Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_068459661.1 APY04_RS03310 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >NCBI__GCF_001541235.1:WP_068459661.1 Length = 305 Score = 119 bits (298), Expect = 8e-32 Identities = 83/253 (32%), Positives = 138/253 (54%), Gaps = 14/253 (5%) Query: 2 ITIKIGGSVVDD--LHPSTIADIKKIAESEGV--ILVHGGGKEVTKVCEQLGKEPKFVTS 57 + IK GG + D L + D+ + +S GV I+VHGGG ++ + ++L + FV Sbjct: 32 VIIKFGGHAMGDAALADAFAKDVVYLKQS-GVNPIVVHGGGPQIAAMLKKLEIKSDFVHG 90 Query: 58 PSGIKSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLL 117 R TDK T E+ MV+SG INK IV + + G A+G+SG DA ++ A R ++ Sbjct: 91 -----LRVTDKPTVEVVEMVLSGLINKDIVSAINRQGGKAVGISGKDANLMIASRITEMP 145 Query: 118 IVNEKGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAA 177 + QA+D GY G EVN + + + PVI+P+A S + E LN++ D A+ Sbjct: 146 DP-QSNLMQAVDIGYVGDPVEVNPHIVDVISKSDIIPVIAPVAASRDGETLNINADSFAS 204 Query: 178 YVAGKVGSDKVLFITNVDGLL-MDDKVVPKLTLAEAKEI--RPKIGPGMEKKILASTEAL 234 +A ++ + ++L +T+V G+L +++ +LT+ EA+ + I GM KI E + Sbjct: 205 ALAARMKAKRLLLLTDVAGVLDKSGELISQLTIEEARGLIKDGTISGGMIPKIEGCIEVV 264 Query: 235 DMGVTTALIANGQ 247 + GV +I +G+ Sbjct: 265 EAGVEAVVIIDGR 277 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: 185 Number of extensions: 10 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: 305 Length adjustment: 26 Effective length of query: 241 Effective length of database: 279 Effective search space: 67239 Effective search space used: 67239 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