Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_019556286.1 F612_RS0103095 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000381085.1:WP_019556286.1 Length = 363 Score = 140 bits (352), Expect = 7e-38 Identities = 92/281 (32%), Positives = 152/281 (54%), Gaps = 21/281 (7%) Query: 101 VAYQGVRGAYSESAAEKAY-PNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIHR 159 VAY G G+YS ++ K + + ++ + FEAVE+ ++P+ENS G + Sbjct: 96 VAYLGPEGSYSHASVIKQFGSSVHSIAVSTIEEVFEAVEKGDASYGMVPVENSSEGVVKS 155 Query: 160 NYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCE----NTLTKLG 215 + L+ +L + GEV L + HCLL+ +E++ ++++H QAL QCE N L Sbjct: 156 TQNALVTTDLKVSGEVALEIHHCLLSK-SKTVENIHKIVAHQQALGQCEQWIKNNLPWAE 214 Query: 216 LVREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAR 275 + EAV A AAK ++ AA+ASE+AA++Y LNI+ I+D DN T+F ++ R Sbjct: 215 I--EAVASNALAAKMAKTDSA--VAAIASEQAAQLYQLNILESHIEDQSDNSTKFWVVGR 270 Query: 276 EPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLK 335 + ++ KT+++ S++ G L L+ F+ R IN+T+I SRP Sbjct: 271 D--ATQSSGEDKTAMIVSMKNQSGALLDILSCFSSRGINMTRIISRPSLD---------T 319 Query: 336 YFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYPV 376 +DY F++D DE + AL ++ + F ++LGS+PV Sbjct: 320 TWDYQFFIDVMGHQEDENLKQALAEVKSKSAFFKLLGSFPV 360 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: 249 Number of extensions: 13 Number of successful extensions: 6 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: 363 Length adjustment: 30 Effective length of query: 351 Effective length of database: 333 Effective search space: 116883 Effective search space used: 116883 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: 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