Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate GFF2973 PGA1_c30200 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >FitnessBrowser__Phaeo:GFF2973 Length = 277 Score = 119 bits (299), Expect = 8e-32 Identities = 84/277 (30%), Positives = 134/277 (48%), Gaps = 8/277 (2%) Query: 105 RIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSG 164 RIA G GSYSH A R + C F D N V +G A+ A++P+EN++ G Sbjct: 4 RIAIQGELGSYSHEACR----KERPDMDVLPCRNFEDAINAVRSGAAELAMLPVENSTYG 59 Query: 165 AINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYP 224 + D++ LL H+ L I+ E + + LL L I +SH QC++FL+ Sbjct: 60 RVADIHRLLPHSGLHIIDEAFVRVHINLLGVPGAQLEDIKEAHSHLVLLPQCARFLSENN 119 Query: 225 -HWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVL 283 H ++ ++ AA + Q H AAL SE G +YGL+VL R + N TRF+ + Sbjct: 120 IHGRVS-PDNARAARDVAEQGDKSH-AALASELAGEIYGLEVLARHIEDHGNNTTRFLTM 177 Query: 284 ARKA-INVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMF 342 +R T+ + AL +A+ + + MT+LES + G+ F Sbjct: 178 SRDPNTERRGNHGMITSFVFQVRNIPAALYKAMGGFATNGINMTKLESYMVDGSFTATQF 237 Query: 343 YLDIQANLESAEMQKALKELGEITRSMKVLGCYPSEN 379 Y DI + + ++ A+ EL T ++++LG YP+ + Sbjct: 238 YADIDGHPDDPNVRLAMDELAYFTTNIEILGVYPAND 274 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: 208 Number of extensions: 8 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 Apr 09 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