Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_006747000.1 THITH_RS14955 amino-acid N-acetyltransferase
Query= curated2:Q67KD3 (293 letters) >NCBI__GCF_000227685.2:WP_006747000.1 Length = 440 Score = 125 bits (313), Expect = 2e-33 Identities = 86/280 (30%), Positives = 148/280 (52%), Gaps = 11/280 (3%) Query: 15 ALPYIREFSGKTVVIKYGGAAMAAADLKAAVMQDIALMKYVGMHPIVVHGGGPEVSELAR 74 A+PYI +T+VI G A A + +++DIA ++ +G ++VHG P++ R Sbjct: 16 AVPYIVAHRDRTMVIAIAGEAAQALEFPT-LLRDIAQLQALGTRVVLVHGARPQIEARLR 74 Query: 75 RMGIEPQFVDGLRVTDAATMEIAQMVLVGKTNREIVTHLCAQGVKAVGLSGQDAGLIRAA 134 G+ P++ GLRVTDAA +E A VG+ I L ++ + G++G A L A+ Sbjct: 75 ERGLTPRYAAGLRVTDAAALE-AVCDAVGRLRLHI-EGLLSRNLGNPGIAG--ARLRVAS 130 Query: 135 RHLHRSRETG--EMVDLGFVGDVAAVDTEVLTTLTTAGYVPVIAPIGVGPGGQPYNINAD 192 + +R G E VD F G+V VD + L G + +++P+G P G+ +N++ + Sbjct: 131 GNFVTARPLGVREGVDFQFTGEVRRVDAPGIVRLLDEGQIVLLSPLGYSPTGEVFNLSGE 190 Query: 193 TVAGAIAAAMKAEKLVLLTDVEGVRADKDDPSSLLSRVTAQEVKSWIAR-GRLQGGMIPK 251 VA +A A+KA+KLV LT+ +R D +L+++T + + L + Sbjct: 191 DVATQVAVALKADKLVFLTEAGPLR---DRQREMLTQLTVSAAERLLTTDSGLPEELAAH 247 Query: 252 LQCCLTALEGGVNRVHIIDGRVPHSLLLEIFTDEGVGTMV 291 L+ + RVH++D + LL+E+F+ +G+GT+V Sbjct: 248 LRSAVDVCTVHDLRVHLVDRHIDGGLLIELFSRQGIGTLV 287 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: 272 Number of extensions: 9 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: 440 Length adjustment: 29 Effective length of query: 264 Effective length of database: 411 Effective search space: 108504 Effective search space used: 108504 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