Align [LysW]-aminoadipate kinase; EC 2.7.2.17 (uncharacterized)
to candidate WP_058929441.1 AU252_RS02895 acetylglutamate kinase
Query= curated2:Q9RUG6 (292 letters) >NCBI__GCF_001484605.1:WP_058929441.1 Length = 325 Score = 95.5 bits (236), Expect = 1e-24 Identities = 77/266 (28%), Positives = 124/266 (46%), Gaps = 27/266 (10%) Query: 27 IVVKVGGSDGIDYD---AVCADLAERWQAGEKLILVHGGSGETNRVAEALGHPPKFVTSP 83 +V+K GG+ ++ + A D+ G ++VHGG + N + LG +F Sbjct: 36 MVIKYGGNAMVNEELRRAFAEDVVFLHHVGIHPVVVHGGGPQINSMLARLGIESEFKGG- 94 Query: 84 SGYTSRFTDRQTLEIFEMVYCGKMNKGLVERLQRLGVNAVGLSGLDGRIFEGKHKDSVRS 143 R T + +++ MV G++ + LV + G AVG+SG DG + +V Sbjct: 95 ----LRVTTPEAMDVVRMVLTGQVGRELVGLINSHGPYAVGMSGEDGGLLRAVRTGTVID 150 Query: 144 VENGKVKVLRGDHTGTVEKVNTGLIELLLGAGYLPVLTPPAASYE--------------G 189 E + ++ G V VN I +L AG +PV++ A E G Sbjct: 151 GEEVDLGLV-----GEVVGVNPEGILDILAAGRIPVISTVAPEIESDGLETAAGEVQTTG 205 Query: 190 VAINVDGDRAAAQLAAALRAEALLLLSNVPGLLRDYPDEASLIREIPANDVESYLEFAQD 249 +NV+ D AAA LA AL A L++L++V GL ++PD +SLI + A+++ L + Sbjct: 206 QVLNVNADTAAAALAEALGASKLVILTDVEGLYANWPDRSSLISSLTASELRQLLPSLES 265 Query: 250 RMKKKVLGAAEAVAGGVGRVVFGDAR 275 M K+ +A+ GGV R D R Sbjct: 266 GMIPKMEACLKAIDGGVERAHIVDGR 291 Lambda K H 0.319 0.137 0.394 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: 194 Number of extensions: 14 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: 292 Length of database: 325 Length adjustment: 27 Effective length of query: 265 Effective length of database: 298 Effective search space: 78970 Effective search space used: 78970 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: 48 (23.1 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