Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate AZOBR_RS20490 AZOBR_RS20490 cyclohexadienyl dehydrogenase
Query= BRENDA::J9XQS6 (287 letters) >lcl|FitnessBrowser__azobra:AZOBR_RS20490 AZOBR_RS20490 cyclohexadienyl dehydrogenase Length = 301 Score = 285 bits (730), Expect = 7e-82 Identities = 142/233 (60%), Positives = 185/233 (79%), Gaps = 2/233 (0%) Query: 43 ADIVADAGMVIVSVPIHVTEQVIGKLPPLPKDCILV-DLASVKEFVARVLAEALP-GVAV 100 A+ + A +V+++ P+ +V +L PL + ++V D+ SVK+ V R + +P GV + Sbjct: 68 AEALEGADLVVLATPVGAFAEVGEQLGPLLRPGMIVTDVGSVKQAVLRDVGPHIPDGVHL 127 Query: 101 IPAHPVAGTERSGPDSGFASLFRNRWCIITPPADADPAKLEALSALWQTLGAKVEIMDAR 160 IP HPVAGTE SGP++GFA+LF+ RWCI+TPP A+ ++ + +W+ +G+ VE+MDA Sbjct: 128 IPGHPVAGTEHSGPEAGFATLFQGRWCIVTPPPGANEGAVDKVVTMWRRIGSTVELMDAN 187 Query: 161 HHDMVLAVTSHLPHLIAYTIVGTASDLEGVTESEVIKYSAGGFRDFTRIAASDPTMWRDV 220 HHD VLA+TSHLPHLIAYTIVGTASDLE T+SEVIK+SAGGFRDFTRIAASDP MWRDV Sbjct: 188 HHDRVLAITSHLPHLIAYTIVGTASDLEDDTKSEVIKFSAGGFRDFTRIAASDPVMWRDV 247 Query: 221 FLSNRDAVLDMLQRFTEDLTALQKAIRVGDGQQLFDHFTRTRAIRRSIIELGQ 273 FL+NR+AVL++LQRFTEDLTALQ+AIR G+G+QL DHFT+TRAIRR II+ Q Sbjct: 248 FLNNREAVLEILQRFTEDLTALQRAIRWGEGEQLQDHFTKTRAIRRGIIDAKQ 300 Lambda K H 0.322 0.138 0.414 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: 300 Number of extensions: 3 Number of successful extensions: 1 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: 287 Length of database: 301 Length adjustment: 26 Effective length of query: 261 Effective length of database: 275 Effective search space: 71775 Effective search space used: 71775 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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