Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_011427008.1 RHE_RS19475 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_000092045.1:WP_011427008.1 Length = 308 Score = 230 bits (586), Expect = 3e-65 Identities = 121/284 (42%), Positives = 173/284 (60%), Gaps = 1/284 (0%) Query: 3 VFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAV 62 +F IA+IG+GLIGSS A + + + +S RA L LGD T Q+AV Sbjct: 4 LFDRIALIGIGLIGSSLAHDIRRLGLTKEIVVATRSADTLKRAEELGLGDRYTTSSQEAV 63 Query: 63 READLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSH 121 R+ADLV++ VPV A VA +A +LK I+ D GS K SVI +Q ++P+ + +P H Sbjct: 64 RDADLVIVSVPVGASESVAKEIAGSLKPGAIVTDVGSTKASVIAQMQPHMPDSVHFIPGH 123 Query: 122 PLAGTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDH 181 PLAGTE +GPDAGF LF+ I TP A T A+ + +WE +G +++ M AEHHD Sbjct: 124 PLAGTEKSGPDAGFPGLFEGRWCIFTPVAGTDETALKRLRGFWEALGSKVDEMDAEHHDK 183 Query: 182 VLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLEN 241 VLA+ SHLPH+IAY ++G E + + +++YSA FRD TR+AAS+P +W+D+ L N Sbjct: 184 VLAIVSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCLHN 243 Query: 242 APALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKARLAL 285 A+L +L F DL L+ AI +GD + E F ++ R ++ Sbjct: 244 RDAILEMLARFSEDLAYLQRAIRWGEGDKIFELFTRTRAIRRSI 287 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: 239 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: 293 Length of database: 308 Length adjustment: 27 Effective length of query: 266 Effective length of database: 281 Effective search space: 74746 Effective search space used: 74746 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