Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_012568544.1 RC1_RS16310 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_000016185.1:WP_012568544.1 Length = 290 Score = 132 bits (332), Expect = 1e-35 Identities = 86/273 (31%), Positives = 135/273 (49%), Gaps = 6/273 (2%) Query: 106 IAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGA 165 IA+ G G+ S LA R F + CA F D F V G+A A++P+EN+ +G Sbjct: 8 IAYQGAPGANSDLACRSV----FPEMEPLPCAAFEDAFAAVREGRARLAMIPVENSVAGR 63 Query: 166 INDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPH 225 + D++ LL L I+GE + HCLL L+ + V+SH Q QC +L Sbjct: 64 VADIHHLLPKGGLHIIGEHYQRVVHCLLAPKGATLAGLRQVHSHVQALGQCRGWLRERGL 123 Query: 226 WKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLAR 285 + + ++ AA + VA+ P A+ S +YGL VL + R N TRFVV+AR Sbjct: 124 APVTHADTAGAAAD-VARWNDPAQGAIASRLAAEIYGLDVLAEGIEDARHNTTRFVVMAR 182 Query: 286 K-AINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYL 344 + + P T+ + AL +AL + + +T+LES + G FY+ Sbjct: 183 EPVVPPRGSGPCVTSFVFRVRSVPAALYKALGGFATNGVNLTKLESYLVDGRFTAAQFYV 242 Query: 345 DIQANLESAEMQKALKELGEITRSMKVLGCYPS 377 +++A+ E ++ AL+EL R + +LG YP+ Sbjct: 243 EVEAHPEDRPLRLALEELAFFAREVTILGVYPA 275 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: 204 Number of extensions: 10 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: 290 Length adjustment: 28 Effective length of query: 358 Effective length of database: 262 Effective search space: 93796 Effective search space used: 93796 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: 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