Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate H281DRAFT_02211 H281DRAFT_02211 N-acetylglutamate kinase
Query= curated2:A8AA51 (264 letters) >FitnessBrowser__Burk376:H281DRAFT_02211 Length = 299 Score = 106 bits (265), Expect = 5e-28 Identities = 79/257 (30%), Positives = 132/257 (51%), Gaps = 23/257 (8%) Query: 2 IVVKAGGRTLLNNM-------DEIVKSISRLEKAVFVHGGGDLVDEWERKMGMEPQFKVS 54 +V+K GG + D I+ + + V VHGGG +D+ +K+G + F Sbjct: 34 VVIKYGGNAMTEERLKQGFARDVILLKLVGINP-VIVHGGGPQIDQALKKVGKQGTFIQG 92 Query: 55 ASGIKFRYTDEKELEVFVAVLGGLLNKKIVASFASYGRGAVGLTGADGPSVIAERKKKVI 114 R TDE+ +EV VLGG + + IV +G AVGLTG DG +I RK + Sbjct: 93 -----MRVTDEETMEVVEWVLGGEVQQDIVTLINHFGGHAVGLTGKDG-GLIHARKMLMP 146 Query: 115 VQEKVGERLVKRAIAGGYTGKIKEVKTDLIKALVERGLVPVVAPIALSPEGELLNVNGDQ 174 ++ G+ + G G+++ + ++KAL + +PV++PI +G N+N D Sbjct: 147 DRDNPGQY-----VDIGQVGEVEAINPAVVKALQDDAFIPVISPIGFGEDGLSYNINADL 201 Query: 175 MAAELAKALSAEYLVLLTDVPGVL-MDGKVVPEIKSSEAEEVAK--KVGPGMNIKIIMAG 231 +A +LA L+AE LV++T++PGV+ +G ++ ++ + E + + + GM KI A Sbjct: 202 VAGKLAVVLNAEKLVMMTNIPGVMDKEGNLLTDLSAREIDGLFADGTISGGMLPKISSAL 261 Query: 232 RVASGGTKVV-ICDGTV 247 A G + V I DG + Sbjct: 262 DAAKSGVRSVHIIDGRI 278 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: 243 Number of extensions: 17 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: 299 Length adjustment: 26 Effective length of query: 238 Effective length of database: 273 Effective search space: 64974 Effective search space used: 64974 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