Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate GFF1941 Psest_1984 chorismate mutase domain of proteobacterial P-protein, clade 2
Query= BRENDA::Q9SSE7 (381 letters) >FitnessBrowser__psRCH2:GFF1941 Length = 365 Score = 158 bits (399), Expect = 3e-43 Identities = 111/330 (33%), Positives = 169/330 (51%), Gaps = 31/330 (9%) Query: 49 VLASLRENDANGRDNSVRAMEVKKIFEDSPLLPKPLSSNQLTESVSNGSRVRVAYQGVRG 108 VL + E + DN A ++I L +PL RVAY G G Sbjct: 60 VLKHIMELNRGPLDNEEMARLFREIMSSCLALEQPL---------------RVAYLGPEG 104 Query: 109 AYSESAAEKAYPNCE-AVPCEEFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRH 167 +S++AA K + + + P D F V V+ V+P+ENS G+++ D L H Sbjct: 105 TFSQAAALKHFGHAVISTPMAAIDEVFREVVAGAVNFGVVPVENSTEGAVNHTLDSFLEH 164 Query: 168 NLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLTK--LGLVREAVDDTA 225 ++ I GEV+L + H LL + + R+ SH Q+LAQC L + R AV A Sbjct: 165 DIVICGEVELRIHHHLLVGETTKTDRITRIYSHAQSLAQCRKWLDAHYPNVERVAVSSNA 224 Query: 226 GAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLMLAREPIIPGTNRL 285 AAK++ E ++AA+A + AA++YGL +A+ I+D DN TRFL++ + + P + Sbjct: 225 DAAKRVKSE--WNSAAIAGDMAAQLYGLTKLAEKIEDRPDNSTRFLIIGSQEVPPTGDD- 281 Query: 286 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGGLKYFDYLFYVDF 345 KTSI+ S+ PG L + L F I+LT+IE+RP R SG + Y+F++DF Sbjct: 282 -KTSIIVSMRNKPGALHELLVPFHANGIDLTRIETRPSR------SG---KWTYVFFIDF 331 Query: 346 EASMADEVAQNALRHLEEFATFLRVLGSYP 375 D + ++ L + + A L+VLGSYP Sbjct: 332 LGHHQDPLIKDVLEKIGQEAVALKVLGSYP 361 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: 277 Number of extensions: 16 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: 365 Length adjustment: 30 Effective length of query: 351 Effective length of database: 335 Effective search space: 117585 Effective search space used: 117585 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