Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate WP_015818798.1 TERTU_RS06130 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::O67636 (311 letters) >NCBI__GCF_000023025.1:WP_015818798.1 Length = 742 Score = 211 bits (537), Expect = 4e-59 Identities = 120/280 (42%), Positives = 165/280 (58%), Gaps = 6/280 (2%) Query: 33 VLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDF-- 90 V+IVG+G +GGS A LR+ ++ G PE+ KA ++G++D S+ V + Sbjct: 7 VVIVGLGLIGGSLAAGLRKRAVCREVIGVARRPETCLKAQEMGVVDSAYCSLDDVLEQLE 66 Query: 91 SPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGK---RFVGGH 147 + D + ++ P T RE+ K L L+E VTD SVKG + D+ I G+ V GH Sbjct: 67 AGDIIFIAVPTLTLREVFKALKGRLAEGVIVTDGASVKGSVERDVREIFGEFPPAVVLGH 126 Query: 148 PIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDY 207 PIAG+EKSGVE + LY +VILTP + D +K V ++W VG V M + HD Sbjct: 127 PIAGSEKSGVEAAESELYVDHRVILTPVAENDPAAVKAVAKLWHAVGAEVLEMPVDEHDM 186 Query: 208 VFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENK 267 V G SHLPH +AF+LVDTL H S E ++F+Y GGF+DFTRIA SD IMWRDI L NK Sbjct: 187 VLGCTSHLPHVIAFSLVDTLAHDSKNE-NIFRYAAGGFRDFTRIASSDAIMWRDIMLANK 245 Query: 268 ENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKR 307 +V+ AI+ F +L+ L+++I RE E+ K R Sbjct: 246 ASVLDAIDLFSDNLSRLRDIISREDAVEMTGVFTRAKSAR 285 Lambda K H 0.318 0.138 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: 473 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 311 Length of database: 742 Length adjustment: 33 Effective length of query: 278 Effective length of database: 709 Effective search space: 197102 Effective search space used: 197102 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: 51 (24.3 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