Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_013537251.1 THEAM_RS02535 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000185805.1:WP_013537251.1 Length = 292 Score = 124 bits (310), Expect = 3e-33 Identities = 82/256 (32%), Positives = 136/256 (53%), Gaps = 18/256 (7%) Query: 2 IVVKAGGRTLLNN--MDEIVKSISRLE----KAVFVHGGGDLVDEWERKMGMEPQFKVSA 55 +V+K GG ++N + + ++ L+ V VHGGG + E +++ +E +F Sbjct: 26 VVIKYGGNAMVNEELKEAFAQDVALLKYVGINPVIVHGGGPQIGELLKRLNIETRF---V 82 Query: 56 SGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVIV 115 G+ R TD + + V VL G +NK+IV S+G AVGL+G DG ++AE K+ Sbjct: 83 GGM--RVTDRETMNVVEMVLVGKVNKEIVKLINSHGGNAVGLSGKDGNLIVAE---KIDS 137 Query: 116 QEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQM 175 +E + E I G+ G++K V D++ L+E +PV+AP+ + + E N+N D + Sbjct: 138 REYLSELKAPEIIDLGFVGRVKRVNPDIVTKLLESKFIPVIAPVGIGEDFEAYNINADLV 197 Query: 176 AAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIMAGR 232 A E+A AL AE L++LTDV G+ +G+++ ++ + ++ V GM K+ Sbjct: 198 AGEMAAALKAEKLIMLTDVEGIKDKEGRLLKSLRRDQLPQLIADGTVSGGMIPKVKACEA 257 Query: 233 VASGGTKVV-ICDGTV 247 GG K I DG V Sbjct: 258 ALMGGVKKAHIIDGRV 273 Lambda K H 0.316 0.136 0.379 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: 240 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: 264 Length of database: 292 Length adjustment: 25 Effective length of query: 239 Effective length of database: 267 Effective search space: 63813 Effective search space used: 63813 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: 42 (22.0 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