Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_028485481.1 A377_RS0110795 3-deoxy-8-phosphooctulonate synthase
Query= BRENDA::Q9YEJ7 (270 letters) >NCBI__GCF_000384235.1:WP_028485481.1 Length = 278 Score = 114 bits (284), Expect = 3e-30 Identities = 80/249 (32%), Positives = 132/249 (53%), Gaps = 21/249 (8%) Query: 35 VIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKP------RTSPYSFQGLGLE-GLKL 87 +IAGPC +ES Q+ A +KE + FK R+S S++G G+E GL++ Sbjct: 16 LIAGPCVIESETQIMTIAERLKELTDELEMPFIFKASYDKANRSSTQSYRGPGIEEGLRI 75 Query: 88 LRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRG 147 L+R DE G+PV+T+V + + V+ D++Q A ++ ++ V R G PV +K+G Sbjct: 76 LQRVKDELGVPVLTDVHEDTPLSEVASVVDVMQTPAFLVRQTNFIQNVCRQGLPVNIKKG 135 Query: 148 FGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVD 207 ++ GN QV++ +RG +F +T + D+ +A++++ T PV+ D Sbjct: 136 QFQAPWDMQQVVNKAREVGNDQVMVCDRGT-SFGYNTLIS-DMRGLAMMRQ-TQAPVVFD 192 Query: 208 PSHPA-----------GRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGE 256 +H G+RS+VP LA+A +AAG G+ +E HP+PE ALSD + Sbjct: 193 ATHSVQQPGGQGTTSGGQRSMVPVLARAAVAAGISGVFMETHPDPENALSDGPNMWPLDQ 252 Query: 257 FARLMGELR 265 A L+ L+ Sbjct: 253 MAPLLRTLK 261 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: 141 Number of extensions: 6 Number of successful extensions: 3 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 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