Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_019555795.1 F612_RS0100585 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000381085.1:WP_019555795.1 Length = 403 Score = 388 bits (997), Expect = e-112 Identities = 206/395 (52%), Positives = 268/395 (67%), Gaps = 6/395 (1%) Query: 16 IDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDEDGVR 75 + G+ L + A +KK G+ DL ++ + G+ A FT N FCAAPV +AK HL R Sbjct: 11 VAGVYLGSCAAKIKKNGNPDLVIMELTEGALTVASFTLNAFCAAPVTLAKEHL-KSHSPR 69 Query: 76 ALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKIIAAL 135 AL+IN+GNANAGTGAQG DA CA A ++GC P QV+PFSTGVI + LP +K+ + Sbjct: 70 ALLINSGNANAGTGAQGMADARQSCAWVAAELGCLPEQVLPFSTGVIGQNLPMEKLHEGI 129 Query: 136 PK----MQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHPNMATM 191 P+ + W EA + IMTTD VPKA SRE KV D H+V TGI+KGSGMIHPNMATM Sbjct: 130 PQALANLSITGWEEACKGIMTTDLVPKAISREVKV-DGHSVMITGISKGSGMIHPNMATM 188 Query: 192 LGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEIDNIAD 251 LGF+ATDAK++Q LQ + + +FN ITVDGDTSTND+ + AT K ID + Sbjct: 189 LGFVATDAKINQACLQQALTDSVNLSFNRITVDGDTSTNDACTLTATQKADMPTIDEVNS 248 Query: 252 PRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARSPLVKT 311 YA + + +ELAQ I+RDGEGATKF+TV VE K+ +E + A+A A SPLVKT Sbjct: 249 NAYADFSNAINDVMIELAQMIIRDGEGATKFVTVAVEGGKSTEECLKVAHAVALSPLVKT 308 Query: 312 AFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQAVMSKD 371 A FASDPN G+ LAA+G + V LD + +++YL D+ + E+GG+A SYTE GQAVM++ Sbjct: 309 ALFASDPNWGRILAAVGRSGVDKLDVNTLKIYLGDVCIVENGGKALSYTEEAGQAVMNET 368 Query: 372 EITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 +IT+ I+L+RG TV+T D S+ YV INA+YRS Sbjct: 369 DITILIQLNRGSVNETVWTTDFSYDYVKINAEYRS 403 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: 384 Number of extensions: 15 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: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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