Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate PfGW456L13_913 N-acetylglutamate synthase (EC 2.3.1.1)
Query= curated2:B3PG71 (301 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_913 Length = 432 Score = 115 bits (289), Expect = 1e-30 Identities = 90/290 (31%), Positives = 144/290 (49%), Gaps = 16/290 (5%) Query: 13 NVLTEALPYIQRFTGKTVVVKFGGNAMEGEALQNSFARDIVLMKLVGMNPVVVHGGGPQI 72 N L A PYI T VV G+ +E N D+VL+ +G+ V+VHG PQI Sbjct: 6 NWLRHASPYINAHRDCTFVVMLPGDGVEHPNFGN-IVHDLVLLHSLGVRLVLVHGSRPQI 64 Query: 73 GSLLEKLNIKSEFINGMRVTDSATMDVVEMVLGG---TVNKQIVSLINRNGGQAIGLTGK 129 + L + + +GMR+TD+AT++ V +G + ++ + + Q L Sbjct: 65 EARLAARGLTPHYHHGMRITDAATLECVIDAVGQLRIAIEARLSMDMASSPMQGSRLRVA 124 Query: 130 DGQLIRAKKLTVTHKTPEMLAPEILDIGHVGEVQSVNTAVIDMLINSDFIPVIAPIGVGE 189 G L+ A+ + V E +D H GEV+ V+ I+ L++ I +++P+G Sbjct: 125 SGNLVTARPIGVL---------EGVDYHHTGEVRRVDRKGINRLLDERSIVLLSPLGYSP 175 Query: 190 DGASYNINADLVAGKIAEFLRAEKLMLLTNVSGLQDKQGNVLTGLSTEQVDA-LIADGTI 248 G +N+ + VA + A L A+KL+L GL D+ G ++ L +QV A L G+ Sbjct: 176 TGEIFNLACEDVATRAAIDLGADKLLLFGADLGLIDEHGRLVRELRPQQVPAHLQRLGSN 235 Query: 249 YGGMLPKIACALDAVKGGVTSAHIIDGRVDHAVLLEIFTDAGVGTLITNK 298 Y L + A +A +GGV +HI+ D A+L E+FT G GTL+ + Sbjct: 236 YQAEL--LDAAAEACRGGVARSHIVSYAEDGALLTELFTRDGGGTLVAQE 283 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: 303 Number of extensions: 12 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: 432 Length adjustment: 29 Effective length of query: 272 Effective length of database: 403 Effective search space: 109616 Effective search space used: 109616 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