Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate 8501012 DvMF_1749 prephenate dehydratase (RefSeq)
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__Miya:8501012 Length = 418 Score = 152 bits (385), Expect = 1e-41 Identities = 103/280 (36%), Positives = 150/280 (53%), Gaps = 19/280 (6%) Query: 100 RVAYQGVRGAYSESAAEKAYPNC-EAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIH 158 +VAY G G +S A + E +P ++ D F AV + V+P+ENSL G++ Sbjct: 144 KVAYLGPEGTFSYFAGVEFLGKAVEYMPQKDLDGVFRAVHDRQCELGVVPLENSLHGTVG 203 Query: 159 RNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTKL--GL 216 ++ DL L H + I E+ + HCLL ++ D+ V SHPQ LAQC L + G Sbjct: 204 QSLDLFLSHEVFIQSELFCRISHCLLTTE-TSLADVTTVYSHPQPLAQCGGWLRQALPGA 262 Query: 217 VREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLARE 276 D TA AA+++ E AAA+ A + GLNI+A+ I+D DN TRF+++ Sbjct: 263 RIIPADSTASAARRVGGE--KGAAAIGHRSLAALLGLNILARGIEDQPDNWTRFVVIGPA 320 Query: 277 PI-IPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLK 335 P PGT+ KTS++FS+ + PG L + L + A IN+ K+ESRPLR G K Sbjct: 321 PAGQPGTD---KTSMLFSVPDRPGALAEVLNLLAREGINMKKLESRPLR--------GEK 369 Query: 336 YFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYP 375 + Y+F+VD E + +E + L LR+LGSYP Sbjct: 370 W-KYVFFVDVECDLGNEDYGRVVHELRRLCHTLRILGSYP 408 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: 335 Number of extensions: 19 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: 418 Length adjustment: 31 Effective length of query: 350 Effective length of database: 387 Effective search space: 135450 Effective search space used: 135450 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