Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_015928079.1 MNOD_RS06685 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000022085.1:WP_015928079.1 Length = 304 Score = 125 bits (313), Expect = 1e-33 Identities = 87/258 (33%), Positives = 137/258 (53%), Gaps = 18/258 (6%) Query: 1 MIVVKAGGRTLLNNM--DEIVKSISRLE----KAVFVHGGGDLVDEWERKMGMEPQFKVS 54 ++V+K GG + + ++ + I LE K V VHGGG + ++G++ +F+ Sbjct: 33 IVVIKYGGHAMGDRAAAEDFAEDIVLLEQSGLKPVIVHGGGPQIGRMLDRLGIKSEFREG 92 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TDE +EV VL G +NK+IV ++ G A+GL G DG V A R + + Sbjct: 93 -----LRVTDEATVEVVEMVLAGSINKQIVGWISAEGGKAIGLCGKDGNMVQARRATRTV 147 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 V + ++R + G G+ + V ++ A+++ L+PV+AP+A+ +G+ NVN D Sbjct: 148 VDP---DSNIERHVDLGLVGEPERVNRAVLDAVLKAELIPVLAPVAVGSDGQTYNVNADT 204 Query: 175 MAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKI-IMA 230 A +A AL A+ L+LLTDVPGVL D K++PE+ + + + GM KI Sbjct: 205 FAGAIAGALRAKRLLLLTDVPGVLDKDKKLIPELSIEDCRRLIADGTITGGMIPKIETCI 264 Query: 231 GRVASGGTKVVICDGTVP 248 + G VVI DG VP Sbjct: 265 YAIEQGVEAVVILDGKVP 282 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: 226 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: 304 Length adjustment: 26 Effective length of query: 238 Effective length of database: 278 Effective search space: 66164 Effective search space used: 66164 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