Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_011382953.1 AMB_RS02625 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000009985.1:WP_011382953.1 Length = 410 Score = 288 bits (737), Expect = 2e-82 Identities = 174/413 (42%), Positives = 237/413 (57%), Gaps = 10/413 (2%) Query: 1 MAVNLTEKTAEQLPD---IDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFC 57 M ++ E+ PD I GI L + GV+ G TDL ++ + G+T VFT + Sbjct: 1 MTTAISPLAPERFPDMPVIAGIRLASHACGVRYAGRTDLLMVEMDKGTTAAGVFTRSLTA 60 Query: 58 AAPVHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPF 117 +APV ++ + + RALV+N+GNANA TG+ G + A +GCK ++V Sbjct: 61 SAPVEWCRAAVA-KGSARALVVNSGNANAFTGSVGVASVKRTVESTAALVGCKDSEVYIA 119 Query: 118 STGVILEPLPADKIIAAL----PKMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVR 173 STG I LP +KI AAL K+QP W EAA+AIMTTDT PK ASR + D TV Sbjct: 120 STGTIGVRLPDEKITAALGDVRAKLQPGNWLEAAQAIMTTDTYPKGASRTAVI-DGTTVI 178 Query: 174 ATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSF 233 GIAKG+GMI P+MATML ++ TDA + VLQ + + D++FN ITVD DTST+D+ Sbjct: 179 INGIAKGAGMIAPDMATMLSYVFTDAALPAEVLQDLLSKGVDKSFNAITVDSDTSTSDTL 238 Query: 234 VIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTC 293 ++ ATGK I + D R A K L L L+LA +VRDGEGATKF+T+ V A Sbjct: 239 MLFATGKAGNKVIKDAKDKRLADFKAKLFDLLLDLALQVVRDGEGATKFVTIHVTGAAGK 298 Query: 294 DEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHG 353 AR + A SPLVKTA D N G+ +AA+G A + D + + + +LVA+ G Sbjct: 299 KAARTIGMSIANSPLVKTAIAGEDANWGRVVAAVGKAG-EKANRDRLSIRMGGVLVADKG 357 Query: 354 GRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 A Y EA A +I + + + G+ +TVYTCDL+H Y+ IN YR+ Sbjct: 358 EMAHGYDEAPVAAHFKGKDIVIEVDVGVGKGRSTVYTCDLTHAYIDINGSYRT 410 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: 364 Number of extensions: 18 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: 410 Length adjustment: 31 Effective length of query: 375 Effective length of database: 379 Effective search space: 142125 Effective search space used: 142125 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 09 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