Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_092481496.1 BM299_RS00470 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_900115975.1:WP_092481496.1 Length = 386 Score = 165 bits (417), Expect = 2e-45 Identities = 107/283 (37%), Positives = 154/283 (54%), Gaps = 23/283 (8%) Query: 100 RVAYQGVRGAYSESAA-----EKAY-PNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSL 153 ++ Y G +G +S +AA + Y P C C D FE V + ++P+ENSL Sbjct: 11 KLGYLGPQGTFSHTAALCWARDHWYTPVC----CASLDAIFEQVADGRLAAGLVPVENSL 66 Query: 154 GGSIHRNYDLLLR-HNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLT 212 GG + DLL +++I GE+ L VR LLA GV + + +V SHPQALAQC + Sbjct: 67 GGPVGETLDLLSTVQSIYITGELMLPVRQHLLARPGVALSAIEKVYSHPQALAQCRKFIK 126 Query: 213 KLGLVREAVDDTAGAAKQIAFENLNDA-AAVASEKAAKIYGLNIVAKDIQDDCDNVTRFL 271 V+ + AA + + AAV SE AA YGL I+ ++ D+ DNVTRFL Sbjct: 127 NNMPGATVVETVSTAAAALTVAGSEEPWAAVGSESAAHAYGLEILVENSHDNPDNVTRFL 186 Query: 272 MLAREPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRAS 331 ML +E G+ KTS+V S+++ PG L++ L FALRQ+NLT+IESRP Sbjct: 187 MLGKERAFTGSPA--KTSLVLSVKDRPGALYRILREFALRQVNLTRIESRP--------- 235 Query: 332 GGLKYFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374 G K DY+F++D + +ALR ++E +L++LG Y Sbjct: 236 AGRKLGDYIFFIDLAGGEDEPKVADALRSVKENTLWLKILGCY 278 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: 306 Number of extensions: 17 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: 386 Length adjustment: 30 Effective length of query: 351 Effective length of database: 356 Effective search space: 124956 Effective search space used: 124956 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: 50 (23.9 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