Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate Dsui_1570 Dsui_1570 amino-acid N-acetyltransferase
Query= curated2:A1ATU7 (292 letters) >FitnessBrowser__PS:Dsui_1570 Length = 448 Score = 149 bits (377), Expect = 9e-41 Identities = 97/284 (34%), Positives = 152/284 (53%), Gaps = 19/284 (6%) Query: 16 PYIRRFAGKTFVIKYGGHAMSDEKLKESFALDVIMLRSLGINAVIVHGGGPQINQTLKRY 75 PY+ F GKTFV+ +GG ++S L +FA DV +L +LG+ V+VHG PQI + L+ Sbjct: 21 PYVNAFRGKTFVVAFGGKSISGP-LARTFAYDVSLLANLGVRLVLVHGSRPQIEEELQEK 79 Query: 76 GIVSQFVKGMRVTDSETMAVVEMVLVGQVNKEVVGYLNQH------GGRAVGLSGKDGTL 129 G+ S+F G R+TD++T+ V + VG V EV L+Q G + + G G Sbjct: 80 GLESRFHAGQRITDADTLDCV-IDAVGSVYLEVEALLSQGLPNTPMAGNTIRVVG--GNF 136 Query: 130 LLSKKLLQDVVGDDGTTEQVDMGYVGDVVKVNTDLLKALENGNYLPVIAPVGVGPQGESY 189 + ++ + G + VD+ Y G V K++ + LKA + +++ +G P GE + Sbjct: 137 ITARPM--------GVLDGVDLQYTGAVRKIDAEGLKAQLGLGNIVLLSNLGASPTGEIF 188 Query: 190 NINADLVAGRVAAALNAEKLILLTDIEGVKDKAGQLLSSIAVADMHRLIR-EEAITGGMI 248 N++ + VA A AL A+KLI LTD +G D G LL + +L R E ++ + Sbjct: 189 NLSMEEVAEEAAKALGADKLIFLTDSQGATDAEGNLLDELTADAAEQLARVGEWLSPDLK 248 Query: 249 PKVVCCADALEEGVKKAHIIDGRVEHAVLLEIFTDVGIGTEIQK 292 + C A GV + HII ++ AVL E+FT G+GT + + Sbjct: 249 RYLPCAVRASRRGVGRVHIIGYELDGAVLHELFTHDGVGTVVTR 292 Lambda K H 0.318 0.138 0.380 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: 337 Number of extensions: 12 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: 292 Length of database: 448 Length adjustment: 29 Effective length of query: 263 Effective length of database: 419 Effective search space: 110197 Effective search space used: 110197 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: 49 (23.5 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