Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_010937222.1 DET_RS07920 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_000011905.1:WP_010937222.1 Length = 276 Score = 134 bits (337), Expect = 3e-36 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 5/276 (1%) Query: 105 RIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSG 164 +I+ G +GS+ + AR E IES + +F V+ G ADY VV IEN+ G Sbjct: 3 KISIQGARGSFHDIVARHKFPGDSE-IIESDTSH--QVFEDVKKGLADYGVVAIENSLYG 59 Query: 165 AINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYP 224 + D YD L IVGE L + L+ + I+ VY+HP Q FL ++P Sbjct: 60 SFLDNYDNLLKYESKIVGETYLHVILNLIALPGVKMEQIHEVYTHPIAMIQAESFLEKHP 119 Query: 225 HWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLA 284 T+ ++ + + AA+ S LY +++L + ++QN+TRF+++A Sbjct: 120 SVIRIEGYDTAGSVRMIKEKNLTTAAAISSNLSAQLYDMKILAKDIETEKQNYTRFLIIA 179 Query: 285 RKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYL 344 ++ KT+L + AG+L + L + + ++++ESRP+ G W FYL Sbjct: 180 KEPKYPPQA--NKTSLAIKAENNAGSLYKCLKCFYDQGINLSKIESRPVMGRTWGYYFYL 237 Query: 345 DIQANLESAEMQKALKELGEITRSMKVLGCYPSENV 380 D + L + E Q+ALKEL ++T ++ VLG Y +V Sbjct: 238 DFERGLNTPETQRALKELAKVTETIHVLGSYEQGSV 273 Lambda K H 0.318 0.132 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: 167 Number of extensions: 7 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: 386 Length of database: 276 Length adjustment: 28 Effective length of query: 358 Effective length of database: 248 Effective search space: 88784 Effective search space used: 88784 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 (21.8 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