Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_019557927.1 F612_RS0111535 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000381085.1:WP_019557927.1 Length = 303 Score = 102 bits (253), Expect = 1e-26 Identities = 80/259 (30%), Positives = 126/259 (48%), Gaps = 24/259 (9%) Query: 2 IVVKAGGRTLLNNM-------DEIVKSISRLEKAVFVHGGGDLVDEWERKMGMEPQFKVS 54 IVVK GG +++ D ++ + + V VHGGG + ++G +F Sbjct: 36 IVVKYGGNAMIDEKLKEGFARDIVLMKLVGMNPIV-VHGGGPQIGNLLARIGKASEFVQG 94 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TD + +++ VLGG +NK+IV +G AVGLTG DG + A + K Sbjct: 95 -----MRVTDTETMDIVEMVLGGQVNKEIVNLIHQHGGNAVGLTGKDGNLISATKLK--- 146 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 + E I G+ G++ ++ T ++ LV+ +PV+AP+ + +G N+N D Sbjct: 147 MHRDAPELNAPEIIDLGHVGEVDKINTKVLDMLVQGDFIPVIAPVGVGVDGHSYNINADL 206 Query: 175 MAAELAKALSAEYLVLLTDVPGVLMDGKVVPEIKSSEAEEVAKKVGP-----GMNIKIIM 229 +A ++A+A+ AE L+LLT+ G+L K + A+ VA V GM KI Sbjct: 207 VAGKIAEAMGAEKLILLTNTAGLL--DKQGQLLTGLNAQSVATLVADGTIYGGMLPKIQC 264 Query: 230 A-GRVASGGTKVVICDGTV 247 A VA+G I DG V Sbjct: 265 ALDAVANGVHSSHIIDGRV 283 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: 231 Number of extensions: 15 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: 264 Length of database: 303 Length adjustment: 26 Effective length of query: 238 Effective length of database: 277 Effective search space: 65926 Effective search space used: 65926 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