Align [LysW]-L-2-aminoadipate 6-kinase monomer (EC 2.7.2.17) (characterized)
to candidate WP_068459661.1 APY04_RS03310 acetylglutamate kinase
Query= metacyc::MONOMER-6801 (269 letters) >NCBI__GCF_001541235.1:WP_068459661.1 Length = 305 Score = 126 bits (316), Expect = 6e-34 Identities = 81/273 (29%), Positives = 140/273 (51%), Gaps = 14/273 (5%) Query: 2 IVVKVGG---AEGINYEAVAKDAASLWKEGVKLLLVHGGSAETNKVAEALGHPPRFLTHP 58 +++K GG + +A AKD L + GV ++VHGG + + + L F+ Sbjct: 32 VIIKFGGHAMGDAALADAFAKDVVYLKQSGVNPIVVHGGGPQIAAMLKKLEIKSDFV--- 88 Query: 59 GGQVSRLTDRKTLEIFEMVYCGLVNKRLVELLQKEGANAIGLSGLDGRLFVGRRKTAVKY 118 R+TD+ T+E+ EMV GL+NK +V + ++G A+G+SG D L + R T + Sbjct: 89 --HGLRVTDKPTVEVVEMVLSGLINKDIVSAINRQGGKAVGISGKDANLMIASRITEMPD 146 Query: 119 VENGKVKVHRGDYTGTVEEVNKALLDLLLQAGYLPVLTPPALSYENEAINTDGDQIAALL 178 ++ ++ Y G EVN ++D++ ++ +PV+ P A S + E +N + D A+ L Sbjct: 147 PQSNLMQAVDIGYVGDPVEVNPHIVDVISKSDIIPVIAPVAASRDGETLNINADSFASAL 206 Query: 179 ATLYGAEALVYLSNVPGLLARYPDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVEA 238 A A+ L+ L++V G+L + L+ ++ +E G M K+ G +E Sbjct: 207 AARMKAKRLLLLTDVAGVLDK---SGELISQLTIEEARGLIKDGTISGGMIPKIEGCIEV 263 Query: 239 VKGGVKRVVFADGRVENPIRRAL---SGEGTVV 268 V+ GV+ VV DGRV + + L G GT++ Sbjct: 264 VEAGVEAVVIIDGRVPHCVLLELFTAHGVGTLL 296 Lambda K H 0.317 0.137 0.385 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: 219 Number of extensions: 15 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: 269 Length of database: 305 Length adjustment: 26 Effective length of query: 243 Effective length of database: 279 Effective search space: 67797 Effective search space used: 67797 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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