Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_084275314.1 B8779_RS04265 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_900176045.1:WP_084275314.1 Length = 356 Score = 237 bits (604), Expect = 4e-67 Identities = 143/359 (39%), Positives = 206/359 (57%), Gaps = 10/359 (2%) Query: 5 DQLKALRVRIDSLDERILDLISERARCAQEVARVKTASWPKAEEAVFYRPEREAWVLKHI 64 ++L+ LR IDS+D+ IL+L+++R ++V +K + A YRPERE +L + Sbjct: 3 EKLQKLREEIDSIDDAILELLNKRMEVVKKVGELKNRT-----NAPIYRPEREIAILNRL 57 Query: 65 MELNKGPLDNEEMARLFREIMSSCLALEQPLRVAYLGPEGTFSQAAALKHFGHSVISKPM 124 E N+GPL+++ + +F EI + LE+P RVAYLGPEG+F+ AA FG P Sbjct: 58 KEKNRGPLNDKAIEAIFLEIFAVSRNLERPERVAYLGPEGSFTHQAAESRFGAMSEYLPT 117 Query: 125 AAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGE 184 +I VF+ V A +GVVP+ENS +G V TLD + D+ I EV + IHH E Sbjct: 118 HSIAAVFKSVEAQRAKYGVVPIENSIDGVVGETLDLLGKSDLKIVAEVYMPIHHSFASLE 177 Query: 185 TTKTDRITRIYSHAQSLAQCRKWLDAHY-PNVERVAVSSNADAAKRVKSEWNSAAIAGDM 243 +I +IYS + QCR +L H+ +VE++ V S A AA E SAAI ++ Sbjct: 178 -EDLKKIKKIYSKDIAFGQCRNFLQEHFLEDVEQIPVESTAKAAMLAAKEPGSAAICSNI 236 Query: 244 AAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEVPPTGDDKTSIIVSMRNKPGALHELLMPF 303 AA+LY L L E IED N TRF+++ + + +G DKTSI+ ++++PGAL L F Sbjct: 237 AAKLYNLPILFENIEDVHTNMTRFIVLSNFKNQRSGFDKTSILAKLQDRPGALVRFLEDF 296 Query: 304 HSNGIDLTRIETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362 + I+LT+IE+RP+ + Y F+ID GH D KNV E +K LGSY K Sbjct: 297 DAAKINLTKIESRPAEDKDFNYWFYIDFDGHVDD---KNVQEVFAKHKKEIKWLGSYAK 352 Lambda K H 0.319 0.133 0.390 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: 293 Number of extensions: 10 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: 365 Length of database: 356 Length adjustment: 29 Effective length of query: 336 Effective length of database: 327 Effective search space: 109872 Effective search space used: 109872 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