Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_011426969.1 RHE_RS19265 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000092045.1:WP_011426969.1 Length = 413 Score = 291 bits (744), Expect = 3e-83 Identities = 166/409 (40%), Positives = 244/409 (59%), Gaps = 10/409 (2%) Query: 5 LTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIA 64 L K+ +P + G+ + TA AG+K TD+ ++ ++V VFT ++ +APV Sbjct: 8 LAPKSFVPMPSLRGVRMATASAGIKYKNRTDVLMMVFDKPASVAGVFTRSKCPSAPVDFC 67 Query: 65 KSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILE 124 +++L RA+V+N+GNANA TG +GR +AA +GC N++ STGVI E Sbjct: 68 RANL-PHGTARAVVVNSGNANAFTGMKGRQATALTAKSAAAAVGCGENEIYLASTGVIGE 126 Query: 125 PLPADKIIAALPKMQPA----FWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKG 180 PL A K L +MQ FW EAA+AIMTTDT PK ++R ++G V GIAKG Sbjct: 127 PLDATKFAGVLDRMQAEATGDFWFEAAKAIMTTDTYPKVSTRSAEIGGV-AVTINGIAKG 185 Query: 181 SGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATG- 239 +GMI P+MATML F+ TDA ++ LQ++ + TFN++TVD DTST+D+ ++ ATG Sbjct: 186 AGMIAPDMATMLSFVVTDADIASEALQVLLSDGVGPTFNSMTVDSDTSTSDTLMLFATGA 245 Query: 240 --KNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEAR 297 ++ Q+ I+ DPR A + L + +L+ +VRDGEGATK + + V A++ A+ Sbjct: 246 AAEDGQARIERADDPRLAAFRAALNEVLKDLSLQVVRDGEGATKMLEITVTGAESDAAAK 305 Query: 298 QAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAA 357 + A + A SPLVKTA D N G+ + A+G + D D + ++ DI VA +G R Sbjct: 306 RIALSIANSPLVKTAAAGEDANWGRIVMAVGKSGEM-ADRDRLAIWFGDIRVAVNGERDP 364 Query: 358 SYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 Y+EA VM +I V++ + G +ATV+TCDL+ YV+IN DYRS Sbjct: 365 DYSEAAASNVMKAQDIPVKVDIGLGTGSATVWTCDLTKEYVAINGDYRS 413 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: 350 Number of extensions: 11 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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