Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_011382953.1 AMB_RS02625 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_000009985.1:WP_011382953.1 Length = 410 Score = 451 bits (1161), Expect = e-131 Identities = 239/413 (57%), Positives = 293/413 (70%), Gaps = 3/413 (0%) Query: 1 MSGSVSPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCP 60 M+ ++SPLAP+ F +MP + G+R+A+ A G++Y RTD+LM+ D+ + AGVFTRS Sbjct: 1 MTTAISPLAPERFPDMPVIAGIRLASHACGVRYAGRTDLLMVEMDKGTTAAGVFTRSLTA 60 Query: 61 SAPVDHCRQNLPGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLAS 120 SAPV+ CR + G ARA+VVNSGNANAFTG G + + T E+ A VGC ++EV++AS Sbjct: 61 SAPVEWCRAAVAKGSARALVVNSGNANAFTGSVGVASVKRTVESTAALVGCKDSEVYIAS 120 Query: 121 TGVIGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAIN 180 TG IG L K L + A W EAA+AIMTTDTYPK A+R+A I G V IN Sbjct: 121 TGTIGVRLPDEKITAALGDVRAKLQPGNWLEAAQAIMTTDTYPKGASRTAVIDGTTVIIN 180 Query: 181 GIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLML 240 GIAKGAGMIAPDMATMLS+V TDA + LQ LL GV+ +FN++TVDSDTSTSDTLML Sbjct: 181 GIAKGAGMIAPDMATMLSYVFTDAALPAEVLQDLLSKGVDKSFNAITVDSDTSTSDTLML 240 Query: 241 FATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAEN 300 FATG A G ++DA D RL F+A L DLL DLALQVVRDGEGA K V + V GA Sbjct: 241 FATGKA---GNKVIKDAKDKRLADFKAKLFDLLLDLALQVVRDGEGATKFVTIHVTGAAG 297 Query: 301 DAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEG 360 AA+ I +SIANSPLVKTA+AGEDANWGRVV AVGK+GE A RDRL+I G + VA +G Sbjct: 298 KKAARTIGMSIANSPLVKTAIAGEDANWGRVVAAVGKAGEKANRDRLSIRMGGVLVADKG 357 Query: 361 ERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 E Y EA A +G+ I I VD+G+G GR+TVYTCDLT Y++ING YR+ Sbjct: 358 EMAHGYDEAPVAAHFKGKDIVIEVDVGVGKGRSTVYTCDLTHAYIDINGSYRT 410 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: 423 Number of extensions: 9 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: 410 Length adjustment: 31 Effective length of query: 382 Effective length of database: 379 Effective search space: 144778 Effective search space used: 144778 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