Align P-protein; EC 4.2.1.51; EC 5.4.99.5 (characterized)
to candidate WP_003544355.1 RL_RS00750 prephenate dehydratase
Query= CharProtDB::CH_024084 (386 letters) >NCBI__GCF_000009265.1:WP_003544355.1 Length = 284 Score = 130 bits (326), Expect = 6e-35 Identities = 90/280 (32%), Positives = 134/280 (47%), Gaps = 8/280 (2%) Query: 99 INPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVVPI 158 +N + RIAF G G+ S +A+R F C F D F V+ G AD ++PI Sbjct: 1 MNIKTNRIAFQGEFGANSDMASRDM----FPTMEPLPCQTFEDAFTAVDNGDADIGMIPI 56 Query: 159 ENTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGTTDLSTINTVYSHPQPFQQCSK 218 ENT +G + D++ LL + L I+GE + I L+V I TV+SH QC K Sbjct: 57 ENTIAGRVADIHHLLPESRLHIIGEYFMPIRFQLMVLPGVTKDEIRTVHSHIHALGQCRK 116 Query: 219 FLNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAGGTLYGLQVLERIEANQRQNFT 278 + R WK T+ A + V + +AAL LYGL+++ + N T Sbjct: 117 IV-RANGWKPVIAGDTAGAAKLVQETGDRSMAALAPRLAADLYGLEIIAENVEDTENNVT 175 Query: 279 RFVVLARK---AINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTRLESRPIHG 335 RFVVL+R A S + TT + AL +AL +N+ MT+LES + G Sbjct: 176 RFVVLSRDEEWAQRNSAEEKVVTTFVFNVRNIPAALYKALGGFATNNINMTKLESYQLGG 235 Query: 336 NPWEEMFYLDIQANLESAEMQKALKELGEITRSMKVLGCY 375 FY DI+ + +++AL+EL + +++LG Y Sbjct: 236 KFVATQFYADIEGHPNDPNVRRALEELRFFSEKVRILGVY 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: 188 Number of extensions: 7 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: 284 Length adjustment: 28 Effective length of query: 358 Effective length of database: 256 Effective search space: 91648 Effective search space used: 91648 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