Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate WP_051327343.1 G491_RS31305 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= BRENDA::P43902 (377 letters) >NCBI__GCF_000429905.1:WP_051327343.1 Length = 291 Score = 135 bits (339), Expect = 2e-36 Identities = 85/286 (29%), Positives = 142/286 (49%), Gaps = 14/286 (4%) Query: 92 GFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVS 151 GF TI I+GG G++G F Y + G+ + I R+ + + VVI+S Sbjct: 16 GFTTIG-------IIGGAGQMGQWFKEYFESLGHTVLISGRKTELTWQDLAEQCQVVIIS 68 Query: 152 VPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMA 211 +P++++++ ++ P + ++ LL D+ S+K + M E V+G HP+FG A MA Sbjct: 69 LPLDVSIDMAHQVGPLMNKDQLLMDMCSMKHDICQAMKESTQAQVIGTHPLFGPSTAGMA 128 Query: 212 KQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLS 271 Q V+ C WL Q++ GA + T+ HD NM +QAL HF T + G L Sbjct: 129 GQNVIVCPMGEGPWLPWLESQLEAKGAVVTITDGYTHDRNMAVVQALTHFMTISFGETLL 188 Query: 272 KQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEAL 331 + ++ + ++PI+RL+L ++GR+FAQD ELY ++I V++ + +E Sbjct: 189 QLGVDPKEIRPYATPIFRLKLGLLGRMFAQDTELYRNLICKNPMASEVLDQFLSSANEVK 248 Query: 332 -TFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQ 376 + + IDAF G + EQ + ES L+ K+ Sbjct: 249 NNICHDPEIMTAIDAF------LGTFPEQGMIESDACLETLAKFKE 288 Lambda K H 0.321 0.137 0.390 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: 217 Number of extensions: 8 Number of successful extensions: 2 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: 377 Length of database: 291 Length adjustment: 28 Effective length of query: 349 Effective length of database: 263 Effective search space: 91787 Effective search space used: 91787 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 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