Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_012470844.1 GLOV_RS13875 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000020385.1:WP_012470844.1 Length = 338 Score = 299 bits (766), Expect = 6e-86 Identities = 151/307 (49%), Positives = 215/307 (70%), Gaps = 9/307 (2%) Query: 48 PVRERTMLNNIIENNDGPFENSTIQHIFKEIFKAGLELQEEDHSKALLVSRKKKPEDTIV 107 P ERT + + N G ++STI+ + G++ LVSR P++TIV Sbjct: 32 PGGERTAIG--VLGNKGYVDDSTIRDL------PGVQQAIHVSKPYKLVSRDFHPDNTIV 83 Query: 108 DIKGEKIGDGQQRFIVG-PCAVESYEQVAEVAAAAKKQGIKILRGGAFKPRTSPYDFQGL 166 D+ G KIG+G++ +VG PCAVES EQ+ + A K+ G +LRGGAFKPRT P+ FQGL Sbjct: 84 DVAGVKIGEGERPVVVGGPCAVESEEQILKTARFVKQCGADLLRGGAFKPRTGPHTFQGL 143 Query: 167 GVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKK 226 EGL++L + L +++E+++P ++ +Y D++Q+GARNMQNF+LL+ G ++K Sbjct: 144 REEGLKLLAKARTATGLPIVTEVMSPDNVALVAEYADLLQVGARNMQNFDLLRELGRIRK 203 Query: 227 PVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQET 286 P+LLKRG++ATI EF+ AAEYI+++GNDQ+ILCERGIRT+ETATRNTLD++ VP++K+ T Sbjct: 204 PILLKRGMSATIEEFLAAAEYILAEGNDQVILCERGIRTFETATRNTLDLAMVPLVKELT 263 Query: 287 HLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSDSAQQMAIPEFEKW 346 HLPV VD +H+TG+R L+ P +KAAL GA GV+ EVHP+P ALSD Q + P FE Sbjct: 264 HLPVMVDPSHATGKRSLVTPMSKAALVAGAHGVLVEVHPEPEKALSDGPQSLTFPGFEAL 323 Query: 347 LNELKPM 353 + +LK + Sbjct: 324 MADLKKL 330 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: 324 Number of extensions: 15 Number of successful extensions: 2 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: 338 Length adjustment: 29 Effective length of query: 329 Effective length of database: 309 Effective search space: 101661 Effective search space used: 101661 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