Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_036260935.1 DL86_RS10190 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >NCBI__GCF_000746085.1:WP_036260935.1 Length = 294 Score = 112 bits (281), Expect = 7e-30 Identities = 87/260 (33%), Positives = 133/260 (51%), Gaps = 30/260 (11%) Query: 1 MIVVKAGGRTLLNNMDEIVKSISR----LEKA----VFVHGGGDLVDEWERKMGMEPQFK 52 ++VVK GG + + D++ + +R LE++ V VHGGG + RK+G++ +F Sbjct: 34 IVVVKYGGHAMGD--DKVGRDFARDMVLLEQSGVNPVVVHGGGPQIGAMLRKLGIKSEF- 90 Query: 53 VSASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKK 112 + G+ R TD +E+ VL G +NK+IV + G A+GL G DG VIA + Sbjct: 91 --SDGL--RVTDRATIEIVEMVLAGSINKQIVGFINAEGGRAIGLCGKDGNMVIANKAPP 146 Query: 113 VIVQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNG 172 A+ G+ G+ +V T ++ ++ R L+PV+APIA +GE NVN Sbjct: 147 T-----------SEAVDLGFVGEPAKVDTTVLDQVLGRELIPVLAPIAQGDDGETYNVNA 195 Query: 173 DQMAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIM 229 D A +A AL A+ L+ LTDVPGVL G ++ E++ E + + GM K+ Sbjct: 196 DTFAGAIAGALKAKRLLFLTDVPGVLDQKGSLIKELRVEEIHALIADGTITGGMIPKVET 255 Query: 230 AGRVASGGTK-VVICDGTVP 248 G + VVI DG P Sbjct: 256 CIYALEQGVEGVVILDGKSP 275 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: 16 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: 294 Length adjustment: 25 Effective length of query: 239 Effective length of database: 269 Effective search space: 64291 Effective search space used: 64291 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