Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_012591514.1 MSIL_RS12860 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000021745.1:WP_012591514.1 Length = 412 Score = 276 bits (707), Expect = 6e-79 Identities = 167/409 (40%), Positives = 234/409 (57%), Gaps = 10/409 (2%) Query: 5 LTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIA 64 L +T LP I+G+ AG++ G TD+ L+ + G+ V VFT ++ +APV Sbjct: 7 LAPQTYPDLPSIEGVRFAAGAAGIRYKGRTDVMLVLMDKGTEVAGVFTKSKCPSAPVDWC 66 Query: 65 KSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILE 124 ++ L RAL++N+GNANA TG G AA+ +G +++ STGVI E Sbjct: 67 RARL-PGGKARALIVNSGNANAFTGKAGADAVKLTATIAAKALGAPKSEIFLASTGVIGE 125 Query: 125 PLPADKIIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKG 180 PL A K AL K+ +P EAA+AIMTTDT PK ++ +G V G+AKG Sbjct: 126 PLDASKFDPALEKLAAKAKPDLMFEAAKAIMTTDTYPKVSTATADLGGVE-VTICGMAKG 184 Query: 181 SGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATG- 239 +GMI P+MATML FI TDA ++ LQ M + + +FN ITVD DTST+D+ ++ ATG Sbjct: 185 AGMIAPDMATMLSFIFTDAPIAAAALQSMLSKGVEGSFNAITVDSDTSTSDTLMLFATGA 244 Query: 240 --KNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEAR 297 K I+ AD R A K L + L+LA +VRDGEGA F+ + V A + A+ Sbjct: 245 AAKRGAPRIELAADRRLASFKAALDKVLLDLAHQVVRDGEGARHFVEITVTGAASTAAAK 304 Query: 298 QAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAA 357 + A + A SPLVKTA D N G+ +AA+G A + DL+ ++ +I VA G R Sbjct: 305 RIALSIANSPLVKTAIAGEDANWGRIVAAVGKAG-EKAERDLLAIWFGEIRVAHRGRRDP 363 Query: 358 SYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 SY EA+ +M + EI + +++ G ATV+TCDL+ YV IN DYRS Sbjct: 364 SYDEAEVSKLMKEKEIKIYVEIGIGTGQATVWTCDLTKEYVEINGDYRS 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: 360 Number of extensions: 14 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: 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 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