Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate 7025858 Shewana3_3007 chorismate mutase / prephenate dehydratase (RefSeq)
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__ANA3:7025858 Length = 667 Score = 162 bits (409), Expect = 3e-44 Identities = 93/283 (32%), Positives = 153/283 (54%), Gaps = 14/283 (4%) Query: 101 VAYQGVRGAYSESAAEKAYPNCEA----VPCEEFDTAFEAVERWLVDRAVLPIENSLGGS 156 +AY G RG+YS AA + + + C+ FD +AVE D LPIEN+ GS Sbjct: 107 IAYLGARGSYSYLAASRYCQRRQVEMLDLGCQSFDEIVQAVESGHADYGFLPIENTSSGS 166 Query: 157 IHRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKLGL 216 I+ YD+L +L IVGE + V HCLL G + D++ V +HPQ ++QC L++ Sbjct: 167 INEVYDVLQHTSLSIVGETTIEVSHCLLGKPGSKLSDIKTVYAHPQPISQCSRYLSQHKD 226 Query: 217 VR-EAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAR 275 +R E +A A +++ N AAA+ S + +Y L + + + N +RF+++AR Sbjct: 227 LRLEYCSSSAEAMEKVNQSADNSAAAIGSTEGGALYQLESIESGLANQKINQSRFIVVAR 286 Query: 276 EPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLK 335 + + KT+++ + + G L +AL V Q+N++K+ESRP+ P Sbjct: 287 KAVAVPEQLPAKTTLIMATGQKAGALVEALLVLKAHQLNMSKLESRPIPGTP-------- 338 Query: 336 YFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYPVDT 378 ++ +FY+D +A+++ E Q L+ LE F++VLG YP +T Sbjct: 339 -WEEMFYLDIDANISSEAMQQGLKQLERITRFIKVLGCYPCET 380 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: 416 Number of extensions: 8 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: 667 Length adjustment: 34 Effective length of query: 347 Effective length of database: 633 Effective search space: 219651 Effective search space used: 219651 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: 52 (24.6 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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