Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_085635512.1 MGEO_RS04535 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_002115805.1:WP_085635512.1 Length = 277 Score = 127 bits (320), Expect = 3e-34 Identities = 86/274 (31%), Positives = 137/274 (50%), Gaps = 6/274 (2%) Query: 106 IAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGA 165 IAF G G+YSH A R Y + + C F D+ + V+TG+AD A++P+ENT G Sbjct: 5 IAFQGELGAYSHEACR-YKRPEMDPY---PCRTFEDVISAVQTGKADLAMLPVENTIYGR 60 Query: 166 INDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPH 225 + D++ LL + L I+ E + + LL L + +SH QC++FL+ + Sbjct: 61 VADIHRLLPESGLKIIDEAFVRVHINLLGVPGARLEDVTEAHSHVVLLPQCARFLSDHGI 120 Query: 226 WKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLAR 285 ++ AA E +++ H AAL SE G +YGL VL R + N TRF+++AR Sbjct: 121 QGRVNADNARAARE-ISERGEKHAAALASELAGEIYGLNVLARHIEDTDSNTTRFLLMAR 179 Query: 286 KAINV-SDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMFYL 344 + + TT + AL +A+ + + MT+LES + G+ FY Sbjct: 180 EGNDARRGDHGMMTTFVFQVRNIPAALYKAMGGFATNGVNMTKLESYMVDGSFTATQFYA 239 Query: 345 DIQANLESAEMQKALKELGEITRSMKVLGCYPSE 378 DI+ + + + AL+EL T + +LG YP + Sbjct: 240 DIEGHPDDPAVALALEELDYFTDMLNILGTYPRD 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: 216 Number of extensions: 11 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: 386 Length of database: 277 Length adjustment: 28 Effective length of query: 358 Effective length of database: 249 Effective search space: 89142 Effective search space used: 89142 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 Jul 26 2024. The underlying query database was built on Jul 25 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