Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_043459303.1 H537_RS0119370 amino-acid N-acetyltransferase
Query= curated2:Q67KD3 (293 letters) >NCBI__GCF_000430725.1:WP_043459303.1 Length = 449 Score = 136 bits (343), Expect = 8e-37 Identities = 91/280 (32%), Positives = 145/280 (51%), Gaps = 7/280 (2%) Query: 17 PYIREFSGKTVVIKYGGAAMAAADLKAAVMQDIALMKYVGMHPIVVHGGGPEVSELARRM 76 PYI + GKT VI G A+AA L V QD++++ +G+ ++VHG P+V+E Sbjct: 21 PYIHAYHGKTFVIGLAGEAIAAGKLNQFV-QDLSILHAMGIKLVLVHGFRPQVNEQLAAK 79 Query: 77 GIEPQFVDGLRVTDAATMEIAQMVLVGKTNREIVTHLCAQGVKAVGLSGQDAGLIRAARH 136 G +F G+R+TD ++ AQ G+ EI +QG+ ++ ++ Sbjct: 80 GHASRFSHGMRITDEVALDCAQEA-AGQLRFEIEAAF-SQGLPNTPMANATVRVVSGNFL 137 Query: 137 LHRSRETGEMVDLGFVGDVAAVDTEVLTTLTTAGYVPVIAPIGVGPGGQPYNINADTVAG 196 R + VD G V VD + + + +++P G P G+ +N+ + VA Sbjct: 138 TARPVGIVDGVDFMHSGFVRKVDAAAIRRTIDSETLVLLSPFGFSPTGEAFNLAMEEVAT 197 Query: 197 AIAAAMKAEKLVLLTDVEGVRADKDDPSSL----LSRVTAQEVKSWIARGRLQGGMIPKL 252 A A A++A+KL+ LT++ G+R D +DP S LS A+ + + + R L L Sbjct: 198 ATAIALQADKLLFLTEMPGIREDLNDPESAIDTELSVAEAERLTASLPRPTLPTDTAFYL 257 Query: 253 QCCLTALEGGVNRVHIIDGRVPHSLLLEIFTDEGVGTMVV 292 Q C+ A GGV R HI+ V +LL+E+FT +G+GTMVV Sbjct: 258 QHCVRACRGGVERSHILPFSVDGALLMEVFTHDGIGTMVV 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: 252 Number of extensions: 20 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: 293 Length of database: 449 Length adjustment: 29 Effective length of query: 264 Effective length of database: 420 Effective search space: 110880 Effective search space used: 110880 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 10 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