Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate WP_011386705.1 AMB_RS22045 acetylglutamate kinase
Query= curated2:B1YB53 (260 letters) >NCBI__GCF_000009985.1:WP_011386705.1 Length = 300 Score = 102 bits (253), Expect = 1e-26 Identities = 73/232 (31%), Positives = 126/232 (54%), Gaps = 16/232 (6%) Query: 2 IVVKIGGSVVCKDP-----TKVVENLPNYADKAVVVHGGGCLVNDLLKRMGVEPKFLTHP 56 +V+K GG + D + V L VVVHGGG ++ +LKR+ ++ + Sbjct: 38 LVIKFGGHAMESDDLARLFARDVVLLKQVGINPVVVHGGGPQIDAMLKRLDIQTPRVD-- 95 Query: 57 GGLVSRYTDLETLKVFVMAMSW-INKSIVASLHALGVEALGLTGADLGVVKARRKEKVLV 115 GL R+TD T++V M ++ INK IV++++ G A+GL+G D +++AR+ + Sbjct: 96 -GL--RFTDEATVEVVEMILAGKINKQIVSAINEAGGFAVGLSGKDGHLIRARKLRRTKK 152 Query: 116 VDERGRQRVVDGGYVGRVVDIAVDKL----RPPPLKVLSPVAVSERGELLNIDGDQLAFD 171 + ++V+D G+VG +I L + + V++PV + GE NI+ D A Sbjct: 153 DPDSNIEKVLDLGFVGEPAEINPHILDQFKKSDTIPVIAPVGMGGAGETYNINADTAAGA 212 Query: 172 VAKRLGAERLVLLSDVDGLI-IGGSVVPRLTAAQAEELVKNEEVRGGMKRKL 222 +A A+RL++L+DV G++ G+++P +TAAQ + + + GGM R L Sbjct: 213 IAGATNAKRLLMLTDVAGVLDKSGNLIPEMTAAQVHAYIADGTISGGMIRPL 264 Lambda K H 0.319 0.139 0.390 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: 178 Number of extensions: 10 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: 260 Length of database: 300 Length adjustment: 26 Effective length of query: 234 Effective length of database: 274 Effective search space: 64116 Effective search space used: 64116 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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