Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate WP_019866296.1 METMI_RS0110740 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:D8IR44_HERSS (295 letters) >NCBI__GCF_000384075.1:WP_019866296.1 Length = 297 Score = 223 bits (568), Expect = 4e-63 Identities = 118/285 (41%), Positives = 170/285 (59%), Gaps = 2/285 (0%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRS--LQSLERARELGIIDAVATDAAS 58 MF K+ I GVGLIGGS A R A IVG GR +Q+L+ AR++G+IDA D A Sbjct: 1 MFNKLCIIGVGLIGGSIAKTARLQNLATVIVGFGREDDVQNLQTARQIGVIDAYYLDIAV 60 Query: 59 AVQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFI 118 AV ADL+++A PVA T +L + P+ + TD GSTK V+AAA+ G F+ Sbjct: 61 AVADADLVIIATPVASTADVLRLLQPYWSANTVYTDVGSTKGSVLAAAQAVFGQVPDNFV 120 Query: 119 PAHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQE 178 PAHPIAG E+ G AA+ L+ K+++IT + D + + W+ G+ + + Sbjct: 121 PAHPIAGAEQSGVLAAVDGLFANKRLIITPVETTDTEALRKIQRFWQGLGSAVSVMEATH 180 Query: 179 HDAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLA 238 HD + A+ SHLPH+LAFALVD + K + +F+YAA GF+DFTRIA+S P MW I A Sbjct: 181 HDQILAATSHLPHILAFALVDMLGHKDEQSEIFKYAAGGFKDFTRIASSDPGMWTAICEA 240 Query: 239 NRDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283 N+ +L +D ++L + ++AA D + +A A+ ARQ++ Sbjct: 241 NKQEILPLIDQLQMELAKLHDLLAADDYSQLFATFAYAKTARQRF 285 Lambda K H 0.320 0.132 0.376 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: 203 Number of extensions: 8 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: 295 Length of database: 297 Length adjustment: 26 Effective length of query: 269 Effective length of database: 271 Effective search space: 72899 Effective search space used: 72899 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 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