Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_013707662.1 DESAC_RS13635 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_000195295.1:WP_013707662.1 Length = 400 Score = 323 bits (827), Expect = 7e-93 Identities = 180/393 (45%), Positives = 249/393 (63%), Gaps = 3/393 (0%) Query: 21 GVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVDHCRQNLPGGIARAVV 80 G R A A IK R D+ +++ + PA+ AGVFT +K +AP+ C++ L G A+A++ Sbjct: 11 GFRAAAVEAAIKKPGRLDLALIVSEYPAAAAGVFTNNKVKAAPILLCQKRLRRGRAQAIL 70 Query: 81 VNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIGEPLDATKFAGVLDKL 140 VNSGNANA TG+ G EA +T+ ++ +G SE + ASTGVIG+PL + L L Sbjct: 71 VNSGNANACTGEAGLEAAVVTSRTISRLLGLSETLILPASTGVIGQPLPLDRMNSALPSL 130 Query: 141 AASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIAKGAGMIAPDMATMLSFV 200 AA D E A+AIMTTDT+PK + A+I G V I GIAKGAGMI PDMATML F+ Sbjct: 131 AAGLRPDGLPEVAQAIMTTDTFPKTSRVQAQINGSVVTIAGIAKGAGMIHPDMATMLVFL 190 Query: 201 VTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATGAAAGDGQAKVEDAADP 260 +TDA +AP L+A L+ G+ +FN +TVD DTST+D +++ A G A G + +E P Sbjct: 191 LTDAVVAPNTLKAALKQGLVTSFNRITVDGDTSTNDCVLVLANGIA---GHSPIEQLQSP 247 Query: 261 RLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAAKRIALSIANSPLVKTA 320 + +L ++ DLA QVVRDGEGA + +V +EGA + A A + A ++A SPLVKTA Sbjct: 248 GGEILSTSLQTVMADLAAQVVRDGEGAAHVFKVIIEGAASAADAVKGARTVALSPLVKTA 307 Query: 321 VAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGERDPAYSEAAATAVMQGETI 380 VAG DANWGR++ A+G++G DR+ I+FG +V +G A +E AA +M + Sbjct: 308 VAGNDANWGRIMAALGRAGIRLNPDRVDIFFGPHQVVRQGVATDAANEQAAHRLMADGSF 367 Query: 381 PIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 +R+ + LG+ TCDLT +YV IN DYRS Sbjct: 368 DLRIHLNLGAYTDYYLTCDLTADYVHINADYRS 400 Lambda K H 0.316 0.130 0.365 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: 363 Number of extensions: 14 Number of successful extensions: 2 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: 413 Length of database: 400 Length adjustment: 31 Effective length of query: 382 Effective length of database: 369 Effective search space: 140958 Effective search space used: 140958 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 (21.6 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