Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate WP_027180205.1 G496_RS0116285 acetylglutamate kinase
Query= BRENDA::Q87EL2 (421 letters) >NCBI__GCF_000429985.1:WP_027180205.1 Length = 291 Score = 101 bits (252), Expect = 3e-26 Identities = 86/274 (31%), Positives = 135/274 (49%), Gaps = 36/274 (13%) Query: 24 VVKVGG-AVLRDDVD-ALTSSLSFLQEVGLTPIVLHGAGPQLDEELTAVGIQKKTVNGFR 81 V+K GG A++ +D+ A ++ L+ +G+ P+V+HG GPQ+ + L+A+ I+ G+R Sbjct: 27 VIKYGGNAMIDEDLKRAFALNIVLLKYIGINPVVVHGGGPQIQKMLSALEIESHFERGYR 86 Query: 82 VTLPETMAIVRKVFHA-TNLQLIEALQRNGARATSITGG------------VFEAHYLDQ 128 VT TM +V V N Q++ + NG A ++G V E+ + Sbjct: 87 VTDEATMDVVEMVLVGQVNKQIVNLINLNGGMAVGLSGKDGTLIKAEKKELVIESEAAPE 146 Query: 129 ET-YGLVGGISAVNIAPIEASLRAASIPVIASLGETPSGQILNINADVAANELVHVLQPY 187 G VG +++VN I + LR IPVIA +G +G NINAD A+ + L Sbjct: 147 LIDLGKVGEVTSVNTTLINSLLRDGFIPVIAPVGVDDNGSTYNINADSVASAVASSLGAK 206 Query: 188 KIIFLTGTGGLLDADGKIINSINLSTEYEQLIQQPWVYGGMKLK----IEQIK------H 237 ++ LT G+LD D ++I+S+ E + I GGM K IE ++ H Sbjct: 207 RLHLLTDISGVLDKDKQLISSMTWH-EAAEAIDSGVAQGGMIPKLTCCIEAVQNGVEKAH 265 Query: 238 LLDRLPLESSVSITRPADLAKELFTHKGSGTLIR 271 ++D +E+ V + ELFT G GT IR Sbjct: 266 IIDG-RIENCVLL--------ELFTKSGIGTEIR 290 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: 275 Number of extensions: 10 Number of successful extensions: 2 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: 291 Length adjustment: 29 Effective length of query: 392 Effective length of database: 262 Effective search space: 102704 Effective search space used: 102704 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 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