Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate WP_012469084.1 GLOV_RS04980 glutamate 5-kinase
Query= curated2:Q1AS30 (253 letters) >NCBI__GCF_000020385.1:WP_012469084.1 Length = 376 Score = 64.7 bits (156), Expect = 3e-15 Identities = 79/262 (30%), Positives = 116/262 (44%), Gaps = 28/262 (10%) Query: 1 MRTVVVKVGGA--SVAGGALEDLPGVVSGGARVAVVHGGGRQ--LTRMLDSLGVPTSFRE 56 +R VV+KVG +V GG L+ +R+ G RQ + +L S G + R+ Sbjct: 9 VRRVVIKVGSRVLTVEGGGLD-----YDAISRLCDEMAGLRQQGIEVILVSSGAVAAGRD 63 Query: 57 GLRVTDERTLEVAEMVFAGSVNKQLARGLLALGVPAAGVSGTDGPVLRVEPVPGLGRVGR 116 LR D TL + + A +V + L G+ T +L E L R Sbjct: 64 ALRSADT-TLTIPQKQAAAAVGQPLLMQAYQQACTRHGLV-TAQILLTAED---LANRNR 118 Query: 117 VVAVETRLLETLWGGGFVPVVAPLGLGPRGAYNVNADDAAAALAVALGAGELLL-LTDVD 175 + T L E L G +PV+ +D +AL +L +LLL LTD++ Sbjct: 119 FLNARTTL-EALLTAGALPVINENDSVAVAEIKFGDNDNLSALVTSLAEADLLLILTDIE 177 Query: 176 GLLR-------DDEPVPALTPA--ECERYVS---SGVASGGMAPKLRAAAEAARGGVPAR 223 GL D E +P + E ER S V +GGMA K+ AA +AAR GVP Sbjct: 178 GLYSANPASDPDAELIPLVRSITREIERMAGGSGSNVGTGGMATKVTAAKKAARFGVPTI 237 Query: 224 IINGGRRGALAGALAGGQVGTL 245 + G + G + A++G ++GTL Sbjct: 238 LAPGKQPGVITAAVSGQEIGTL 259 Lambda K H 0.317 0.138 0.395 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: 119 Number of extensions: 2 Number of successful extensions: 1 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: 253 Length of database: 376 Length adjustment: 27 Effective length of query: 226 Effective length of database: 349 Effective search space: 78874 Effective search space used: 78874 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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