Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_083509499.1 APY04_RS05140 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_001541235.1:WP_083509499.1 Length = 314 Score = 130 bits (328), Expect = 4e-35 Identities = 89/276 (32%), Positives = 135/276 (48%), Gaps = 6/276 (2%) Query: 101 PHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIEN 160 P S RIA+ G G+ SHLA R+ F C F D V+ G+A A++PIEN Sbjct: 19 PASGRIAYQGEPGANSHLACREA----FPDMEAVACPTFEDALLAVKNGEARLAMIPIEN 74 Query: 161 TSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFL 220 + +G + D++ LL L IVGE L + H L+ L ++ V SH Q QC + L Sbjct: 75 SVAGRVADIHHLLPQAELYIVGEHFLRVRHQLMAIPGASLQSVKKVLSHTQALGQCRRKL 134 Query: 221 NRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRF 280 + + T+ + V++ K +AA+ S +YGL +L ++ N TRF Sbjct: 135 IELGLKPVPEAD-TAGSARIVSEMKDAGLAAIASTLAAEIYGLDILMNDVEDEMHNTTRF 193 Query: 281 VVLARKAIN-VSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWE 339 VVLA +A + + + P TT + AL +AL + + MT+LES + G Sbjct: 194 VVLASEADDALPEDGPVITTFIFRVRNVPAALYKALGGFATNGVNMTKLESYQLEGTFNA 253 Query: 340 EMFYLDIQANLESAEMQKALKELGEITRSMKVLGCY 375 MFY DI+ + ++ AL+EL + +VLG Y Sbjct: 254 TMFYADIEGHPSDRMVRLALEELSFFSSEKRVLGTY 289 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: 207 Number of extensions: 9 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: 314 Length adjustment: 29 Effective length of query: 357 Effective length of database: 285 Effective search space: 101745 Effective search space used: 101745 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 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