Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_013721476.1 ALIDE2_RS04315 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000204645.1:WP_013721476.1 Length = 409 Score = 446 bits (1147), Expect = e-130 Identities = 231/410 (56%), Positives = 291/410 (70%), Gaps = 5/410 (1%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 M VNL+ A L + G+ + A+AGV+K DLT+ + G+TV VFT NRFCAAP Sbjct: 1 MPVNLSAPQAADLHPVAGVRIGVAEAGVRKANRKDLTVFLLDEGTTVAGVFTQNRFCAAP 60 Query: 61 VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTG 120 V + + HL +RA+V+NTGNANAGTG+ G A A C A A Q+G +QV+PFSTG Sbjct: 61 VQVCREHLDGGQAIRAMVVNTGNANAGTGSDGLARARATCEALAGQLGLAASQVLPFSTG 120 Query: 121 VILEPLPADKIIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATG 176 VI+EPLP ++I AALP QPA W AA IMTTDTVPKA + ++G TV TG Sbjct: 121 VIMEPLPVERITAALPAALADAQPAHWARAAEGIMTTDTVPKAFGTQVQIGGA-TVSVTG 179 Query: 177 IAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVII 236 I+KG+GMI PNMATMLGF+ATDA ++ +++ + +++A+++FN IT+DGDTSTNDSFV++ Sbjct: 180 ISKGAGMIRPNMATMLGFLATDACIAPDLVRDLVRDLAEQSFNRITIDGDTSTNDSFVLV 239 Query: 237 ATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296 AT K + + I ++ LK L +A +LAQAIVRDGEGATKFITVRVE +T E Sbjct: 240 ATHKAAHAPITSLESSEGRALKAALLQVAQQLAQAIVRDGEGATKFITVRVEGGRTAGEC 299 Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356 RQ AYA A SPLVKTAFFASDPNLG+ LAA+GYA +ADLD L+++YLDD+ VA GGR Sbjct: 300 RQVAYAIAHSPLVKTAFFASDPNLGRILAAVGYAGIADLDQTLIDLYLDDVHVAVQGGRN 359 Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 Y E GQ VM + EITVR+ L RG A TV+TCDLSH YV+INADYRS Sbjct: 360 PQYREEDGQRVMKQQEITVRVVLGRGDAQDTVWTCDLSHDYVTINADYRS 409 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: 451 Number of extensions: 13 Number of successful extensions: 3 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: 409 Length adjustment: 31 Effective length of query: 375 Effective length of database: 378 Effective search space: 141750 Effective search space used: 141750 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