Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_013450392.1 CALNI_RS01290 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >NCBI__GCF_000183405.1:WP_013450392.1 Length = 291 Score = 124 bits (310), Expect = 3e-33 Identities = 89/255 (34%), Positives = 145/255 (56%), Gaps = 19/255 (7%) Query: 2 ITIKIGGSVV--DDLHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTS 57 I IK GG + +DL + DI + + G+ I+VHGGG ++ + ++L + FV+ Sbjct: 26 IVIKYGGHAMVDEDLKNNFARDIV-LLKYVGINPIIVHGGGPQIGDMLKKLNIQSTFVSG 84 Query: 58 PSGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLL 117 R TDKET + MV+ G +NK IV ++ +NG AIGLSG D +I A+ KL Sbjct: 85 -----MRVTDKETMNVVEMVLVGLVNKNIVSLINRNGGKAIGLSGKDGNLILAE---KLF 136 Query: 118 IVNEKGRK--QAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRA 175 I + K + ID G+ GK++ VN S + +L+ + PVI+P+ I E+SE N++ D Sbjct: 137 IEEDSFYKTPEIIDLGHVGKVKSVN-SDVLNLISKDYIPVIAPVGIGEDSEPYNINADLV 195 Query: 176 AAYVAGKVGSDKVLFITNVDGLL-MDDKVVPKLTLAEAKEIRPK--IGPGMEKKILASTE 232 A VA VG++K++ +T+V G+L D ++ L+++E ++++ I GM K+ + Sbjct: 196 AGAVASAVGAEKLILLTDVKGVLDKDGNLISSLSVSEIEDLKNNNIIYGGMLPKMDSVKS 255 Query: 233 ALDMGVTTALIANGQ 247 AL GV I +G+ Sbjct: 256 ALLGGVKKVHIIDGR 270 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: 208 Number of extensions: 12 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: 267 Length of database: 291 Length adjustment: 26 Effective length of query: 241 Effective length of database: 265 Effective search space: 63865 Effective search space used: 63865 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 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