Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_085218902.1 B9N75_RS11360 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q59280 (388 letters) >NCBI__GCF_900177405.1:WP_085218902.1 Length = 407 Score = 280 bits (715), Expect = 7e-80 Identities = 163/388 (42%), Positives = 235/388 (60%), Gaps = 10/388 (2%) Query: 6 ITAPKGFVASATTAGIKASGNPDMALVVNQ-GPEFSAAAVFTRNRVFAAPVKVSRENVA- 63 +TA +GFVA+ AG+K PDMAL+ + G AAVFT+N+ FA PV VSRE +A Sbjct: 24 VTAAEGFVAAGLHAGVKQR-RPDMALLATEDGKPVPCAAVFTQNKFFAPPVGVSRERLAA 82 Query: 64 -DGQIRAVLYNAGNANACNGLQGEKDARESVSHLAQNLGLEDSDIGVCSTGLIGELLPMD 122 G+ A++ N+GNANA G QG +DA + A LG+ D+ VCSTG+IG LPM+ Sbjct: 83 NGGRAAAIIVNSGNANAGTGAQGRRDADAMCTETAAALGIAVDDVLVCSTGIIGTHLPME 142 Query: 123 KLNAGIDQLTAEGALGDNGAAAAKAIMTTDTVDKETVVFADGWTVGGMGKGVGMMAPSLA 182 K+ I +L + ++ + AA+ I+TTD+ K+ V+ +T+GGM KG GM+AP++A Sbjct: 143 KIAPAIPKLARQRSV-EGAQDAARGILTTDSKPKQAVISGSTFTLGGMAKGCGMIAPNMA 201 Query: 183 TMLVCLTTDASVTQEMAQIALANATAVTFDTLDIDGSTSTNDTVFLLASGASGITPTQDE 242 TML LTTDA++ ++ Q LA+A+ TF+TL++DG+TSTND+ FLL SG G +E Sbjct: 202 TMLAFLTTDAALDRDTLQRVLADASDRTFNTLNVDGATSTNDSAFLLTSGRRG-PADPEE 260 Query: 243 LNDAVYAACSDIAAKLQADAEGVTKRVAVTVVGTTNNEQAINAARTVARDNLFKCAMFGS 302 DAV+ C D+ ++ DAEG+TK V +TV G ++ +A AA+ +A +NL KC+ +GS Sbjct: 261 FADAVHRLCEDLTLQMAHDAEGMTKMVRLTVSGAASDAEARAAAKAIAENNLVKCSWYGS 320 Query: 303 DPNWGRVLAAVGMADADMEPEKISVFFNGQAVCLDSTGA---PGAREVDLSGADIDVRID 359 DP WGR+LAA G A E + +V + G V G G + +I + + Sbjct: 321 DPYWGRLLAAAGSAGIGFEADSATVAYGGTIVSRGGEGVDHDAGKVAAHMQHKEIAIEVA 380 Query: 360 LGTSGEGQATVRTTDLSFSYVEINSAYS 387 LG G G+A V DL Y++ NS S Sbjct: 381 LGL-GRGRAQVIGIDLGPGYIKENSVTS 407 Lambda K H 0.313 0.128 0.357 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: 398 Number of extensions: 19 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: 388 Length of database: 407 Length adjustment: 31 Effective length of query: 357 Effective length of database: 376 Effective search space: 134232 Effective search space used: 134232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 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