Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate HSERO_RS17320 HSERO_RS17320 amino acid acetyltransferase
Query= curated2:B3PG71 (301 letters) >FitnessBrowser__HerbieS:HSERO_RS17320 Length = 440 Score = 130 bits (328), Expect = 4e-35 Identities = 90/291 (30%), Positives = 142/291 (48%), Gaps = 7/291 (2%) Query: 6 ESAMNIANVLTEALPYIQRFTGKTVVVKFGGNAMEGEALQNSFARDIVLMKLVGMNPVVV 65 E N L PY+ F GKT VV F G + LQ A+D+ L+ +G+ VVV Sbjct: 5 EKQTEFVNWLRSVAPYVHAFRGKTFVVAFPGELVTAGDLQ-VLAQDLSLLHALGIRVVVV 63 Query: 66 HGGGPQIGSLLEKLNIKSEFINGMRVTDSATMDVVEMVLGGTVNKQIVSLINRNGGQAIG 125 HG PQ+ L N+++ F NG+RV DSA ++ + G ++ I Q + Sbjct: 64 HGSRPQVAEQLALRNVEARFHNGLRVADSAALECAKEAAG-----ELRLDIEAAFSQGLP 118 Query: 126 LTGKDGQLIRAKKLTVTHKTPEMLAPEILDIGHVGEVQSVNTAVIDMLINSDFIPVIAPI 185 T IR P M + +D+ G V+ + VI ++N+ I +++P+ Sbjct: 119 NTPMAHSAIRVISGNFVTARP-MGVIDGVDLQLTGVVRKIAADVIQPIMNAGGIVLLSPL 177 Query: 186 GVGEDGASYNINADLVAGKIAEFLRAEKLMLLTNVSGLQDKQGNVLTGLSTEQVDALIAD 245 G G ++N+ + VA A LRAEKL+ L+ + D G + LS+ Q +A+++ Sbjct: 178 GFSPTGEAFNLTMEDVAVSAAIALRAEKLIFLSETPMMTDAGGAEIRELSSHQAEAVLSA 237 Query: 246 GTIYGGMLPKIACALDAVKGGVTSAHIIDGRVDHAVLLEIFTDAGVGTLIT 296 G + +A + A GV+ AHI+ D + LLE+FT GVGT++T Sbjct: 238 GFLSPEAAFYLASVVKACNAGVSRAHIVPFATDGSALLELFTHDGVGTMVT 288 Lambda K H 0.317 0.136 0.374 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: 291 Number of extensions: 18 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: 301 Length of database: 440 Length adjustment: 29 Effective length of query: 272 Effective length of database: 411 Effective search space: 111792 Effective search space used: 111792 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: 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