Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_002719447.1 RSPH17029_RS04900 prephenate dehydrogenase
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_000015985.1:WP_002719447.1 Length = 311 Score = 218 bits (556), Expect = 1e-61 Identities = 118/283 (41%), Positives = 173/283 (61%), Gaps = 1/283 (0%) Query: 1 MTVFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQD 60 M +++ +A+IGLGLI SS A A +A ++ + +S R A + L D V + + Sbjct: 1 MALYERVALIGLGLIASSMAHAIRAAGLATEITGHARSAETRAAAVEIGLCDRVFETAAE 60 Query: 61 AVREADLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVP 119 AV ADLV+L VPV AMG +AA +AP L + D GSVK +VI + ++P + VP Sbjct: 61 AVAGADLVVLAVPVGAMGAIAAEIAPHLAPGATVTDVGSVKQAVITAVAPHVPEGVHFVP 120 Query: 120 SHPLAGTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHH 179 HPLAGTE++GP +GFA LF++ +LTP +A+A + E +G + M A HH Sbjct: 121 GHPLAGTEHSGPRSGFATLFRNRWWLLTPPEGADPEAVARLRALCEGMGANVEEMDAAHH 180 Query: 180 DHVLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIML 239 D VLA+TSH PH+IAY ++G+ + +++ I+RYSA FRD TR+AAS+P +W+D+ L Sbjct: 181 DLVLAVTSHTPHLIAYTMVGVADHLRRVTQSEIIRYSAAGFRDFTRIAASDPTMWRDVFL 240 Query: 240 ENAPALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKAR 282 N A L +L F +L L+ AI DGD+L E+F ++ R Sbjct: 241 TNKEATLDILGRFTEELFALQRAIRLGDGDHLFEYFTRTRAIR 283 Lambda K H 0.321 0.136 0.398 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: 244 Number of extensions: 14 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: 293 Length of database: 311 Length adjustment: 27 Effective length of query: 266 Effective length of database: 284 Effective search space: 75544 Effective search space used: 75544 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 (21.8 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