Align Cyclohexadienyl dehydrogenase; Arogenate dehydrogenase; ADH; Prephenate dehydrogenase; PDH; EC 1.3.1.43; EC 1.3.1.12 (characterized)
to candidate CCNA_02307 CCNA_02307 cyclohexadienyl dehydrogenase
Query= SwissProt::Q04983 (293 letters) >FitnessBrowser__Caulo:CCNA_02307 Length = 312 Score = 215 bits (547), Expect = 1e-60 Identities = 113/285 (39%), Positives = 172/285 (60%), Gaps = 6/285 (2%) Query: 3 VFKHIAIIGLGLIGSSAARATKAYCPDVTVSLYDKSEFVRDRARALNLGDNVTDDIQDAV 62 ++ + +IG GLIG S RA + + +++ D SE R R L + ++VT DI +AV Sbjct: 7 LYPKLTVIGCGLIGGSVIRAARQHGVVGEITVADASEAHRARVTELGIAEHVTGDIAEAV 66 Query: 63 READLVLLCVPVRAMGIVAAAMAPALKKDVIICDTGSVKVSVIKTLQ-DNLPNHIIVPSH 121 ++ADLV++ PV ++ +A + PA+K + D GS K +V + + +L +P H Sbjct: 67 KDADLVVIATPVLSVPELARVVIPAMKPGATLTDVGSTKGNVAEAFRAQDLSKIFAIPGH 126 Query: 122 PLAGTENNGPDAGFAELFQDHPVILTP----DAHTPAQAIAYIADYWEEIGGRINLMSAE 177 P+AGTE +GPDAGFAELF++ ILTP D H A A+A ++ +W G ++ LM + Sbjct: 127 PIAGTEQSGPDAGFAELFENRWTILTPFESEDDHYAA-AVAKLSAFWRAFGAQVELMDDK 185 Query: 178 HHDHVLALTSHLPHVIAYQLIGMVSGYEKKSRTPIMRYSAGSFRDATRVAASEPRLWQDI 237 HHD VLA+ SHLPH+IAY ++G + E + +++YSA FRD TR+AAS+P +W+DI Sbjct: 186 HHDLVLAVVSHLPHLIAYTIVGSAADLENVTENEVIKYSASGFRDFTRIAASDPTMWRDI 245 Query: 238 MLENAPALLPVLDHFIADLKKLRTAIASQDGDYLLEHFKESQKAR 282 + N A+L +L F DL+ + AI D D L HF ++ R Sbjct: 246 FVANKDAVLEMLGRFTEDLQAMSRAIRWGDADTLHAHFTRTRAIR 290 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: 238 Number of extensions: 13 Number of successful extensions: 3 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: 312 Length adjustment: 27 Effective length of query: 266 Effective length of database: 285 Effective search space: 75810 Effective search space used: 75810 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