Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Echvi_0123 Echvi_0123 Prephenate dehydratase
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__Cola:Echvi_0123 Length = 279 Score = 142 bits (357), Expect = 1e-38 Identities = 89/277 (32%), Positives = 146/277 (52%), Gaps = 12/277 (4%) Query: 100 RVAYQGVRGAYSESAAEKAY-PNCEAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIH 158 +VA QG++G+Y A + + + C F +++ D VL +ENS+ G+I Sbjct: 9 KVAIQGIKGSYHYQVALNQFGQDIHVIECLTFSDLVKSITSNDADIGVLALENSIAGAIL 68 Query: 159 RNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKLGLVR 218 NYDL+ R+NL ++GE L + H L+ G +I+D+ V SHP AL QC+ + ++ Sbjct: 69 PNYDLMDRNNLQVIGEFYLPISHQLMVLKGQSIDDITEVRSHPMALLQCKAFFEQYPQIK 128 Query: 219 EAVD-DTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREP 277 D DTA AK+I+ ++L A+A + AA+ YGL+I+A DIQ +N+TRF ++ Sbjct: 129 LIEDLDTASVAKEISEQHLQGVGAIAGKSAAEFYGLDILASDIQTIKNNITRFCIVKNAA 188 Query: 278 IIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYF 337 K SI +++ G L K L + +++LTKI+S P+ P + Sbjct: 189 DAKPVIGFDKASIKVTIKNEQGSLAKVLTTMSAYRLDLTKIQSLPVIDQP---------W 239 Query: 338 DYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374 Y F++D ++ Q AL+ L+ ++VLG Y Sbjct: 240 HYAFFIDLLFENLEDY-QQALKELKANGHQIKVLGEY 275 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: 211 Number of extensions: 15 Number of successful extensions: 2 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: 279 Length adjustment: 28 Effective length of query: 353 Effective length of database: 251 Effective search space: 88603 Effective search space used: 88603 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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