Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate WP_013459295.1 SULKU_RS02200 prephenate dehydrogenase
Query= BRENDA::O67636 (311 letters) >NCBI__GCF_000183725.1:WP_013459295.1 Length = 278 Score = 146 bits (369), Expect = 5e-40 Identities = 86/269 (31%), Positives = 137/269 (50%), Gaps = 7/269 (2%) Query: 35 IVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSP-- 92 IVG+G MGGS A +L+ F I G D N E A+ +++ S E+ Sbjct: 5 IVGLGLMGGSMALALKHLSFISSIVGCDHNEEHQKIALQRKLVE----SFMSFEELKQEC 60 Query: 93 DFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGT 152 D + L+ PV E +K + + D T+ D GS K +V + ++ V HP+ GT Sbjct: 61 DVIFLAIPVNGVIEFLQKSTDLAGSDKTLIDLGSTKALIVDAIPPVIRSNVVAAHPMTGT 120 Query: 153 EKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVV 212 E+ G +L+ LY K V+L + + + R+++ +G + M HD + Sbjct: 121 EQFGPSAALEGLYAEKVVVLCDLEHSGATQRDTALRIFQAIGMQIRTMGAAQHDRHAAFI 180 Query: 213 SHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMK 272 SH+PH +++AL +T++ E ++ GGF+ +R+AKS P MW DIF +N+ENV++ Sbjct: 181 SHMPHVISYALANTVLAQEEKE-NILTLAAGGFRSMSRLAKSSPAMWEDIFRQNRENVLE 239 Query: 273 AIEGFEKSLNHLKELIVREAEEELVEYLK 301 A+E FE L LK + E EL +K Sbjct: 240 AVELFEVELQTLKTALKNEDYAELRREMK 268 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: 187 Number of extensions: 11 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: 311 Length of database: 278 Length adjustment: 26 Effective length of query: 285 Effective length of database: 252 Effective search space: 71820 Effective search space used: 71820 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: 48 (23.1 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