Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_085640565.1 MGEO_RS17020 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_002115805.1:WP_085640565.1 Length = 289 Score = 112 bits (279), Expect = 2e-29 Identities = 87/283 (30%), Positives = 143/283 (50%), Gaps = 19/283 (6%) Query: 1 MASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDDVDALTS---SLSFLQEVGLTPIVLH 57 +A+A+ +S+ L + Q A VVK GG + DD DA+ + +++VG+ P+V+H Sbjct: 11 IATARTLSEALP-YMQRYAGAIVVVKFGGNAMGDD-DAMAEFARDIVLMRQVGINPVVVH 68 Query: 58 GAGPQLDEELTAVGIQKKTVNGFRVTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSI 116 G GP +++ LT +GI+ V G RVT T+ +V V N ++++A+ G RA + Sbjct: 69 GGGPMINDMLTKLGIKSDFVRGKRVTDKATVQVVEMVLTGLVNKRIVQAIMDEGGRAVGL 128 Query: 117 TGG-----VFEAHYLDQETYGLVGGISAVNIAPIEASLRAASIPVIA--SLGETPSGQIL 169 +G V EA D G VG +N + +A IPV+A + G P+ + Sbjct: 129 SGKDDDLMVCEA---DDPELGFVGRPVEMNPQVLRDLFKAGIIPVVAPVATGMQPN-ETF 184 Query: 170 NINADVAANELVHVLQPYKIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMK 229 N+N D AA + L+ +++ LT G+ D DG ++ ++ + E +I + GGM Sbjct: 185 NVNGDTAAGAIAGALKADRLLLLTDVSGVKDRDGNVVTAMT-PEDVEAMIADGTIAGGMI 243 Query: 230 LKIE-QIKHLLDRLPLESSVSITRPADLAKELFTHKGSGTLIR 271 K E +K + D + + P ELFT G+G+LIR Sbjct: 244 PKTETALKAIEDGVRAVVILDGRVPNACLLELFTEHGAGSLIR 286 Lambda K H 0.320 0.136 0.399 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: 227 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: 421 Length of database: 289 Length adjustment: 29 Effective length of query: 392 Effective length of database: 260 Effective search space: 101920 Effective search space used: 101920 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 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