Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_017547588.1 C792_RS0101060 prephenate dehydrogenase
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_000330705.1:WP_017547588.1 Length = 287 Score = 113 bits (283), Expect = 4e-30 Identities = 83/275 (30%), Positives = 128/275 (46%), Gaps = 7/275 (2%) Query: 7 IAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAVREAD 66 I I GLG IG S A A K+ P+ V D A L + + + AD Sbjct: 3 IVIAGLGNIGGSFALAIKSNAPEHEVYAIDIDAESLRNAEDSGLIKKGYETPESIIPHAD 62 Query: 67 LVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSHPLAG 125 LV+ V + + A AP K++VI+ D VK S+I+ ++ L ++ V HP+AG Sbjct: 63 LVIFSVYPMILKSLVAEYAPYFKENVILTDVTGVKRSIIEEIEPLLSDNADFVFGHPMAG 122 Query: 126 TENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGR-INLMSAEHHDHVLA 184 EN G E+F+ + TP + I ++ + EIG R + ++ + HD V+ Sbjct: 123 RENRGLSFASGEVFRGANYLFTPTPGNKPENIEMLSSFVREIGFRNVTSITPDFHDEVIG 182 Query: 185 LTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLENAPA 244 TS L HVIA LI + Y+ S+RD TR+ +LW ++ + N Sbjct: 183 FTSQLAHVIAVSLIN-----SDDTNRDTKAYTGDSYRDLTRITNINEKLWPELFIMNKDH 237 Query: 245 LLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQ 279 LL +D F L +L AI ++D + + E ES+ Sbjct: 238 LLNHIDGFKEQLDQLTKAIENEDVETMQEMMIESR 272 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: 201 Number of extensions: 13 Number of successful extensions: 5 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: 287 Length adjustment: 26 Effective length of query: 267 Effective length of database: 261 Effective search space: 69687 Effective search space used: 69687 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 Jul 26 2024. The underlying query database was built on Jul 25 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