Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_013076224.1 BTUS_RS11390 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >NCBI__GCF_000092905.1:WP_013076224.1 Length = 289 Score = 134 bits (337), Expect = 2e-36 Identities = 88/255 (34%), Positives = 135/255 (52%), Gaps = 24/255 (9%) Query: 1 MITIKIGGSVVDDLHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTSP 58 + IK GGS + + I DI + + G+ ++VHGGGKE+T + E+LG +FV Sbjct: 24 IFVIKYGGSAMGERFTDVILDIIWLKQV-GIRPVVVHGGGKEITAMLERLGHRAQFVEG- 81 Query: 59 SGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLLI 118 R TD+ E+ MV+SG +N +V ++ A+GLSG D ++E +K Sbjct: 82 ----LRVTDEAVMEVVEMVLSGAVNPRLVAAFNQHDGGAVGLSGADGMLLEVAKK----- 132 Query: 119 VNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAAY 178 A D GY G++ VN + I+ LLD+ L PVI+P+ + E NV+ D AA Sbjct: 133 -----HHPAGDIGYVGEVVHVNTALIEGLLDRHLIPVIAPVGVDREGRRYNVNADEAAGA 187 Query: 179 VAGKVGSDKVLFITNVDGLL----MDDKVVPKLTLAEAKEI--RPKIGPGMEKKILASTE 232 VAG +G++K+ IT+V G+L +VV K+T E +++ +I GM K+ A Sbjct: 188 VAGALGAEKLFLITDVPGILRRGPKGSEVVSKITAEEIRQLVEGGEIYGGMIPKVKACLT 247 Query: 233 ALDMGVTTALIANGQ 247 AL+ G I NG+ Sbjct: 248 ALEAGAKHVHIINGE 262 Lambda K H 0.313 0.133 0.360 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: 214 Number of extensions: 14 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: 267 Length of database: 289 Length adjustment: 25 Effective length of query: 242 Effective length of database: 264 Effective search space: 63888 Effective search space used: 63888 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 47 (22.7 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