Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_011736457.1 PPRO_RS12825 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000015045.1:WP_011736457.1 Length = 339 Score = 287 bits (734), Expect = 3e-82 Identities = 137/260 (52%), Positives = 190/260 (73%), Gaps = 1/260 (0%) Query: 95 LVSRKKKPEDTIVDIKGEKIGDGQQRFIV-GPCAVESYEQVAEVAAAAKKQGIKILRGGA 153 LVSR PEDTIVD+ G ++G G + +V GPCAVES EQ+ A KK G +LRGGA Sbjct: 71 LVSRDFHPEDTIVDVAGVRVGQGCRPVVVAGPCAVESEEQIVRTALFVKKAGADMLRGGA 130 Query: 154 FKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQ 213 FKPRT P+ FQGL EGL++L E L V++E+++P + DY D++Q+GARNMQ Sbjct: 131 FKPRTGPHTFQGLREEGLELLALAGRESGLPVVTEVMSPDSVGLVADYADLLQVGARNMQ 190 Query: 214 NFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNT 273 NF+LL+ G ++KPVLLKRG++AT+ EF+ AAEYI+++GN+Q+ILCERGIRT+ETATRNT Sbjct: 191 NFDLLRELGRIRKPVLLKRGMSATVEEFLAAAEYILAEGNEQVILCERGIRTFETATRNT 250 Query: 274 LDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSD 333 LD++ P++++ +HLPV +D +H+TG+R L+ P AAL GA GV+ EVHP+P ALSD Sbjct: 251 LDLAVAPLIRELSHLPVMIDPSHATGKRSLVPPMTLAALVAGAHGVLVEVHPEPEKALSD 310 Query: 334 SAQQMAIPEFEKWLNELKPM 353 Q + FE+ + +++ M Sbjct: 311 GPQSLTFQGFERLMADVRRM 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: 314 Number of extensions: 13 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: 339 Length adjustment: 29 Effective length of query: 329 Effective length of database: 310 Effective search space: 101990 Effective search space used: 101990 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