Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_059152706.1 V474_RS17425 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_001046635.1:WP_059152706.1 Length = 299 Score = 122 bits (305), Expect = 2e-32 Identities = 88/273 (32%), Positives = 131/273 (47%), Gaps = 10/273 (3%) Query: 106 IAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPIENTSSGA 165 +A G G H AA +Y A + C F D + V+ G+A A++PIEN+ G Sbjct: 27 VALQGAPGCNGHRAALEYDA----DCLPLPCFSFEDALDAVKEGRAARAIIPIENSQHGR 82 Query: 166 INDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSKFLNRYPH 225 + D++ LL + LSIVGE ++I H L+ + YSHPQ Q +L Sbjct: 83 VADIHFLLPESGLSIVGEHFMSIHHALMALPGAK-GPFSAAYSHPQALGQSRHYLRERGI 141 Query: 226 WKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFTRFVVLAR 285 + Y + T+ A V +A P+ A+ + LYGL V+E + N TRFVVLAR Sbjct: 142 VPMAYAD-TAGAAALVREAGDPNSCAIAPKLAAQLYGLDVIEENVEDAADNTTRFVVLAR 200 Query: 286 KAIN---VSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHGNPWEEMF 342 + ++ + DQ PA TT + AL +AL + + MT+LES + F Sbjct: 201 EPLDPFELKDQ-PAMTTFIFEVKNIPAALYKALGGFATNGVNMTKLESYQAQASFAATTF 259 Query: 343 YLDIQANLESAEMQKALKELGEITRSMKVLGCY 375 Y DI+ A + AL+EL + ++ LG Y Sbjct: 260 YADIEGAPGEARVDMALQELAFHCKYVRPLGTY 292 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: 231 Number of extensions: 12 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: 299 Length adjustment: 28 Effective length of query: 358 Effective length of database: 271 Effective search space: 97018 Effective search space used: 97018 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 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