Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_015932245.1 MNOD_RS27460 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_000022085.1:WP_015932245.1 Length = 309 Score = 254 bits (649), Expect = 2e-72 Identities = 132/277 (47%), Positives = 181/277 (65%), Gaps = 1/277 (0%) Query: 7 IAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAVREAD 66 +A++GLGLIGSS AR +A T+ D+ V +R R L L D+VTDD+ V EAD Sbjct: 11 LALVGLGLIGSSIARGARANDLVDTIVAIDRDPAVLERVRTLGLADHVTDDLAAGVAEAD 70 Query: 67 LVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSHPLAG 125 LV+LCVPV A+G V AA+A ALK I+ D GSVK +V+ ++P+H VP+HP+AG Sbjct: 71 LVILCVPVGAVGPVTAALAGALKPGAILSDVGSVKGAVMAAAAPHVPDHAAFVPAHPVAG 130 Query: 126 TENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDHVLAL 185 TE +GPDAGFA LFQ ILTP TP +A+A + +WE +G + M+A HHD VLA+ Sbjct: 131 TEQSGPDAGFATLFQGRWCILTPPEGTPPEAVARVRGFWEGLGSVVETMTAAHHDLVLAI 190 Query: 186 TSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDIMLENAPAL 245 TSH+PH+IAY ++G + E +++ ++++SAG FRD TR+AAS+P +W+D+ L N A+ Sbjct: 191 TSHVPHLIAYNIVGTAADLETVTQSEVIKFSAGGFRDFTRIAASDPTMWRDVFLNNKEAV 250 Query: 246 LPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKAR 282 L VL F DL L AI DGD L F ++ R Sbjct: 251 LEVLGRFNEDLAALARAIRWDDGDALHALFTRTRAIR 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: 241 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: 309 Length adjustment: 27 Effective length of query: 266 Effective length of database: 282 Effective search space: 75012 Effective search space used: 75012 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