Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate H281DRAFT_00444 H281DRAFT_00444 N-acetylglutamate synthase
Query= curated2:A4J169 (287 letters) >FitnessBrowser__Burk376:H281DRAFT_00444 Length = 462 Score = 144 bits (364), Expect = 3e-39 Identities = 86/273 (31%), Positives = 151/273 (55%), Gaps = 5/273 (1%) Query: 16 PYIKKFSGKTIVIKYGGHAMLNADLKKAVMTDLVLMKFVGINPVVVHGGGPEITGMLHRL 75 PYI F KT V+ +GG +++ L A+++D+ L++ +GI V+VHG P++ + Sbjct: 39 PYIHAFRNKTFVVGFGGE-VVHQGLLNALVSDIALLQAMGIQIVLVHGSRPQVEEQMSLH 97 Query: 76 GIESQFVSGLRVTDAPTMEVVEMVLGKLNKEIVALIN-GLGGRSVG---LSGKDANLIMA 131 G+ES+F G+R+TDA +E + G++ +I A I+ GL + +S N + A Sbjct: 98 GVESEFSHGMRITDARALESAKEAAGEVRLDIEAAISQGLPNTPMAHAHISVVSGNFVTA 157 Query: 132 NKKYSNDCQDIGFVGEVTGVNPQLLQTVIQEGYIPVVSPVGISTEGETYNINADTVASAI 191 D D G V ++ ++ + + ++SP+G S GE +N+ + VASA Sbjct: 158 RPVGILDGVDFAHTGVVRKIDADSIRHSLASRKLVLLSPLGFSPTGEAFNLAMEDVASAA 217 Query: 192 ATALKADKLIILTDVEGILEDRQDKGTLISTVKMEDIPRLIERGVIQGGMIPKVECCMQA 251 A AL+ADK++ LT+ G+++ +D LI + ++D +L E G + G ++ ++A Sbjct: 218 AIALRADKIVFLTETPGLMQAGEDGTELIRELSLDDAYKLHESGEVTGDAGFYLKHSIRA 277 Query: 252 IQTGVATTHILDGRVPHSILLEVFTDKGIGTMV 284 + GVA HI+ + S+LLE+F G+GTM+ Sbjct: 278 CRGGVARAHIIPYALDGSLLLELFLHDGVGTMI 310 Lambda K H 0.318 0.138 0.387 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: 304 Number of extensions: 14 Number of successful extensions: 3 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: 287 Length of database: 462 Length adjustment: 29 Effective length of query: 258 Effective length of database: 433 Effective search space: 111714 Effective search space used: 111714 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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