Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate WP_012569198.1 RC1_RS19550 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:Q92MG1 (307 letters) >NCBI__GCF_000016185.1:WP_012569198.1 Length = 296 Score = 365 bits (937), Expect = e-106 Identities = 182/289 (62%), Positives = 221/289 (76%), Gaps = 1/289 (0%) Query: 5 FQTIALIGIGLIGSSIARDIR-EKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAEAV 63 F +A+IG+GLIGSS+AR +R + LAG +V RS A R ELGL DR A AV Sbjct: 7 FPRVAVIGLGLIGSSLARVLRADPTLAGELVAADRSAAVCARVLELGLADRAETDPACAV 66 Query: 64 EGADLVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVPGH 123 GADLV+++VP+GA +AA I HLKPGAI+TDVGS K +VI +AP +P VHFVPGH Sbjct: 67 AGADLVILAVPIGACADLAAAIGPHLKPGAILTDVGSVKQAVIRDVAPQVPDGVHFVPGH 126 Query: 124 PIAGTEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHHDK 183 PIAGTEHSGPDAGFA LFRGRWCILTPP GTD AV ++ W GSM++ M+P HHD+ Sbjct: 127 PIAGTEHSGPDAGFADLFRGRWCILTPPPGTDPAAVEKVVELWRRAGSMIEVMEPGHHDR 186 Query: 184 VLAIVSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCLHN 243 VLAI SHLPH+IAY IVGTA DLE +SEVI++SASGFRDFTR+AASDP MWRD+ L+N Sbjct: 187 VLAITSHLPHLIAYTIVGTATDLEEHLKSEVIRFSASGFRDFTRIAASDPVMWRDIFLNN 246 Query: 244 KDAILEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIVQAGQ 292 ++A+LE++ RF+EDL +LQRAIRWG+ + L LFTRTR IRR I+ A Q Sbjct: 247 REAVLEIIQRFTEDLTALQRAIRWGEAETLEHLFTRTRDIRRGIIDARQ 295 Lambda K H 0.320 0.135 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: 330 Number of extensions: 16 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: 307 Length of database: 296 Length adjustment: 27 Effective length of query: 280 Effective length of database: 269 Effective search space: 75320 Effective search space used: 75320 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