Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_089322531.1 CHB58_RS02525 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >NCBI__GCF_900188395.1:WP_089322531.1 Length = 292 Score = 122 bits (306), Expect = 9e-33 Identities = 78/259 (30%), Positives = 143/259 (55%), Gaps = 15/259 (5%) Query: 2 ITIKIGGS-VVDDLHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTSP 58 + IK GG+ +VDD + A+ + + G+ ++VHGGG ++ + ++L + +F+ Sbjct: 26 VVIKYGGNAMVDDELKRSFAEDVVLLKYIGINPVIVHGGGPQIGEFLKKLDIKTRFIGG- 84 Query: 59 SGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLLI 118 R TDKET I MV+ G++NK IV+++ +G NA+GLSG D +IEA + Sbjct: 85 ----MRVTDKETMNIVEMVLVGKVNKEIVKLINSHGGNAVGLSGKDGNLIEARKIDYKKY 140 Query: 119 VNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAAY 178 ++E + ID G+ G++ +VN + + LL+ PVI+P+ + ++ E N++ D A Sbjct: 141 LSEVKATEIIDLGFVGEVEKVNPAIVFKLLESKFIPVIAPVGVGKDYEAYNINADIVAGE 200 Query: 179 VAGKVGSDKVLFITNVDGLLMDDKVVPKLTLAEAKEIRP-----KIGPGMEKKILASTEA 233 VA + ++K++ +T+++G+ DK +++ +I I GM K+ A A Sbjct: 201 VAAALKAEKLIMLTDIEGI--KDKNGDLMSVLSKDDIPQLIEDGTISGGMIPKVKACQIA 258 Query: 234 LDMGVTTALIANGQKENPI 252 L GV A I +G+ ++ + Sbjct: 259 LGGGVKKAHIIDGRVKHAV 277 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: 223 Number of extensions: 12 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: 267 Length of database: 292 Length adjustment: 26 Effective length of query: 241 Effective length of database: 266 Effective search space: 64106 Effective search space used: 64106 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