Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_041778980.1 BIND_RS16900 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >NCBI__GCF_000019845.1:WP_041778980.1 Length = 284 Score = 108 bits (271), Expect = 1e-28 Identities = 80/260 (30%), Positives = 134/260 (51%), Gaps = 23/260 (8%) Query: 1 MITIKIGGSVVDDLHPS-TIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTS 57 ++ +K GG +DD + A + E GV ++VHGGG ++ + +LG + F Sbjct: 24 IVVVKYGGHAMDDEESARNFAKDMVLLEQSGVNPVVVHGGGPQIGAMLAKLGIKSVF--- 80 Query: 58 PSGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLL 117 G+ R TD+ T EI MV++G INK IV + G AIGL G D ++ A + Sbjct: 81 SQGL--RITDRATIEIVEMVLAGSINKQIVGFINAEGGRAIGLCGKDGNMVTAHK----- 133 Query: 118 IVNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAA 177 + + G A+D G+ G+ +V+ + + +L + L PV++P+A + E N++ D A Sbjct: 134 -LGQPG--DAVDLGFVGEPAKVDTTVLDQVLGRELIPVLAPVAQGVDGETYNINADTFAG 190 Query: 178 YVAGKVGSDKVLFITNVDGLLMDDKVVPKLTLAEAKEIRPKIGP-----GMEKKILASTE 232 +AG + + ++LF+T+V G+L K + K E EIR I GM K+ Sbjct: 191 AIAGALQAKRLLFLTDVPGVLDRQKRLIKQLRVE--EIRTLIADGTITGGMIPKVETCIY 248 Query: 233 ALDMGVTTALIANGQKENPI 252 AL+ GV +I +G+ + + Sbjct: 249 ALEQGVEGVVILDGKTPHAV 268 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: 201 Number of extensions: 12 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: 267 Length of database: 284 Length adjustment: 25 Effective length of query: 242 Effective length of database: 259 Effective search space: 62678 Effective search space used: 62678 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 Jul 25 2024. The underlying query database was built on Jul 25 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