Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_011386516.1 AMB_RS21090 prephenate dehydratase
Query= BRENDA::Q9SA96 (392 letters) >NCBI__GCF_000009985.1:WP_011386516.1 Length = 289 Score = 166 bits (420), Expect = 8e-46 Identities = 106/280 (37%), Positives = 146/280 (52%), Gaps = 14/280 (5%) Query: 108 ISFQGIPGAYSETAALKAFPNCETVPCEQFEAAFQAVELWLVDKAVLPIENSVGGSIHRN 167 I+FQG PGAYS A A+P + +PC FE F AV A++PI+NSV G + Sbjct: 11 IAFQGEPGAYSHLACRNAYPGMQPLPCATFEDTFAAVREGRARYAMIPIDNSVAGRVADV 70 Query: 168 YDLLLRHRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVNSLNNLGIQRIS 227 + L+ LHI+ E ++H LL VPG + IK V SH AL QC N + LG++ I Sbjct: 71 HHLMPYAGLHIIAEHFERISHHLLVVPGATLDTIKTVKSHVHALGQCRNLIRELGLKVIV 130 Query: 228 AKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNVTRFLILAREPMIP 287 DTA AA ++ + AIAS AA YGL L I+D +N TRF++LARE + P Sbjct: 131 GTDTAGAAAELAERQDPTMAAIASELAAEAYGLVSLKAGIEDAEHNTTRFVVLAREALEP 190 Query: 288 RTDRPYKTSIVFSLEEGPGVLFKALAVFALRSINLSKIESRPQRRRPLRVVDGSNNGSAK 347 ++P T+ VF + L+KAL FA IN++++ES +V G + Sbjct: 191 NPNQPCVTTFVFRVRNVAAALYKALGGFATNGINMTRLES--------YMVGG------E 236 Query: 348 YFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYP 387 + FY D E + AL L F+ +RILG YP Sbjct: 237 FAATQFYADVEGHPTQRNLRLALEELDFFSHEVRILGVYP 276 Lambda K H 0.321 0.135 0.402 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: 244 Number of extensions: 10 Number of successful extensions: 2 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: 392 Length of database: 289 Length adjustment: 28 Effective length of query: 364 Effective length of database: 261 Effective search space: 95004 Effective search space used: 95004 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 (21.9 bits) S2: 49 (23.5 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