Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate GFF3375 HP15_3317 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >FitnessBrowser__Marino:GFF3375 Length = 298 Score = 127 bits (320), Expect = 2e-34 Identities = 86/256 (33%), Positives = 143/256 (55%), Gaps = 19/256 (7%) Query: 2 ITIKIGGSVVD--DLHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTS 57 + IK GG+ ++ DL S D+ + + G+ I+VHGGG ++ ++ E+L + +FV Sbjct: 30 VVIKYGGNAMENEDLKSSFARDVV-LMKLVGINPIVVHGGGPQIGELLERLNIQSRFVNG 88 Query: 58 PSGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLL 117 R TD ET ++ MV+ G++NK IV ++ +G A+GL+G DA +I R +KL Sbjct: 89 -----MRVTDSETMDVVEMVLGGQVNKEIVSLINSHGGMAVGLTGKDANLI---RARKLE 140 Query: 118 IVN---EKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDR 174 +V+ E R + ID G+ G++ VN I+ L L PVI+PI + + N++ D Sbjct: 141 VVDRSPELERPEIIDIGHVGEVASVNVDVIEMLTRSNLIPVIAPIGVGPDGASYNINADL 200 Query: 175 AAAYVAGKVGSDKVLFITNVDGL-LMDDKVVPKLTLAEAKEI--RPKIGPGMEKKILAST 231 A VA + ++K++ +TNV GL +DKV+ LT + ++ I GM KI + Sbjct: 201 VAGKVAEAMKAEKLMLLTNVSGLKSKEDKVLTGLTAKQVNDLIEDGTIHGGMLPKIRCAL 260 Query: 232 EALDMGVTTALIANGQ 247 A++ GV T+ I +G+ Sbjct: 261 SAVENGVRTSHIIDGR 276 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: 237 Number of extensions: 15 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: 298 Length adjustment: 26 Effective length of query: 241 Effective length of database: 272 Effective search space: 65552 Effective search space used: 65552 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