database: 257 Effective search space: 79927 Effective search space used: 79927 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