Align N-acetylglutamate synthase; N-acetylglutamate kinase (EC 2.3.1.1; EC 2.7.2.8) (characterized)
to candidate 8499536 DvMF_0306 acetylglutamate kinase (RefSeq)
Query= reanno::Dyella79:N515DRAFT_3768 (438 letters) >FitnessBrowser__Miya:8499536 Length = 320 Score = 96.3 bits (238), Expect = 1e-24 Identities = 81/276 (29%), Positives = 127/276 (46%), Gaps = 26/276 (9%) Query: 41 VVKVGGAVLRDDL--PALTSSLTFLQQVGLTPIVLHGAGPQLDEELSAAGIQKQTVNGLR 98 V+K GG ++D+ A ++ L+QVG+ P+V+HG GPQ+ L IQ Q GLR Sbjct: 41 VIKYGGHAMKDEALKKAFALNIALLKQVGINPVVVHGGGPQIGRMLEQLHIQSQFREGLR 100 Query: 99 VTSPKALAIV---------RKVFQEQNLRLVEA--LQGMDTRATS-------VPSGVFTS 140 VT + +V +++ NL V+A L G D + V G Sbjct: 101 VTDDATMDVVEMVLVGKVNKEIVNLLNLSGVKAVGLSGKDGQLIRARKMEMIVNGGNHAP 160 Query: 141 EYLDRDVYGLVGKVSSINLAPIEASLRAGSIPVIASLGETAEGQILNINADFAANELVRV 200 E +D G VG+V + + + R +PVIA +G G+ NINAD A + Sbjct: 161 EIID---LGKVGEVMRVETTLLRSLERDNFVPVIAPVGVDENGETYNINADAVAGAVAAA 217 Query: 201 LQPYKIVFLTGTGGLLDDKGRIIDSINLSTEYEHLMAQPWINGGMRVKIEQIADLL-SSL 259 L+ +++ LT G+LD + +I S+ + E L + GGM K++ + L + Sbjct: 218 LRAKRLLLLTDVAGILDKQKELIRSLT-TREAVELFTDGTLTGGMIPKVKCCLEALEEGV 276 Query: 260 PLTSSVSITQPSELAKELFTHKGSGTLVRRGEKVLR 295 V + + ELFT KG T + GE+ +R Sbjct: 277 EKAMIVDGRVENCILLELFTDKGISTEI-VGERGMR 311 Lambda K H 0.319 0.135 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: 285 Number of extensions: 14 Number of successful extensions: 2 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: 438 Length of database: 320 Length adjustment: 30 Effective length of query: 408 Effective length of database: 290 Effective search space: 118320 Effective search space used: 118320 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 (21.8 bits) S2: 50 (23.9 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