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_013643903.1 METBO_RS01520 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000191585.1:WP_013643903.1 Length = 276 Score = 181 bits (460), Expect = 2e-50 Identities = 109/267 (40%), Positives = 159/267 (59%), Gaps = 7/267 (2%) Query: 97 VAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNH 156 + + GP GTF++ AA G+ ++ +I +V V G VN GVVP+ENS EG V Sbjct: 11 IGFFGPSGTFTEQAA-SQVGNDLLG--FDSILDVLEAVKNGDVNLGVVPIENSIEGPVGV 67 Query: 157 TLDSFL-EHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNV 215 TLD + ++D+ I E+ + I H+LL+ + I +YSH Q+L+QCRK+ D+ V Sbjct: 68 TLDLMVHDYDLKIKREIIIPISHNLLINTDASIEDIKYVYSHIQALSQCRKFTDSMGVVV 127 Query: 216 ERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGSQEV 275 + S + AA+ V+ +SAAI AA++YGL A I+D N TRF+++G + Sbjct: 128 N--STPSTSAAAEMVRGRKDSAAIGTRRAAEIYGLKIAASDIQDYKNNLTRFIVLGKTDH 185 Query: 276 PPTGDDKTSIIVS-MRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVFFIDCMGH 334 TG+DKTS++ S M +KPG L+ +L F I+LT+IE+RPS+ Y+FFID GH Sbjct: 186 EFTGNDKTSVVFSLMEDKPGGLYHILELFAKLDINLTKIESRPSKEKLGNYIFFIDFDGH 245 Query: 335 HQDPLIKNVLEKIGHEAVALKVLGSYP 361 D I N+L+ I + LKVLGSYP Sbjct: 246 RTDESISNILDVIKSKVGFLKVLGSYP 272 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: 220 Number of extensions: 11 Number of successful extensions: 5 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: 276 Length adjustment: 27 Effective length of query: 338 Effective length of database: 249 Effective search space: 84162 Effective search space used: 84162 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 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