Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_046010347.1 OLEAN_RS17770 amino-acid N-acetyltransferase
Query= curated2:Q0RFA8 (343 letters) >NCBI__GCF_000967895.1:WP_046010347.1 Length = 440 Score = 125 bits (314), Expect = 2e-33 Identities = 90/285 (31%), Positives = 150/285 (52%), Gaps = 19/285 (6%) Query: 50 PWLSRFQGATIVIKYGGNAMTEPALRAAFAADIVFLRYSGLRVVVVHGGGPQITAHLARL 109 P+++ +G T V+ G+A+ + A DI L G+R+V+VHG PQI L L Sbjct: 15 PYINAHRGKTFVLMLEGDAIADDNF-AHIVQDIALLNSLGVRLVIVHGARPQIDQALNVL 73 Query: 110 GVESTFVGGLRVTTPETMDVVRMVLLGQVNRDV-----VGLVND--HGPFAVGLSGEDAN 162 ++S F G LR+T ++ VR +G V D+ VGL N HG +SG N Sbjct: 74 NIKSQFHGDLRITDQAALNAVR-AAIGIVKSDIEARLSVGLPNTPMHGARIRVVSG---N 129 Query: 163 LFTARRRPAIVDGQEVDVGLVGDIVEVRAETVDALLDSGKVPVVASVARGIDGGVYNVNA 222 TA+ + ++DG VD G++ + + + LD G + +++S G ++N+ A Sbjct: 130 FVTAKPK-GVIDG--VDFQHTGEVRRIDRQAISQQLDQGNIVLLSSCGYSPSGEMFNLAA 186 Query: 223 DTAAAELAVALGATKLVVLTDVEGLYADWPTSDE----VLSELSITELEQLLPTLAAGMI 278 + A + A++L A KL+++ + EGL A SD V+S+L+ EL +++ +L+ Sbjct: 187 EDVATQTAISLTAEKLILMGESEGLPATAKESDSDSSMVISQLTTDELSRIIDSLSGEHK 246 Query: 279 PKMEACRRAVRGGVPQAHVLDGRVPHAVLLEIFTDDGIGTLITPD 323 A A++ + + H+L +V A+L E+FT +G GTLIT D Sbjct: 247 FHALAASTAIKAHINRVHLLSYKVDGALLQELFTHEGAGTLITAD 291 Lambda K H 0.318 0.135 0.387 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: 268 Number of extensions: 18 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: 343 Length of database: 440 Length adjustment: 30 Effective length of query: 313 Effective length of database: 410 Effective search space: 128330 Effective search space used: 128330 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: 50 (23.9 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