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_083818547.1 PYRFU_RS06195 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000223395.1:WP_083818547.1 Length = 324 Score = 175 bits (443), Expect = 2e-48 Identities = 101/266 (37%), Positives = 150/266 (56%), Gaps = 3/266 (1%) Query: 96 RVAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVN 155 RV++LGP G+FS A FG + P +I +V G V++ VVP ENS EG V Sbjct: 58 RVSFLGPRGSFSHEAVRAVFGGAAREMPAHSISAAVTMLVEGVVDYAVVPYENSIEGPVG 117 Query: 156 HTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNV 215 TL + E V+ E +H +LV + ++Y H +L + R WL+ + P+ Sbjct: 118 ETLRALAESADVVRVWAEY-VHPIVLVLAARSDGEVRKVYGHPHALGEARDWLERNLPHA 176 Query: 216 ERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEV 275 E + V+S + AA+ E +AA+ +AA+LYGL +AE + RP N TRFL++ ++ Sbjct: 177 ELIPVASTSKAAEMAAREDGAAAVCSRLAAELYGLRIVAEGLATRP-NFTRFLVLHHRDN 235 Query: 276 PPTGDDKTSIIVSMRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGHH 335 P TG KTSI+ ++R++PG+L+ LL F I+LT I + P W+Y FFID G Sbjct: 236 PETGS-KTSIVAAVRHEPGSLYRLLEVFAERRINLTMIYSYPVPGSPWSYYFFIDMEGSR 294 Query: 336 QDPLIKNVLEKIGHEAVALKVLGSYP 361 +D I+ LE+ A+ L+VLGSYP Sbjct: 295 RDEKIREALEEAEKRALWLRVLGSYP 320 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: 286 Number of extensions: 15 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 365 Length of database: 324 Length adjustment: 29 Effective length of query: 336 Effective length of database: 295 Effective search space: 99120 Effective search space used: 99120 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