Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_013257308.1 DEBA_RS02395 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000143965.1:WP_013257308.1 Length = 410 Score = 159 bits (403), Expect = 1e-43 Identities = 102/279 (36%), Positives = 148/279 (53%), Gaps = 13/279 (4%) Query: 99 VRVAYQGVRGAYSESAAEKAY-PNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSI 157 +RVA+ G +S AA + + +CE P F VER V+P+ENS G + Sbjct: 131 LRVAFLGPATTFSHQAAMRHFGSSCEFAPHRSIIDVFHEVERSHAQVGVVPVENSSEGQV 190 Query: 158 HRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKLGLV 217 DL L +L++ GE+ + L++ IE ++RV SHPQAL QC N L + + Sbjct: 191 SVTLDLFLESDLNVCGEIYARISQVLMSKEAA-IEGIQRVYSHPQALNQCRNWLARNMPM 249 Query: 218 REAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREP 277 ++ T+ AA + +AAV S AA+ GLN +A DIQD+ N TRF ++ R+ Sbjct: 250 ATLIESTSTAAAAQKAAQEDGSAAVGSILAARQGGLNALAIDIQDNPHNTTRFFVIGRQK 309 Query: 278 IIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYF 337 P N KTSI+F PG+LF AL FA INLT+IESRPL+ P + Sbjct: 310 CPPTGND--KTSILFVTHHKPGMLFSALKHFADSGINLTRIESRPLKNTP---------W 358 Query: 338 DYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYPV 376 +Y+F++D + D + + L+E L+VLGSYP+ Sbjct: 359 EYVFFIDMAGHVEDAQVRQVINTLDEETRLLKVLGSYPM 397 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: 329 Number of extensions: 14 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: 381 Length of database: 410 Length adjustment: 31 Effective length of query: 350 Effective length of database: 379 Effective search space: 132650 Effective search space used: 132650 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