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_048102761.1 MBAR_RS10240 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000195895.1:WP_048102761.1 Length = 293 Score = 171 bits (433), Expect = 2e-47 Identities = 111/289 (38%), Positives = 161/289 (55%), Gaps = 26/289 (8%) Query: 97 VAYLGPEGTFSQAAA----LKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEG 152 + LGPEG++S+ AA L+H +V + A I++ F V+ G + +VP+ENS EG Sbjct: 3 IGVLGPEGSYSEKAAQIWTLRHRLDNVKIQYFADIEDAFLAVIQGKSDLSIVPIENSIEG 62 Query: 153 AVNHTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHY 212 +V TLD LE+ + I GE+ ++I H LL ++I + SH Q LAQCR +L ++ Sbjct: 63 SVGITLDLLLENGVEIVGEIVVKIEHCLL--SKGGPEKIKVVLSHPQGLAQCRHFLKKYF 120 Query: 213 PNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLI--- 269 P E + S + AA+ AAIA AA+ Y L L I+DR N TRF+ Sbjct: 121 PEAELRSTGSTSHAARLAGEFEEMAAIASPEAAECYRLKVLLPNIQDRKENYTRFIALQA 180 Query: 270 ---IGSQEVPPTGDDKT-------------SIIVSM-RNKPGALHELLMPFHSNGIDLTR 312 I ++V + +DKT SIIV + +++PGAL+E+L F N I+LTR Sbjct: 181 AGKISDEQVLCSTEDKTGKPENSSHSAFKTSIIVYLEKDRPGALYEILGAFAKNKINLTR 240 Query: 313 IETRPSRSGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361 IE+RPS+ Y F+ID GH D LI+ L+ I ++ LK+LGSYP Sbjct: 241 IESRPSKKELGDYYFYIDFEGHTGDALIEKTLKDIENKIDTLKILGSYP 289 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: 281 Number of extensions: 18 Number of successful extensions: 4 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: 293 Length adjustment: 28 Effective length of query: 337 Effective length of database: 265 Effective search space: 89305 Effective search space used: 89305 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