Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate 16694 b2599 fused chorismate mutase P/prephenate dehydratase (NCBI)
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__Keio:16694 Length = 386 Score = 152 bits (384), Expect = 2e-41 Identities = 98/313 (31%), Positives = 158/313 (50%), Gaps = 16/313 (5%) Query: 73 IFEDSPLLPKPLSSNQLTESVSNGSRVRVAYQGVRGAYSESAAE----KAYPNCEAVPCE 128 I EDS L + L L + N R+A+ G +G+YS AA + + C Sbjct: 80 IIEDSVLTQQALLQQHLNKI--NPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCA 137 Query: 129 EFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHNLHIVGEVKLAVRHCLLANHG 188 +F F VE D AV+PIEN+ G+I+ YDLL +L IVGE+ L + HCLL + Sbjct: 138 KFADIFNQVETGQADYAVVPIENTSSGAINDVYDLLQHTSLSIVGEMTLTIDHCLLVSGT 197 Query: 189 VNIEDLRRVLSHPQALAQCENTLTKLGLVR-EAVDDTAGAAKQIAFENLNDAAAVASEKA 247 ++ + V SHPQ QC L + + E + T+ A +++A AA+ SE Sbjct: 198 TDLSTINTVYSHPQPFQQCSKFLNRYPHWKIEYTESTSAAMEKVAQAKSPHVAALGSEAG 257 Query: 248 AKIYGLNIVAKDIQDDCDNVTRFLMLAREPIIPGTNRLFKTSIVFSLEEGPGVLFKALAV 307 +YGL ++ + + N TRF++LAR+ I KT+++ + + G L +AL V Sbjct: 258 GTLYGLQVLERIEANQRQNFTRFVVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLV 317 Query: 308 FALRQINLTKIESRPLRKHPLRASGGLKYFDYLFYVDFEASMADEVAQNALRHLEEFATF 367 + +T++ESRP+ +P ++ +FY+D +A++ Q AL+ L E Sbjct: 318 LRNHNLIMTRLESRPIHGNP---------WEEMFYLDIQANLESAEMQKALKELGEITRS 368 Query: 368 LRVLGSYPVDTTM 380 ++VLG YP + + Sbjct: 369 MKVLGCYPSENVV 381 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: 270 Number of extensions: 19 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: 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 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