Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_010937222.1 DET_RS07920 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000011905.1:WP_010937222.1 Length = 276 Score = 168 bits (426), Expect = 1e-46 Identities = 105/278 (37%), Positives = 157/278 (56%), Gaps = 13/278 (4%) Query: 99 VRVAYQGVRGAYSESAAEKAYP-NCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSI 157 ++++ QG RG++ + A +P + E + + FE V++ L D V+ IENSL GS Sbjct: 2 IKISIQGARGSFHDIVARHKFPGDSEIIESDTSHQVFEDVKKGLADYGVVAIENSLYGSF 61 Query: 158 HRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTK-LGL 216 NYD LL++ IVGE L V L+A GV +E + V +HP A+ Q E+ L K + Sbjct: 62 LDNYDNLLKYESKIVGETYLHVILNLIALPGVKMEQIHEVYTHPIAMIQAESFLEKHPSV 121 Query: 217 VREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLARE 276 +R DTAG+ + I +NL AAA++S +A++Y + I+AKDI+ + N TRFL++A+E Sbjct: 122 IRIEGYDTAGSVRMIKEKNLTTAAAISSNLSAQLYDMKILAKDIETEKQNYTRFLIIAKE 181 Query: 277 PIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKY 336 P P + KTS+ E G L+K L F + INL+KIESRP+ + Sbjct: 182 PKYP--PQANKTSLAIKAENNAGSLYKCLKCFYDQGINLSKIESRPVMG---------RT 230 Query: 337 FDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374 + Y FY+DFE + Q AL+ L + + VLGSY Sbjct: 231 WGYYFYLDFERGLNTPETQRALKELAKVTETIHVLGSY 268 Lambda K H 0.319 0.134 0.384 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: 246 Number of extensions: 11 Number of successful extensions: 5 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: 381 Length of database: 276 Length adjustment: 28 Effective length of query: 353 Effective length of database: 248 Effective search space: 87544 Effective search space used: 87544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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