Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)
Query= curated2:A9A1K7 (267 letters) >FitnessBrowser__Korea:Ga0059261_2530 Length = 299 Score = 119 bits (298), Expect = 8e-32 Identities = 81/252 (32%), Positives = 137/252 (54%), Gaps = 15/252 (5%) Query: 4 IKIGGSVVDDLHPSTIADIKK---IAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTSP 58 +K GG + D P D + + ++ G+ ++VHGGG ++ ++ ++LG E +FV Sbjct: 34 VKYGGHAMGD--PELARDFAEDVVLLKAVGINPVVVHGGGPQIGQMLKRLGVESEFV--- 88 Query: 59 SGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLLI 118 G+ R TD ETA I MV++G INK IV + G AIG+SG D+ ++ A + + Sbjct: 89 GGL--RVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLVTARKVTRSEA 146 Query: 119 VNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAAY 178 +G ++ +D G+ G+ V+AS + +L QG PVI+PIA+ + N++ D A Sbjct: 147 DPLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADGHTYNINADTMAGA 206 Query: 179 VAGKVGSDKVLFITNVDGLLMDDK-VVPKLTLAEAKEIRP--KIGPGMEKKILASTEALD 235 +AG +G+ + +T+V G+L DK ++ L ++ I GM K+ A+D Sbjct: 207 IAGALGASRFFLLTDVPGVLSKDKQLLSDLDPGRIAALKADGTISGGMIPKVETCVAAVD 266 Query: 236 MGVTTALIANGQ 247 GV A+I +G+ Sbjct: 267 AGVDAAVILDGR 278 Lambda K H 0.313 0.133 0.360 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: 202 Number of extensions: 11 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: 267 Length of database: 299 Length adjustment: 26 Effective length of query: 241 Effective length of database: 273 Effective search space: 65793 Effective search space used: 65793 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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