Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_012567821.1 RC1_RS12785 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000016185.1:WP_012567821.1 Length = 414 Score = 298 bits (764), Expect = 2e-85 Identities = 175/403 (43%), Positives = 236/403 (58%), Gaps = 11/403 (2%) Query: 12 QLPDIDGIALYTAQAGVKKPGHTDLTLIAV-AAGSTVGAVFTTNRFCAAPVHIAKSHLFD 70 QLP + G+ L + G++ D T++A+ G+TV V T + +APVH + L Sbjct: 15 QLPPVAGVRLAAGRCGIRYKTPRDETMVALFEPGTTVAGVLTRSLTASAPVHRCRRSLAG 74 Query: 71 EDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADK 130 +RALV+N GN+NA TG G A AAAAR GC P++V STGVI +P+PAD Sbjct: 75 -GSIRALVVNAGNSNAFTGKAGEAFVDATVAAAARLAGCDPSEVFTASTGVIGQPMPADL 133 Query: 131 IIAALPKMQPAF-------WNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGM 183 I LP + P W AARAIMTTDT PK A ++ D V G AKGSGM Sbjct: 134 IARHLPAIWPTLGPAQGGAWETAARAIMTTDTFPKGAFAVAEI-DGVPVTVAGFAKGSGM 192 Query: 184 IHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQ 243 I P+MATMLGF+ TDA ++ LQ + + +FN+ITVDGDTST+D+ ++ ATGK + Sbjct: 193 IAPDMATMLGFLFTDAAIAPAALQRLLARATERSFNSITVDGDTSTSDTVILAATGKAAH 252 Query: 244 SEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAA 303 + + +DPR + L ++ L+LAQ IVRDGEGATKF+T+RV A++ A++ A Sbjct: 253 APVTEASDPRLDGFRAALEAVCLDLAQQIVRDGEGATKFVTLRVTGAESHAAAKRVALTV 312 Query: 304 ARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQ 363 A SPLVKTA D N G+ +AA+G A + D + + + + + G Y EA Sbjct: 313 ANSPLVKTAVAGEDANWGRIVAAVGRAG-ERAERDRLVIAIGGVPICRDGMEVPGYDEAP 371 Query: 364 GQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 A M EI + I L GQ ATV+TCDL+HGY+ IN YRS Sbjct: 372 VAAHMKGTEIGIDIDLGVGQGEATVWTCDLTHGYIDINGSYRS 414 Lambda K H 0.317 0.130 0.367 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: 398 Number of extensions: 19 Number of successful extensions: 6 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: 406 Length of database: 414 Length adjustment: 31 Effective length of query: 375 Effective length of database: 383 Effective search space: 143625 Effective search space used: 143625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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