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_012784187.1 AFER_RS00495 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000023265.1:WP_012784187.1 Length = 306 Score = 182 bits (463), Expect = 8e-51 Identities = 108/273 (39%), Positives = 159/273 (58%), Gaps = 5/273 (1%) Query: 96 RVAYLGPEGTFSQAAALKHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVN 155 RV+YLGP GTF++ A + FG V I++V V G V+ P+EN+ EGAV Sbjct: 5 RVSYLGPTGTFTEEALRRSFGDRVEPVAYPTIEDVLEAVDHGDVDLAFSPIENALEGAVL 64 Query: 156 HTLDSFLEH-DIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPN 214 TLD+ + D++ E L +HH LL + DRITR+ SH Q+L+Q R +L P Sbjct: 65 ATLDALVHRFDLLAVAEAILPVHHQLLGVVGSSLDRITRVLSHPQALSQSRGFLRTRLPG 124 Query: 215 VERVAVSSNADAAKRVK--SEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLIIGS 272 RVAV+S A+AA+ V ++ +AAI AA L+ L LA IED P N TRF ++ Sbjct: 125 ATRVAVASTAEAARTVADANDPTTAAIGTMTAAHLWHLDVLASDIEDDPRNETRFWLLAK 184 Query: 273 QEVP-PTGDDKTSIIV-SMRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYVFFID 330 +P PTG D+T++ + ++PG+L LL F + GI+LT++E+RP+R+ Y+F I+ Sbjct: 185 GRLPEPTGSDRTALACFQVTDRPGSLLALLSAFAARGINLTKLESRPTRTSLGAYLFVIE 244 Query: 331 CMGHHQDPLIKNVLEKIGHEAVALKVLGSYPKA 363 GH DP + + L+ + V K+LGS+ A Sbjct: 245 LEGHVTDPAVASALDDLAASGVRAKLLGSFASA 277 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: 240 Number of extensions: 14 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: 306 Length adjustment: 28 Effective length of query: 337 Effective length of database: 278 Effective search space: 93686 Effective search space used: 93686 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