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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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