Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Dsui_1940 Dsui_1940 chorismate mutase, clade 2
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__PS:Dsui_1940 Length = 374 Score = 147 bits (371), Expect = 5e-40 Identities = 108/305 (35%), Positives = 158/305 (51%), Gaps = 23/305 (7%) Query: 83 PLSSNQLT--------ESVSNGSRVRVAYQGVRGAYSESAAEKAYPNC-EAVPCEEFDTA 133 PLSS +T +S + +A+ G G +SESA+ K + + +P D Sbjct: 79 PLSSESVTWFFREVMSACLSLEQPLGIAFLGPLGTFSESASTKHFGHAARLLPQASIDDV 138 Query: 134 FEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIED 193 F VE + V P+ENS G++ R DLLL +L I GEV L + LL +++ Sbjct: 139 FREVEAGHANYGVAPVENSTEGAVGRTLDLLLGTSLKICGEVVLRIHQHLLTK-APSLDR 197 Query: 194 LRRVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIY 251 + +V SH Q+LAQC L + + R +V A AA+ A E AAA+A E AA Y Sbjct: 198 VTKVYSHAQSLAQCHEWLNRHLPNVPRISVGSNAQAAQMAAQEE--GAAAIAGEAAADRY 255 Query: 252 GLNIVAKDIQDDCDNVTRFLMLAREPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALR 311 L +A+ I+D+ +N TRF++L R P T KTS++ S+ G L L FA Sbjct: 256 DLPRLAESIEDEPNNTTRFVVLGRHDAGPSTAGKDKTSLIMSIPNNTGALHTLLVPFADA 315 Query: 312 QINLTKIESRPLRKHPLRASGGLKYFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVL 371 ++LT++ESRP R H L ++Y+F+VD + + + AL L A +L+VL Sbjct: 316 GVSLTRLESRPAR-HTL--------WEYVFFVDVDGHRDEPRVKAALDELARRAAYLKVL 366 Query: 372 GSYPV 376 GSYPV Sbjct: 367 GSYPV 371 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: 286 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 381 Length of database: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 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