Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 8499666 DvMF_0432 2-dehydro-3-deoxyphosphooctonate aldolase (RefSeq)
Query= BRENDA::Q9YEJ7 (270 letters) >FitnessBrowser__Miya:8499666 Length = 270 Score = 108 bits (269), Expect = 2e-28 Identities = 76/231 (32%), Positives = 120/231 (51%), Gaps = 21/231 (9%) Query: 35 VIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKP------RTSPYSFQGLGL-EGLKL 87 + AGPC++ES E + A AV+EA FK RTS F+G GL G++ Sbjct: 16 IFAGPCALESLELAMDTAHAVREAAEAAGLFAVFKSSWDKANRTSLDGFRGPGLARGMEW 75 Query: 88 LRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRG 147 L R E GLPVVT++ +P + V+ AD+LQI A + LL ++G+ V +K+G Sbjct: 76 LARIKQETGLPVVTDIHEPDQAKPVAEVADVLQIPAFLCRQTSLLLAAAQTGRVVNVKKG 135 Query: 148 FGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVD 207 ++ A + + GN +++L ERG +D ++ ++ + +PV+ D Sbjct: 136 QFVAPWDMAPALDKLRSTGNQRILLTERGASF--GYNNLVVDFRSLPIM-QGYGVPVVFD 192 Query: 208 PSH----PAGR-------RSLVPALAKAGLAAGADGLIVEVHPNPEEALSD 247 +H P G+ R VP L++A +AAG DG+ +E HP+P+ AL D Sbjct: 193 ATHSVQLPGGKGTSSGGDRRFVPMLSRAAVAAGVDGVFLETHPDPDHALCD 243 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: 163 Number of extensions: 7 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: 270 Length adjustment: 25 Effective length of query: 245 Effective length of database: 245 Effective search space: 60025 Effective search space used: 60025 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 09 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