Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_013519257.1 ALIDE2_RS13005 amino-acid N-acetyltransferase
Query= curated2:B1ZUD7 (292 letters) >NCBI__GCF_000204645.1:WP_013519257.1 Length = 448 Score = 105 bits (263), Expect = 1e-27 Identities = 86/288 (29%), Positives = 140/288 (48%), Gaps = 22/288 (7%) Query: 18 PYVQDFRGSIFVVKYGGSFMDDPDPAGRTR-VARDLAFLAAVGINVVVVHGGGKAITRAM 76 PY+ FR FVV G + AG+ + + +DLA + A+G+ +V+VHG + + Sbjct: 18 PYIHKFRHQTFVVGLTGEAI----AAGKLQSIVQDLAMIQAMGVKIVLVHGFRPQVNEQL 73 Query: 77 ESSGLKANFVNGMRQTDEATIAVVKKTLDEVVNRDVCDAIGGAGGKPKGMPGDSVLVCQK 136 + G A + +GMR TD + ++ ++ R +A G M G V V Sbjct: 74 AAKGHAARYSHGMRITDPVALDCAQEAAGQL--RYEIEAAFSQGLPNTPMAGARVRVISG 131 Query: 137 --LTTDDNG--NPVDLGYVGDVTEVKVKLIKKEIADGFIPVISPVAEGYDGKPYNVNADL 192 LT G + VD + G V +V V I++ + + +ISP G+ +N+ + Sbjct: 132 NFLTARPVGIVDGVDFQHTGLVRKVDVAGIRRSLESEAMVLISPFGFSPTGEAFNLAMEE 191 Query: 193 VAGRVASALRARRLVYMSDVPGLLANPADP----ESLISTVKVGQIDDLKKKGIIDKGMR 248 VA RVAS L+A +L+++S+VPG+ P DP + + + + Q L + + R Sbjct: 192 VATRVASELKADKLLFLSEVPGIRTRPDDPAGEDNPIDTELPLAQARQLLSR--LPAAQR 249 Query: 249 PK-----VQSAMRALQEGVQRVHFIDGRLAHSLLLEIFTDKGIGTEFV 291 P +Q +RA + GV+R H I + +LLLEI+ GIGT V Sbjct: 250 PTDAAFYLQHCVRACEHGVERSHIIPFAVDGALLLEIYVHDGIGTMVV 297 Lambda K H 0.318 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: 236 Number of extensions: 11 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: 292 Length of database: 448 Length adjustment: 29 Effective length of query: 263 Effective length of database: 419 Effective search space: 110197 Effective search space used: 110197 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 (21.7 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