Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_041098943.1 SUTH_RS09880 chorismate mutase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_000828635.1:WP_041098943.1 Length = 360 Score = 165 bits (418), Expect = 2e-45 Identities = 108/278 (38%), Positives = 155/278 (55%), Gaps = 14/278 (5%) Query: 101 VAYQGVRGAYSESAAEKAYPNCEAV-PCEEFDTAFEAVERWLVDRAVLPIENSLGGSIHR 159 +AY G G YSESAA K + + PC D F +E V+PIENS G+I R Sbjct: 90 IAYLGPAGTYSESAARKHFGGAPTLLPCPAIDDVFRVIESGNAHYGVVPIENSTEGAIGR 149 Query: 160 NYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTK-LGLV- 217 + DLLL L I GE+ L + H L+ + D+ R+ SH Q+LAQC L + L LV Sbjct: 150 SLDLLLSSPLQICGEINLPIHHNLM-TRCATLADVTRIYSHAQSLAQCHEWLNRNLPLVP 208 Query: 218 REAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREP 277 R V A AA+ A E AAAVA + AA++Y L I+A I+DD +N TRF+++A Sbjct: 209 RVPVASNAEAARLAAGE--AGAAAVAGDAAAELYALPIIAASIEDDPNNTTRFVIVAEHD 266 Query: 278 IIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYF 337 G + +TS+V S + PG +++ LA FA ++++++ESR P R GG ++ Sbjct: 267 --AGVSGSDRTSLVCSAQNRPGAVYQLLAPFADNGVSMSRLESR-----PARGFGGSRW- 318 Query: 338 DYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSYP 375 +Y+FY+D E ++ AL L A F++ LGSYP Sbjct: 319 EYVFYIDIEGHRSEPAVARALEELRHRAGFVKELGSYP 356 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: 309 Number of extensions: 20 Number of successful extensions: 6 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: 360 Length adjustment: 30 Effective length of query: 351 Effective length of database: 330 Effective search space: 115830 Effective search space used: 115830 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 10 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