Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate HSERO_RS21495 HSERO_RS21495 acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__HerbieS:HSERO_RS21495 Length = 297 Score = 110 bits (274), Expect = 4e-29 Identities = 84/261 (32%), Positives = 131/261 (50%), Gaps = 23/261 (8%) Query: 2 IVVKAGGRTLLNNM-------DEIVKSISRLEKAVFVHGGGDLVDEWERKMGMEPQFKVS 54 IVVK GG + D I+ + + V VHGGG +D +K+G + F Sbjct: 32 IVVKYGGNAMTEESLKHGFARDVILLKLVGMNPVV-VHGGGPQIDAALKKIGKQGTFVQG 90 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TDE+ +EV VLGG + + IV YG AVGLTG DG +I RK ++ Sbjct: 91 -----MRITDEETMEVVEWVLGGEVQQDIVMLINHYGGQAVGLTGKDG-GLIRARKMQMP 144 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 +E G L GY G+I+ + ++KAL + +P+++PI +G+ N+N D Sbjct: 145 DKEHPGAFLDI-----GYVGEIEAINPAVVKALQDDAFIPIISPIGFGDDGQAYNINADV 199 Query: 175 MAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIMAG 231 +A ++A+ L AE L+++T++ GV G ++ ++ + E +E+ + GM KI A Sbjct: 200 VAGKIAEILHAEKLIMMTNIAGVQDKAGNLLTDLSAREIDEMFADGTISGGMLPKISSAL 259 Query: 232 RVASGGTKVV-ICDGTVPDPL 251 A G V I DG + L Sbjct: 260 DAAKSGVNTVHIIDGRIEHSL 280 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: 246 Number of extensions: 19 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: 297 Length adjustment: 26 Effective length of query: 238 Effective length of database: 271 Effective search space: 64498 Effective search space used: 64498 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 09 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