Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_012975120.1 AZL_RS13670 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000010725.1:WP_012975120.1 Length = 412 Score = 298 bits (762), Expect = 3e-85 Identities = 176/400 (44%), Positives = 228/400 (57%), Gaps = 9/400 (2%) Query: 13 LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72 LP I G+ + TA +G++ G DL L + G++V V T + C+APV + L + Sbjct: 16 LPPIAGVRIATANSGIRYKGRDDLLLAVLDPGTSVAGVLTRSLTCSAPVIWCRDSL-PKG 74 Query: 73 GVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKII 132 RA+V+N GNANA TG G A AAAA GC P++V STGVI PL AD I Sbjct: 75 SARAVVVNAGNANAFTGKAGDATVQATVAAAAAVAGCAPDEVYIASTGVIGIPLAADAIG 134 Query: 133 AALPKMQP------AFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186 L M P A W AARAIMTTDT PK + R K+G TV G AKGSGMI P Sbjct: 135 KCLAPMAPSLKADSAAWENAARAIMTTDTFPKGSVRTAKIGGT-TVTIAGFAKGSGMIAP 193 Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246 +MATMLGF+ TDA ++ LQ M E + TFN ITVDGDTST+D+ ++ ATGK + + Sbjct: 194 DMATMLGFVFTDAAIAATALQDMLSEFTERTFNAITVDGDTSTSDTLLLFATGKAGNAPV 253 Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306 + A+ + L L L+LA +VRDGEGATKFI + V A + A++ A S Sbjct: 254 SSADAAELAEFRAALEDLLLDLALQVVRDGEGATKFIAITVRGADSDAAAKRIGMTVANS 313 Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366 PLVKTA D N G+ +AAIG A D DL+++ + L+ G Y E A Sbjct: 314 PLVKTAVAGEDANWGRIVAAIGRAG-ERADRDLIKITVGGTLICAEGMEVPGYDETPVAA 372 Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 M E+ + I L G+ A V+TCDL+HGY+ IN +YRS Sbjct: 373 HMKGKEVDIDIDLGLGKGTAKVWTCDLTHGYIDINGNYRS 412 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: 393 Number of extensions: 17 Number of successful extensions: 5 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: 412 Length adjustment: 31 Effective length of query: 375 Effective length of database: 381 Effective search space: 142875 Effective search space used: 142875 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 Jul 25 2024. The underlying query database was built on Jul 25 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