Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_002724637.1 RSPH17029_RS20565 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >NCBI__GCF_000015985.1:WP_002724637.1 Length = 278 Score = 115 bits (289), Expect = 8e-31 Identities = 86/265 (32%), Positives = 132/265 (49%), Gaps = 22/265 (8%) Query: 19 TVVEVEGVRIGGGSK-AVIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKP------R 71 T+V + + IGGG A+I GPC +ES + R A + EA A FK R Sbjct: 6 TIVTIGDIAIGGGHPIALITGPCQLESLDHARMMAERIAEACAPTGTKFIFKASYDKANR 65 Query: 72 TSPYSFQGLGLE-GLKLLRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFP 130 +S + +GLG+E GL++L R +E G+PV+T+V +P H T + D+LQI A + Sbjct: 66 SSLSTARGLGMEKGLEILGRIREEFGVPVLTDVHEPGHCATAAEVCDVLQIPAFLCRQTD 125 Query: 131 LLREVGRSGKPVLLKRGFGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDV 190 LL G +G+ V +K+G ++ A+ + GN +++L ERG +F +T T D Sbjct: 126 LLLAAGETGRAVNVKKGQFLAPWDMKNVADKVASTGNRRILLCERG-TSFGYNTLVT-DF 183 Query: 191 AAVAVLKEATHLPVIVDPSH-----------PAGRRSLVPALAKAGLAAGADGLIVEVHP 239 + + AT PV+ D +H G+R P LA+A A G L +E H Sbjct: 184 RGLPTM-AATGWPVVFDATHSVQQPGGLGGSSGGQREFAPVLARAACAVGVSALFIETHE 242 Query: 240 NPEEALSDAKQQLTPGEFARLMGEL 264 +P+ A SD + RL+ +L Sbjct: 243 DPDRAPSDGPNMIPVDRMGRLIADL 267 Lambda K H 0.318 0.136 0.392 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: 135 Number of extensions: 5 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: 270 Length of database: 278 Length adjustment: 25 Effective length of query: 245 Effective length of database: 253 Effective search space: 61985 Effective search space used: 61985 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 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 16 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