Align Acetylglutamate kinase; EC 2.7.2.8; N-acetyl-L-glutamate 5-phosphotransferase; NAG kinase; NAGK (uncharacterized)
to candidate GFF3372 HP15_3314 N-acetyllutamate synthase
Query= curated2:Q3MFQ8 (297 letters) >FitnessBrowser__Marino:GFF3372 Length = 435 Score = 134 bits (337), Expect = 4e-36 Identities = 95/285 (33%), Positives = 149/285 (52%), Gaps = 24/285 (8%) Query: 25 PYIQQFAGRTVVVKYGGAAMKDSHLKDQVIRDIVFLSCVGLRPILVHGGGPEINSWLDKL 84 PYI GRTVV+ G A++ + + +I DI LS +G+R ++ G P+I + LD Sbjct: 15 PYINAHRGRTVVLTIPGDAIEHGNFIN-IIHDIALLSSLGVRLVVAFGARPQIQTRLDAA 73 Query: 85 GIEAQFKNGLRVTDAPTMDVVEMVLVGRVNKEIVSLINQAGGLAVGLCGKD--------- 135 GIE+ F GLR+T + +V M VG + + S L++GL Sbjct: 74 GIESSFSKGLRITPQEHLSMV-MEAVGGLRAYLES------HLSMGLVNSPMHNARIRVS 126 Query: 136 -GNLITARPQGQ-EGIGF--VGEVSNVNIKILETLASNGYIPVVSSVAADDSGQAYNINA 191 GN + A+P G +GI F G+V V++ +E L G+I ++ + +G A+N++ Sbjct: 127 GGNYVAAKPVGVLDGIDFGHTGKVRRVDVAGIEKLLELGHIVLLPPMGYSPTGDAFNLSY 186 Query: 192 DTVAGEIAAALGAEKLILLTDTRGILKDYKDPGTLIPKVDIREARELINGGVVSGGMIPK 251 + V ++AAAL AEKL++ D G+ ++ GTLI ++ R+A E + G V+G Sbjct: 187 EDVGSQVAAALQAEKLMVFIDDPGL---QEEDGTLIRELSARQASERLAAGAVTGHDADL 243 Query: 252 VTCCVRSLAQGVRAAHIIDGRIPHALLLEIFTDVGIGTMILGSQY 296 + + +GVR AHII ALL E+FT G GT++ G Y Sbjct: 244 LRAACDACVKGVRRAHIISYVDDGALLKELFTRDGAGTLVSGDHY 288 Lambda K H 0.320 0.139 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: 306 Number of extensions: 18 Number of successful extensions: 4 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: 297 Length of database: 435 Length adjustment: 29 Effective length of query: 268 Effective length of database: 406 Effective search space: 108808 Effective search space used: 108808 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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