Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_072909467.1 BUB13_RS14360 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_900142125.1:WP_072909467.1 Length = 341 Score = 272 bits (696), Expect = 8e-78 Identities = 136/264 (51%), Positives = 186/264 (70%), Gaps = 3/264 (1%) Query: 95 LVSRKKKPEDTIVDIKGEKIGDGQQRFIV--GPCAVESYEQVAEVAAAAKKQGIKILRGG 152 L SR+ +PE + ++I +G G + F+V GPC+VES +Q+ E A A K+ G ++LRGG Sbjct: 72 LASREVQPEPSEIEIV-PGLGIGGKEFVVVAGPCSVESQKQICETAEAVKQSGARLLRGG 130 Query: 153 AFKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNM 212 AFKPRTSPY FQG+ +GL++L L +++E+V P +E Y D++Q+GARN Sbjct: 131 AFKPRTSPYSFQGMEEDGLKLLAEARKLTGLPIVTEVVNPRDVELVAKYADIMQVGARNT 190 Query: 213 QNFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRN 272 QNF LLK G + KP+LLKRG+A TI EF+ +AEYI+S+GN ++ILCERGIRT+ETATRN Sbjct: 191 QNFALLKMLGQLDKPILLKRGMAVTIQEFLMSAEYILSEGNRRVILCERGIRTFETATRN 250 Query: 273 TLDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALS 332 TLDISAVP+LKQ+THLPV +D +H+TG L+ AA A GADG++ EVHP P A S Sbjct: 251 TLDISAVPVLKQQTHLPVMIDPSHATGHSHLVPSMCYAAAAAGADGLLVEVHPCPEEASS 310 Query: 333 DSAQQMAIPEFEKWLNELKPMVKV 356 D Q + EF+ + +L+ V+V Sbjct: 311 DGPQSLRPAEFDAMMKKLRAFVEV 334 Lambda K H 0.316 0.134 0.369 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: 337 Number of extensions: 17 Number of successful extensions: 1 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: 358 Length of database: 341 Length adjustment: 29 Effective length of query: 329 Effective length of database: 312 Effective search space: 102648 Effective search space used: 102648 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: 49 (23.5 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