Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate 8499666 DvMF_0432 2-dehydro-3-deoxyphosphooctonate aldolase (RefSeq)
Query= BRENDA::P39912 (358 letters) >FitnessBrowser__Miya:8499666 Length = 270 Score = 92.4 bits (228), Expect = 1e-23 Identities = 76/234 (32%), Positives = 110/234 (47%), Gaps = 22/234 (9%) Query: 119 QRFI-VGPCAVESYEQVAEVAAAAKKQGIKILRGGAFKP------RTSPYDFQGLGV-EG 170 +RFI GPCA+ES E + A A ++ FK RTS F+G G+ G Sbjct: 13 RRFIFAGPCALESLELAMDTAHAVREAAEAAGLFAVFKSSWDKANRTSLDGFRGPGLARG 72 Query: 171 LQILKRVADEFDLAVISEIVTPAHIEEALDYIDVIQIGARNMQNFELLKAAGAVKKPVLL 230 ++ L R+ E L V+++I P + + DV+QI A + LL AA + V + Sbjct: 73 MEWLARIKQETGLPVVTDIHEPDQAKPVAEVADVLQIPAFLCRQTSLLLAAAQTGRVVNV 132 Query: 231 KRGLAATISEFINAAEYIMSQGNDQIILCERGIRTYETATRNTLDISAVPILKQETHLPV 290 K+G + A + + S GN +I+L ERG +D ++PI+ Q +PV Sbjct: 133 KKGQFVAPWDMAPALDKLRSTGNQRILLTERGASF--GYNNLVVDFRSLPIM-QGYGVPV 189 Query: 291 FVDVTHST-----------GRRDLLLPTAKAALAIGADGVMAEVHPDPSVALSD 333 D THS G R + ++AA+A G DGV E HPDP AL D Sbjct: 190 VFDATHSVQLPGGKGTSSGGDRRFVPMLSRAAVAAGVDGVFLETHPDPDHALCD 243 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: 205 Number of extensions: 14 Number of successful extensions: 4 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: 270 Length adjustment: 27 Effective length of query: 331 Effective length of database: 243 Effective search space: 80433 Effective search space used: 80433 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: 48 (23.1 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