Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate Ac3H11_900 N-acetylglutamate synthase (EC 2.3.1.1)
Query= curated2:Q67KD3 (293 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_900 Length = 448 Score = 127 bits (320), Expect = 4e-34 Identities = 86/283 (30%), Positives = 145/283 (51%), Gaps = 10/283 (3%) Query: 17 PYIREFSGKTVVIKYGGAAMAAADLKAAVMQDIALMKYVGMHPIVVHGGGPEVSELARRM 76 PYI +F +T VI G A+AA L + QD+AL++ +G+ ++VHG P+V+E Sbjct: 18 PYIHKFRNQTFVIGLTGEAIAAGKLHN-IAQDLALIQAMGVKIVLVHGFRPQVNEQLAAK 76 Query: 77 GIEPQFVDGLRVTDAATMEIAQMVLVGKTNREIVTHLCAQGVKAVGLSGQDAGLIRAARH 136 G ++ G+R+TD+ ++ AQ G+ EI +QG+ ++G +I Sbjct: 77 GHAAKYSHGIRITDSVALDCAQEA-AGQLRYEIEAAF-SQGLPNTPMAGATVRVISGNFL 134 Query: 137 LHRSRETGEMVDLGFVGDVAAVDTEVLTTLTTAGYVPVIAPIGVGPGGQPYNINADTVAG 196 R + VD G V VD + G + +++P G P G+ +N++ + VA Sbjct: 135 TARPVGIVDGVDFQHSGLVRKVDVAGIRQTLDMGALVLLSPFGFSPTGEAFNLSMEEVAT 194 Query: 197 AIAAAMKAEKLVLLTDVEGVRADKDDPSS-------LLSRVTAQEVKSWIARGRLQGGMI 249 ++A ++A+KL+ LT+V+G+R +P S L AQ + + + + Sbjct: 195 SVAIELRADKLIFLTEVQGIRMSPTEPESDDNPIDTELPLAAAQALLAQLPPAQQPTDTG 254 Query: 250 PKLQCCLTALEGGVNRVHIIDGRVPHSLLLEIFTDEGVGTMVV 292 LQ C+ A + GV R HI+ V SLLLE++ +G+GTMV+ Sbjct: 255 FYLQHCVKACKAGVERSHILPFAVDGSLLLEVYVHDGIGTMVI 297 Lambda K H 0.319 0.136 0.386 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: 269 Number of extensions: 13 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: 293 Length of database: 448 Length adjustment: 29 Effective length of query: 264 Effective length of database: 419 Effective search space: 110616 Effective search space used: 110616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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