Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 207075 DVU1624 2-dehydro-3-deoxyphosphooctonate aldolase
Query= BRENDA::Q9YEJ7 (270 letters) >MicrobesOnline__882:207075 Length = 273 Score = 110 bits (274), Expect = 4e-29 Identities = 79/248 (31%), Positives = 123/248 (49%), Gaps = 21/248 (8%) Query: 35 VIAGPCSVESWEQVREAALAVKEAGAHMLRGGAFKP------RTSPYSFQGLGL-EGLKL 87 ++AGPC++E ++ E A AV+EA FK RTS SF+G GL G++ Sbjct: 19 ILAGPCALEDFDVAMETAHAVREAAEAAGLFAVFKSSWDKANRTSITSFRGPGLVRGMEW 78 Query: 88 LRRAGDEAGLPVVTEVLDPRHVETVSRYADMLQIGARNMQNFPLLREVGRSGKPVLLKRG 147 L R +E+GLPVVT++ P V+ AD++QI A + LL +G+ V +K+G Sbjct: 79 LARIREESGLPVVTDIHLPEQAAPVAEVADIIQIPAFLCRQTDLLVAAAATGRVVNVKKG 138 Query: 148 FGNTVEELLAAAEYILLEGNWQVVLVERGIRTFEPSTRFTLDVAAVAVLKEATHLPVIVD 207 ++ A E + GN +++L ERG +D ++ + + +PV+ D Sbjct: 139 QFVAPWDMRPAVEKLRAAGNERILLTERGASF--GYNNLVVDYRSIPTM-QGFGVPVVFD 195 Query: 208 PSH-----------PAGRRSLVPALAKAGLAAGADGLIVEVHPNPEEALSDAKQQLTPGE 256 +H G R VP LA+A +AAG DG+ +E HP+P++AL D Sbjct: 196 ATHSVQLPGGLGGSSGGERRHVPVLARAAVAAGVDGVFLECHPDPDKALCDGPNSWPLDR 255 Query: 257 FARLMGEL 264 L+ EL Sbjct: 256 LPALLKEL 263 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: 166 Number of extensions: 8 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: 273 Length adjustment: 25 Effective length of query: 245 Effective length of database: 248 Effective search space: 60760 Effective search space used: 60760 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