Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_013705910.1 DESAC_RS04605 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P39912 (358 letters) >NCBI__GCF_000195295.1:WP_013705910.1 Length = 336 Score = 265 bits (676), Expect = 2e-75 Identities = 134/260 (51%), Positives = 183/260 (70%), Gaps = 1/260 (0%) Query: 95 LVSRKKKPEDTIVDI-KGEKIGDGQQRFIVGPCAVESYEQVAEVAAAAKKQGIKILRGGA 153 LVSR+ K E++I+ + +G KIG G + GPCAVES Q +A A K G ++ RGGA Sbjct: 71 LVSREMKRENSIIVLPQGVKIGGGHFVVMAGPCAVESELQAFTIARAVKAAGAQVFRGGA 130 Query: 154 FKPRTSPYDFQGLGVEGLQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQ 213 FKPRTSPY +QGL EGL+IL RV DE L VI+E + ++ Y D+IQIGARNMQ Sbjct: 131 FKPRTSPYSYQGLEEEGLKILARVRDEIGLPVITEAIDHYSLDLVEQYADIIQIGARNMQ 190 Query: 214 NFELLKAAGAVKKPVLLKRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNT 273 NF LL+ AG +KPVLLKRG++AT+ EF AAEYI+++GN Q+ILCERGIR RNT Sbjct: 191 NFSLLRRAGQARKPVLLKRGMSATLDEFFMAAEYILAEGNTQVILCERGIRGIGAHARNT 250 Query: 274 LDISAVPILKQETHLPVFVDVTHSTGRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSD 333 LD++A+P +K+E+HLP+ D +H+ GRR L+ P A+ A+A+GADG++ EVH DP+ ALSD Sbjct: 251 LDLAAIPYVKKESHLPIIADPSHAAGRRLLVPPLARGAVAVGADGLIIEVHHDPTHALSD 310 Query: 334 SAQQMAIPEFEKWLNELKPM 353 Q + +F + +++ + Sbjct: 311 GPQSLYPEQFAALMRDIQTL 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: 334 Number of extensions: 14 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: 336 Length adjustment: 29 Effective length of query: 329 Effective length of database: 307 Effective search space: 101003 Effective search space used: 101003 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