Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Ac3H11_2574 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2574 Length = 351 Score = 137 bits (344), Expect = 6e-37 Identities = 98/285 (34%), Positives = 140/285 (49%), Gaps = 19/285 (6%) Query: 100 RVAYQGVRGAYSESAAEKAYPNC-EAVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIH 158 RVA G G + E AA + + + + C FD F A V+ +ENS G + Sbjct: 80 RVAVLGPEGTFCEQAAIEFFGGAADLMYCANFDEVFHATAAGSAQYGVVGVENSTEGVVT 139 Query: 159 RNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTK--LGL 216 R+ DL L H+VGEV L VRH LL +++ + VL+HPQALAQC+ L+K Sbjct: 140 RSLDLFLHTPTHVVGEVSLLVRHNLLRTTN-SLDGIEAVLAHPQALAQCQAWLSKHLPHA 198 Query: 217 VREAVDDTAGAAKQIAFENLNDA-AAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAR 275 R V A A+ N A AA++SE+AA +GL+IV+ IQDD N TRF ++ Sbjct: 199 ERRPVSSNAEGAR---LATTNPAWAALSSERAATQFGLHIVSHAIQDDAYNRTRFAIICL 255 Query: 276 EPII--PGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGG 333 + P + TS+V S+ PG + L +++T+ ESRP R Sbjct: 256 PHTLQTPPPSGKDCTSLVVSVPNQPGAVHDLLVPLKTHGVSMTRFESRPAR--------- 306 Query: 334 LKYFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYPVDT 378 ++Y FY+D + A AL L F +VLG+YPV + Sbjct: 307 TGQWEYYFYIDLDGHPAQPHVARALEELRSLCAFYKVLGTYPVSS 351 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: 272 Number of extensions: 14 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: 351 Length adjustment: 30 Effective length of query: 351 Effective length of database: 321 Effective search space: 112671 Effective search space used: 112671 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 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