Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_012784187.1 AFER_RS00495 prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000023265.1:WP_012784187.1 Length = 306 Score = 142 bits (359), Expect = 9e-39 Identities = 104/279 (37%), Positives = 148/279 (53%), Gaps = 13/279 (4%) Query: 100 RVAYQGVRGAYSESAAEKAYPN-CEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIH 158 RV+Y G G ++E A +++ + E V + EAV+ VD A PIEN+L G++ Sbjct: 5 RVSYLGPTGTFTEEALRRSFGDRVEPVAYPTIEDVLEAVDHGDVDLAFSPIENALEGAVL 64 Query: 159 RNYDLLL-RHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTL-TKL-G 215 D L+ R +L V E L V H LL G +++ + RVLSHPQAL+Q L T+L G Sbjct: 65 ATLDALVHRFDLLAVAEAILPVHHQLLGVVGSSLDRITRVLSHPQALSQSRGFLRTRLPG 124 Query: 216 LVREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAR 275 R AV TA AA+ +A N AA+ + AA ++ L+++A DI+DD N TRF +LA+ Sbjct: 125 ATRVAVASTAEAARTVADANDPTTAAIGTMTAAHLWHLDVLASDIEDDPRNETRFWLLAK 184 Query: 276 EPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLK 335 + T F + + PG L L+ FA R INLTK+ESR P R S G Sbjct: 185 GRLPEPTGSDRTALACFQVTDRPGSLLALLSAFAARGINLTKLESR-----PTRTSLGA- 238 Query: 336 YFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374 YLF ++ E + D +AL L ++LGS+ Sbjct: 239 ---YLFVIELEGHVTDPAVASALDDLAASGVRAKLLGSF 274 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: 233 Number of extensions: 12 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: 306 Length adjustment: 29 Effective length of query: 352 Effective length of database: 277 Effective search space: 97504 Effective search space used: 97504 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