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_012046870.1 BBTA_RS33060 prephenate dehydratase
Query= SwissProt::P57472 (385 letters) >NCBI__GCF_000015165.1:WP_012046870.1 Length = 286 Score = 134 bits (336), Expect = 4e-36 Identities = 85/275 (30%), Positives = 145/275 (52%), Gaps = 12/275 (4%) Query: 107 SFLGPKGSYSHIA---AYKYADLNFQKCITNECSTFEEVVLSVENNQSDYAVLPIENTCS 163 +F G G+ SHIA AY A+ C TFE+ + ++ + ++D ++PIEN+ + Sbjct: 8 AFQGEPGANSHIAISEAYPTAE-------AMPCPTFEDALSAISSGEADLGMIPIENSVA 60 Query: 164 GSINEVFDILKKTNLFIIGEINIFINHNLLTLKKIELNKIKTIYSHPQPFQQCSDFIKKF 223 G + ++ +L + L IIGE + I H L+ LK +L IKT+ SH QC I++ Sbjct: 61 GRVADIHHLLPASGLSIIGEWFLPIRHQLMALKGTKLADIKTVESHVHALGQCRRIIRQL 120 Query: 224 PEWKIKYTKSTADAMKKIKKYNDVTNAALGSEIGSKIYGLEILMKNLANKENNITRFILL 283 I TA + + + + D + AA+ S + ++IYGLEIL +++ ++ +N TRF++L Sbjct: 121 GVRPI-VAGDTAGSARDVSQRGDRSVAAIASRLAAEIYGLEILAEDIEDEAHNTTRFVVL 179 Query: 284 NRNPKKISKNI-PTTTTLIFTTGQEAGSLSKVLSILQEKKLIMKKLTSQKIYKNPWEEMF 342 R P+ +N P T+ +F +L K L + M KL S + N + F Sbjct: 180 AREPQWAEQNSGPLVTSFVFRVRNLPAALYKALGGFATNGVNMTKLESYMVDGNFFATQF 239 Query: 343 YIDIQVNLSSTLMQDALEKIKKITRFIKILGCYPS 377 Y D+ + + ALE++K +R ++I+G YP+ Sbjct: 240 YADVDGHPEDKGLAFALEELKFFSRELRIVGVYPA 274 Lambda K H 0.318 0.134 0.374 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: 180 Number of extensions: 6 Number of successful extensions: 3 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: 385 Length of database: 286 Length adjustment: 28 Effective length of query: 357 Effective length of database: 258 Effective search space: 92106 Effective search space used: 92106 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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