Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate AZOBR_RS20490 AZOBR_RS20490 cyclohexadienyl dehydrogenase
Query= SwissProt::Q04983 (293 letters) >FitnessBrowser__azobra:AZOBR_RS20490 Length = 301 Score = 226 bits (577), Expect = 4e-64 Identities = 115/281 (40%), Positives = 174/281 (61%), Gaps = 1/281 (0%) Query: 3 VFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAV 62 +F +AI+G+GLIGSS ARA Y V D+S +A L + + T D+ +A+ Sbjct: 12 LFDRVAIVGVGLIGSSLARALTHYGVARQVVCADRSPEHCAKAMELGIVERATTDLAEAL 71 Query: 63 READLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSH 121 ADLV+L PV A V + P L+ +I+ D GSVK +V++ + ++P+ + ++P H Sbjct: 72 EGADLVVLATPVGAFAEVGEQLGPLLRPGMIVTDVGSVKQAVLRDVGPHIPDGVHLIPGH 131 Query: 122 PLAGTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDH 181 P+AGTE++GP+AGFA LFQ I+TP A+ + W IG + LM A HHD Sbjct: 132 PVAGTEHSGPEAGFATLFQGRWCIVTPPPGANEGAVDKVVTMWRRIGSTVELMDANHHDR 191 Query: 182 VLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLEN 241 VLA+TSHLPH+IAY ++G S E +++ ++++SAG FRD TR+AAS+P +W+D+ L N Sbjct: 192 VLAITSHLPHLIAYTIVGTASDLEDDTKSEVIKFSAGGFRDFTRIAASDPVMWRDVFLNN 251 Query: 242 APALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKAR 282 A+L +L F DL L+ AI +G+ L +HF +++ R Sbjct: 252 REAVLEILQRFTEDLTALQRAIRWGEGEQLQDHFTKTRAIR 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: 218 Number of extensions: 7 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: 301 Length adjustment: 26 Effective length of query: 267 Effective length of database: 275 Effective search space: 73425 Effective search space used: 73425 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 09 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