Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_028489948.1 Q394_RS0114840 amino-acid N-acetyltransferase
Query= curated2:B8D1G8 (290 letters) >NCBI__GCF_000621325.1:WP_028489948.1 Length = 424 Score = 108 bits (271), Expect = 2e-28 Identities = 81/291 (27%), Positives = 139/291 (47%), Gaps = 24/291 (8%) Query: 1 MEELINKAQTLVEALPYIRNFYGKTFVIKYGGSTMGDKRLKEKIMEDITLLKYVGVNPVL 60 M + N L EA PYI+ KTFVI + G + ++ ++++DI + +G V+ Sbjct: 1 MNDPSNSVNLLREASPYIQQHRNKTFVIAFPGEVV-EQPTFSRLIQDIATVSALGSRIVI 59 Query: 61 IHGGGPAISEAMESMDKEARFIQGLRITDSETMSLVEMVLVG----KVNKELVSIINRLG 116 +HG I++ + + + A +R+T + + LVE VG K+ L +N+ G Sbjct: 60 VHGTRAQINQRLAAAGRVAHIHHNIRVTHPDDIPLVEEA-VGYLRIKIESLLSHALNQPG 118 Query: 117 GEAVGICGKDGGLIEADKLIFEDKSIDLGHVGSVKKINPEIVLNLIKGGYIPVISPVGSS 176 E I G I A L D +D GH G +++I + + I ++SP+G S Sbjct: 119 LENASIGVSSGNYITAQPLGIID-GVDYGHTGKIRRIAHRFIQQQLDSHNIVLMSPIGYS 177 Query: 177 KEGDTYNINADTVAGKLAVSLKAEKLIFLTDVDGVWSDPSNEKTRVSSLTVNEVKSWIGE 236 G+TYNI+ + VA A +L A+K+IF++D N+ +T ++ + Sbjct: 178 PSGETYNIDYEHVALSTAKALNADKIIFISD---------NDAQLPHEITAGQIDA---- 224 Query: 237 GKIKGGMVPKVEACIEAVTCGVN-RTHILNGLIPHALLLEIFTDRGIGTMI 286 P ++ + G + R H+LN ALLLE++T G+G++I Sbjct: 225 ---DANASPFLKKIARILLDGDSERVHLLNAATDGALLLEVYTRDGVGSLI 272 Lambda K H 0.316 0.138 0.389 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: 253 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 290 Length of database: 424 Length adjustment: 29 Effective length of query: 261 Effective length of database: 395 Effective search space: 103095 Effective search space used: 103095 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 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