Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_018306370.1 DHAF_RS05785 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000021925.1:WP_018306370.1 Length = 319 Score = 260 bits (665), Expect = 3e-74 Identities = 128/255 (50%), Positives = 177/255 (69%) Query: 101 KPEDTIVDIKGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSP 160 K E + + I IG + + GPCAVES EQ+ A K G KILRGG +KPRTSP Sbjct: 53 KDERSTIRIGDTTIGAREVVLMAGPCAVESGEQMRAAAQGVKAAGGKILRGGVYKPRTSP 112 Query: 161 YDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKA 220 Y FQGLG EG+ L+ A E+ L ++E++ ++ +D +D++Q+G+RNMQNF LLK Sbjct: 113 YSFQGLGEEGIDYLREAAAEYGLLTVTEVMDERSLDVLVDKVDILQVGSRNMQNFHLLKL 172 Query: 221 AGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVP 280 G V+ PV+LKRGLAAT+ E++ AAEYI++ GN Q+ILCERGIRT+E +TRNTLD+SAV Sbjct: 173 LGEVRNPVILKRGLAATVEEWLAAAEYILAGGNAQVILCERGIRTFEPSTRNTLDLSAVS 232 Query: 281 ILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAI 340 ++K +HLPV VD +H+ GR D++ AKAA+A+GADG++ EVHP P A SD Q + Sbjct: 233 LVKVLSHLPVIVDPSHAAGRVDIIPALAKAAVAVGADGLLIEVHPHPEEAQSDGMQSLTP 292 Query: 341 PEFEKWLNELKPMVK 355 +F + EL+P+ + Sbjct: 293 EQFARLAAELRPIAQ 307 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: 299 Number of extensions: 13 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: 319 Length adjustment: 28 Effective length of query: 330 Effective length of database: 291 Effective search space: 96030 Effective search space used: 96030 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