Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_083758898.1 SULAZ_RS07475 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000021545.1:WP_083758898.1 Length = 300 Score = 120 bits (301), Expect = 3e-32 Identities = 78/227 (34%), Positives = 124/227 (54%), Gaps = 12/227 (5%) Query: 29 VFVHGGGDLVDEWERKMGMEPQFKVSASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFA 88 V VHGGG + ++ +KMG+E +F G+ R TD++ +++ VLGGL+NK IV Sbjct: 60 VIVHGGGPQIGQYLKKMGLESKF---VGGL--RVTDKETMDIVEMVLGGLVNKSIVQLIN 114 Query: 89 SYGRG---AVGLTGADGPSVIAERKKKVIVQEKVGERLVKRAIAGGYTGKIKEVKTDLIK 145 SY G AVG+TG DG + A++ + +G+ + G+ G+++EV L+ Sbjct: 115 SYSGGHVKAVGITGKDGGLIKAKKLDAEEYFKSMGDFRPTELLDLGHVGEVEEVDPSLLI 174 Query: 146 ALVERGLVPVVAPIALSPEGELLNVNGDQMAAELAKALSAEYLVLLTDVPGVL-MDGKVV 204 L E +PV+API EG N+N D +A+ +A +L AE ++ LTD+ G+ +GK + Sbjct: 175 NLDEDNYIPVIAPIGYDDEGNAYNINADLVASAIAVSLKAEKVIFLTDIEGLKDSEGKTL 234 Query: 205 PEIKSSEAEEVAKK--VGPGMNIKI-IMAGRVASGGTKVVICDGTVP 248 + + E EE+ K + GM K+ V +G K I DG +P Sbjct: 235 SSVSTKEIEEMIKTGVIKGGMIPKVKACTYAVENGVNKAHILDGRIP 281 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: 249 Number of extensions: 15 Number of successful extensions: 4 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: 300 Length adjustment: 26 Effective length of query: 238 Effective length of database: 274 Effective search space: 65212 Effective search space used: 65212 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