Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_027457665.1 K420_RS0108410 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000519045.1:WP_027457665.1 Length = 408 Score = 444 bits (1142), Expect = e-129 Identities = 236/410 (57%), Positives = 298/410 (72%), Gaps = 6/410 (1%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 M VN A+QL + G+ L A+A ++K DLTL+A+ G TV VFT NRFCAAP Sbjct: 1 MPVNYATPAADQLLPVAGVRLGVAEAEIRKKNRRDLTLVALDGGCTVAGVFTQNRFCAAP 60 Query: 61 VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTG 120 V + ++HL +RALVINTG ANAGTG GR A A C A A +G +QV+PFSTG Sbjct: 61 VQLCRNHLATGKEIRALVINTGIANAGTGEPGRQTAQASCEAVAALLGIAADQVLPFSTG 120 Query: 121 VILEPLPADKIIAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATG 176 VILEPLP D++ A LP + W+ AA AIMTTDTV KAASR VG + T+ +G Sbjct: 121 VILEPLPVDRLKAGLPAAKADLKADNWHAAAHAIMTTDTVAKAASRRITVGGK-TITVSG 179 Query: 177 IAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVII 236 I+KG+GMI PNMATMLGF+ATDA ++Q +L + +E AD +FN ITVDGDTSTNDSFV+I Sbjct: 180 ISKGAGMIKPNMATMLGFVATDAGIAQSLLDKLVKEAADASFNCITVDGDTSTNDSFVMI 239 Query: 237 ATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296 ATG+ S + + AD + +++ + ++A+ELAQAIVRDGEGATKFIT+ V+ KT +E Sbjct: 240 ATGQ-SGAAFASEADAGWDEVRAAIVAVAVELAQAIVRDGEGATKFITIAVQGGKTVEEC 298 Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356 RQ YA SPLVKTAFFASDPNLG+ LAA+GYA +ADLD D V+++LDD+LVAE+GGRA Sbjct: 299 RQVGYAIGHSPLVKTAFFASDPNLGRILAAVGYAGIADLDVDGVKVWLDDVLVAENGGRA 358 Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 A+Y EA+G VM++ EITVR+ L RG A A+V+TCD S+ YV INADYRS Sbjct: 359 AAYQEAEGARVMAQAEITVRVDLGRGNAQASVFTCDFSYDYVKINADYRS 408 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: 444 Number of extensions: 16 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: 406 Length of database: 408 Length adjustment: 31 Effective length of query: 375 Effective length of database: 377 Effective search space: 141375 Effective search space used: 141375 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