Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate YP_428345.1 Rru_A3263 cyclohexadienyl dehydrogenase
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_000013085.1:YP_428345.1 Length = 298 Score = 231 bits (590), Expect = 1e-65 Identities = 125/284 (44%), Positives = 177/284 (62%), Gaps = 1/284 (0%) Query: 3 VFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAV 62 +F +A+IG+GLIGSS ARA + + T+++ D+ E V RA AL L D +D AV Sbjct: 9 LFDRVALIGVGLIGSSLARAIRRHGLARTIAVADQGEGVAARALALGLCDEAGEDAVAAV 68 Query: 63 READLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSH 121 R ADLV+LC PV A +A A+ PAL I+ D GSVK VI+ + +LP + +VP H Sbjct: 69 RGADLVMLCTPVGAGEAIARAIGPALAPGAIVSDVGSVKARVIEMIAPHLPAGVHLVPGH 128 Query: 122 PLAGTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDH 181 P+AGTE +GP++GFAELF+ ILTP T A+A+ +A+ W +G I M + HD Sbjct: 129 PVAGTEKSGPESGFAELFEGRWCILTPLPTTDARAVDKVAELWRRVGMVIETMDPDTHDK 188 Query: 182 VLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLEN 241 VLA+TSHLPH+IAY ++G + E ++ +SAG FRD TR+A S+P +W+D+ L N Sbjct: 189 VLAITSHLPHLIAYTIVGTAADLEDHLSQKVIAFSAGGFRDFTRIAGSDPVMWRDVFLNN 248 Query: 242 APALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKARLAL 285 A+L +L F DL L+ AI +GD L F +++ R A+ Sbjct: 249 REAVLEILQRFTEDLTALQRAIRWGEGDTLEALFTKTRAIRQAV 292 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: 231 Number of extensions: 12 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: 298 Length adjustment: 26 Effective length of query: 267 Effective length of database: 272 Effective search space: 72624 Effective search space used: 72624 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