Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate WP_058929409.1 AU252_RS02695 prephenate dehydrogenase
Query= SwissProt::Q04983 (293 letters) >NCBI__GCF_001484605.1:WP_058929409.1 Length = 369 Score = 98.6 bits (244), Expect = 2e-25 Identities = 76/257 (29%), Positives = 125/257 (48%), Gaps = 17/257 (6%) Query: 7 IAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLG-DNVTDDIQDAVREA 65 + +IG GL+G+S + V V L D S ++A A+++G D + D E Sbjct: 16 VVVIGTGLLGASIGLGLRGR--GVPVFLSDPSP--TNQAVAVDIGAGQPLDQLGDEAPEL 71 Query: 66 DLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQDNLPNHI-IVPSHPLA 124 +V+ P +VA A+A D ++ D SVK +++ L + V +HP+A Sbjct: 72 -VVVAAPPDVTADVVARALADY--PDSVVVDIASVKAAILAELGGRGADLARYVGTHPMA 128 Query: 125 GTENNGPDAGFAELFQDHPVILTPDAHTPAQAIAYIADYWEEIGGRINLMSAEHHDHVLA 184 G E +GP A ELF P ++ P + A A+ ++G ++ +A+ HD +A Sbjct: 129 GREKSGPVAARGELFTSMPWVVCPGPESSAAAVQTARSLATDLGAVVSQFTADEHDEAVA 188 Query: 185 LTSHLPHVIAYQLIGMVSGYEKKSRTPI--MRYSAGSFRDATRVAASEPRLWQDIMLENA 242 L SHLP +++ L + G TP+ + + RD TR+AAS+P LW I+ NA Sbjct: 189 LVSHLPQIMSSLLASRLQG------TPLHALSLAGNGLRDVTRIAASDPTLWVQILGGNA 242 Query: 243 PALLPVLDHFIADLKKL 259 ++ +L DL +L Sbjct: 243 GKVVEILYGVREDLNRL 259 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: 234 Number of extensions: 9 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: 369 Length adjustment: 28 Effective length of query: 265 Effective length of database: 341 Effective search space: 90365 Effective search space used: 90365 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: 49 (23.5 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