Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_038019486.1 G579_RS0110705 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000423825.1:WP_038019486.1 Length = 295 Score = 108 bits (269), Expect = 2e-28 Identities = 80/261 (30%), Positives = 130/261 (49%), Gaps = 21/261 (8%) Query: 2 IVVKAGGRTLLNN-------MDEIVKSISRLEKAVFVHGGGDLVDEWERKMGMEPQFKVS 54 IV+K GG + D ++ + + V VHGGG + +MG+ +F Sbjct: 28 IVIKYGGNAMTEEHLKTRFARDVVLMKLVGMNPVV-VHGGGPQIGATLARMGVSTEFVQG 86 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TD++ ++V VLGGL+NK+IV G AVGLTG DG + A +K++ Sbjct: 87 -----MRVTDQETMQVVEMVLGGLVNKEIVNLINQAGGCAVGLTGKDGGLIQA---RKLL 138 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 V+ E + G G+++ V L++ L + ++PV+API + P+G+ N+N D Sbjct: 139 VRNAASES-PDDLLDVGLVGEVERVNPALLQILERQDIIPVIAPIGVGPDGQTYNINADL 197 Query: 175 MAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIMAG 231 +A +LA+ L AE +L+T+V GVL G+++ + +++ + GM K+ Sbjct: 198 VAGKLAETLHAEKFILMTNVAGVLDKSGELLTGLTPGRVQDLIADGTIYGGMLPKLACCL 257 Query: 232 RVASGGTKVV-ICDGTVPDPL 251 S G K I DG V L Sbjct: 258 SAVSNGVKTAHIIDGRVEHAL 278 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: 245 Number of extensions: 18 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: 295 Length adjustment: 26 Effective length of query: 238 Effective length of database: 269 Effective search space: 64022 Effective search space used: 64022 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