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 Synpcc7942_0881 Synpcc7942_0881 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >FitnessBrowser__SynE:Synpcc7942_0881 Length = 291 Score = 140 bits (353), Expect = 4e-38 Identities = 97/273 (35%), Positives = 147/273 (53%), Gaps = 12/273 (4%) Query: 97 VAYLGPEGTFSQAAALKHFG-----HSVISKPMA--AIDEVFREVVAGAVNFGVVPVENS 149 +A+LGP GT+++ AAL+ S+ +A +I + + GAV++ VVPVENS Sbjct: 6 IAHLGPVGTYAEMAALRFQAWLTQQDQQPSRLLACRSIPATLQTLADGAVDYAVVPVENS 65 Query: 150 TEGAVNHTLDSFLE-HDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWL 208 EG+V TLDS + + I + L I H L+ E+ +T I ++ SH Q+LAQC++WL Sbjct: 66 VEGSVAATLDSLWQLPQLSIQRALILPIAHALISFESDRT-AIRQVLSHPQALAQCQQWL 124 Query: 209 DAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFL 268 H P E + +S +A + ++ A IA AA+LY + + I D P N TRF Sbjct: 125 QRHLPQAELIPANSTTEALQDLERHPQRAVIASTRAAELYQMPIQSFPINDSPDNRTRFW 184 Query: 269 IIGSQEVPPTGDDKTSIIVSM-RNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVF 327 +I P G TS+ S+ N PGAL + L I+L+RIE+RP++ Y+F Sbjct: 185 VISRSPTP--GGACTSLNFSLDANVPGALVKPLQILADRRINLSRIESRPTKRSLGEYLF 242 Query: 328 FIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 F+D +DP I ++ + L+VLGSY Sbjct: 243 FLDLEADLRDPAIAAAVQAVADCTEQLRVLGSY 275 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: 235 Number of extensions: 13 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: 291 Length adjustment: 28 Effective length of query: 337 Effective length of database: 263 Effective search space: 88631 Effective search space used: 88631 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