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_084572759.1 DL86_RS06755 prephenate dehydratase
Query= SwissProt::P27603 (365 letters) >NCBI__GCF_000746085.1:WP_084572759.1 Length = 279 Score = 146 bits (369), Expect = 6e-40 Identities = 96/276 (34%), Positives = 146/276 (52%), Gaps = 11/276 (3%) Query: 96 RVAYLGPEGTFSQAAAL---KHFGHSVISKPMAAIDEVFREVVAGAVNFGVVPVENSTEG 152 R YLGPE TF++AA + G ++ P A+ V +GAV+ ++P+ENS EG Sbjct: 4 RYGYLGPEATFTEAALRSLPETAGAEYVAYPSASA--ALGAVRSGAVDAAMLPLENSVEG 61 Query: 153 AVNHTLDSFLEHD-IVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAH 211 V TL F+ D + I E L++ L+ + I ++++H+ + QCR+W Sbjct: 62 GVPATLREFVSDDPLQIVAEANLKVEFALMGNPGARVHTIKQVFTHSHAHGQCRRWQREW 121 Query: 212 YPNVERVAVSSNADAAKRVKSEWNS--AAIAGDMAAQLYGLSKLAEKIEDRPVNSTRFLI 269 P + + S A AA + AAIA +AA+ YGL LA I DR TRF++ Sbjct: 122 LPAAQFESTPSTAAAALEIAQRGGRDIAAIAAVVAAERYGLEVLASDIGDRANVVTRFVL 181 Query: 270 IGSQE--VPPTGDDKTSII-VSMRNKPGALHELLMPFHSNGIDLTRIETRPSRSGKWTYV 326 + P TG D+TSI+ ++ ++PG L +L F S + +TR+E+RPS G Y Sbjct: 182 LRRPGPLAPRTGADRTSIVAMASGDRPGWLVHVLDEFASREVPVTRVESRPSGEGLGRYH 241 Query: 327 FFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYPK 362 F IDC GH DP +++ L + A++ LGSYP+ Sbjct: 242 FLIDCEGHAVDPQVRDALVSLALHCRAVRFLGSYPR 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: 242 Number of extensions: 17 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: 279 Length adjustment: 28 Effective length of query: 337 Effective length of database: 251 Effective search space: 84587 Effective search space used: 84587 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