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_041456041.1 AVA_RS06500 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000204075.1:WP_041456041.1 Length = 290 Score = 149 bits (377), Expect = 7e-41 Identities = 98/280 (35%), Positives = 146/280 (52%), Gaps = 14/280 (5%) Query: 95 LRVAYLGPEGTFSQAAAL---KHFGHS----VISKPMAAIDEVFREVVAGAVNFGVVPVE 147 L VA+LGP GT+++ A + K HS +P ++I + + + G VVPVE Sbjct: 3 LSVAHLGPPGTYAEQATIFYVKWLSHSSGLEASLRPYSSIAQSLQALAQGETQLAVVPVE 62 Query: 148 NSTEGAVNHTLDSFLEHDIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKW 207 NS EG+V T+D+ + D + + H L+ D I +YSH Q+LAQC+ W Sbjct: 63 NSIEGSVTMTMDTMWQLDSLQIQSALILPIAHALISCADSLDGIKTVYSHPQALAQCQGW 122 Query: 208 LDAHYPNVERVAVSSNADAAKRVKSEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRF 267 L A PNV+ + +S +A ++++ + + AIA AA+LY L LA +I D N TRF Sbjct: 123 LRAFLPNVQLIPSNSTTEALEKLEYDLSIGAIASSRAAELYNLPILASRINDYAENCTRF 182 Query: 268 LIIGSQE------VPPTGDDKTSIIVSM-RNKPGALHELLMPFHSNGIDLTRIETRPSRS 320 +I E +P TSI S+ N PGAL + L F I+L+RIE+RP++ Sbjct: 183 WVISQAESDITHQLPLQKLTHTSIAFSVPANVPGALLKTLQVFAHLDINLSRIESRPTKR 242 Query: 321 GKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSY 360 Y+FFID P +K+ L ++ LK+ GSY Sbjct: 243 SLGEYLFFIDLEADVNTPQMKSALLELTTYTEVLKIFGSY 282 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: 213 Number of extensions: 12 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: 290 Length adjustment: 28 Effective length of query: 337 Effective length of database: 262 Effective search space: 88294 Effective search space used: 88294 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 Jul 25 2024. The underlying query database was built on Jul 25 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