Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate WP_012567460.1 RC1_RS10975 acetylglutamate kinase
Query= BRENDA::Q0ASS9 (441 letters) >NCBI__GCF_000016185.1:WP_012567460.1 Length = 305 Score = 119 bits (299), Expect = 1e-31 Identities = 96/316 (30%), Positives = 153/316 (48%), Gaps = 38/316 (12%) Query: 1 MNPNAPGVRQTIVQLLSHMRDGKEIREYLHRFSGIDQERFAVIKVGGAVIQDDLPG--LA 58 M+ +P + + L+ R E ++ R++G R V+K GG + D+ G A Sbjct: 1 MSTPSPAAAPSREEWLAKARTLSEALPFMRRYAG----RTVVVKYGGHAMGDESLGRRFA 56 Query: 59 SALAFLQTVGLTPVVVHGGGPQLDAALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QAN 117 + + ++ +G++PVVVHGGGPQ+ LE I +E VDGLRVT E + I L+ N Sbjct: 57 NDIVLMKQMGISPVVVHGGGPQIGQMLERLKIKSEFVDGLRVTDKETVEIAEMVLSGSIN 116 Query: 118 LALVDAIRDAGGRAAAVPRGVFEADIVDADK-----------------LGRVGEPRHIHL 160 +V I DAGG A + + D+++A K LG VG+P ++ Sbjct: 117 KQIVALINDAGGDAVGLSGK--DDDLIEARKVTRSKRDPDSNIEKVIDLGFVGDPFRVNP 174 Query: 161 DLVGSAARAGQAAILACLGETPDGTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDED 220 L+ +A ++A +G DG NINAD A A+ A+ +++ LT G+LD+ Sbjct: 175 GLLHKLQQADIIPVIAPIGIGEDGQTYNINADTAAGAIAAAVNATRLLLLTDVAGVLDKQ 234 Query: 221 GDILSSINL-----ATDFGDLMQADWVNGGMRLKLEEIKRLLDDLPLSSSVSITR-PSEL 274 ++ +++ A D G GGM K+E R ++ ++ + R P + Sbjct: 235 KRLIPEMSVEAAQRAIDDGT------ATGGMIPKIETCLRAVNGGVEAAVILDGRVPHAI 288 Query: 275 ARELFTHAGSGTLIRR 290 ELFT G+GTLI R Sbjct: 289 VLELFTEGGAGTLIGR 304 Lambda K H 0.320 0.139 0.411 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: 312 Number of extensions: 17 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: 441 Length of database: 305 Length adjustment: 30 Effective length of query: 411 Effective length of database: 275 Effective search space: 113025 Effective search space used: 113025 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