Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_093394337.1 BM091_RS06270 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::Q9SSE7 (381 letters) >NCBI__GCF_900114975.1:WP_093394337.1 Length = 630 Score = 166 bits (420), Expect = 2e-45 Identities = 104/281 (37%), Positives = 155/281 (55%), Gaps = 21/281 (7%) Query: 100 RVAYQGVRGAYSESAAEKAYPNCEAVPCEE---FDTAFEAVERWLVDRAVLPIENSLGGS 156 ++ + GV G++S AA + + E P E+ F FE V ++P+ENSL GS Sbjct: 357 KILHAGVPGSFSHKAALQYFG--EDAPIEQVPTFRNVFENVASGKAKWGIVPLENSLTGS 414 Query: 157 IHRNYDLLLRHNLHIVGEVKLAVRHCLLANHGVNIEDLRRVLSHPQALAQCENTLT---K 213 IH NYDLL+ +L +VGE+ L + H L+ G IED++ V SHPQ QC L+ Sbjct: 415 IHANYDLLMEFDLFLVGELTLRIVHNLIGLDGAKIEDIKTVYSHPQVFEQCSEFLSGYPH 474 Query: 214 LGLVREAVDDTAGAAKQIAFENLNDAAAVASEKAAKIYGLNIVAKDIQDDCDNVTRFLML 273 LV A D+A A ++ AAA+ASE+AA+++G+ I+ I+ N TRF ++ Sbjct: 475 WDLV--ACKDSATAVLRVQERQDPSAAAIASEEAARLFGMTIIKAGIETHPLNFTRFGVI 532 Query: 274 AREPIIPGTNRLFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRKHPLRASGG 333 + E + G K+SI+FS+ PG L++ L +FA RQIN+ K+ESRP+ P Sbjct: 533 SAEKLENGPKD--KSSIIFSVSNRPGALYEVLKIFAERQINMVKLESRPVHGRP------ 584 Query: 334 LKYFDYLFYVDFEASMADEVAQNALRHLEEFATFLRVLGSY 374 ++YLFY D E + + ++ + L E F R LGSY Sbjct: 585 ---WEYLFYADLEVDLELDEYRSVIEALRERTEFFRYLGSY 622 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: 495 Number of extensions: 15 Number of successful extensions: 4 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: 630 Length adjustment: 34 Effective length of query: 347 Effective length of database: 596 Effective search space: 206812 Effective search space used: 206812 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: 52 (24.6 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