Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Ga0059261_2530 Ga0059261_2530 N-acetylglutamate kinase (EC 2.7.2.8)
Query= BRENDA::Q0ASS9 (441 letters) >FitnessBrowser__Korea:Ga0059261_2530 Length = 299 Score = 100 bits (248), Expect = 8e-26 Identities = 90/284 (31%), Positives = 133/284 (46%), Gaps = 28/284 (9%) Query: 28 YLHRFSGIDQERFAVIKVGGAVIQDDLPGLASALA----FLQTVGLTPVVVHGGGPQLDA 83 Y+ R++G + V+K GG + D P LA A L+ VG+ PVVVHGGGPQ+ Sbjct: 23 YMQRYAG----KTFVVKYGGHAMGD--PELARDFAEDVVLLKAVGINPVVVHGGGPQIGQ 76 Query: 84 ALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAAAV---PRGVF 139 L+ + +E V GLRVT E I L N +V I AGG+A + G+ Sbjct: 77 MLKRLGVESEFVGGLRVTDAETARIAEMVLAGSINKEIVSWISAAGGKAIGISGKDSGLV 136 Query: 140 EADIV---DAD---------KLGRVGEPRHIHLDLVGSAARAGQAAILACLGETPDGTLV 187 A V +AD LG VGEP + ++ + + G ++A + DG Sbjct: 137 TARKVTRSEADPLQGIERHVDLGFVGEPVAVDASVLTTLSAQGFIPVIAPIALGADGHTY 196 Query: 188 NINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVNGGMR 247 NINAD A+ AL + LT G+L +D +LS ++ L ++GGM Sbjct: 197 NINADTMAGAIAGALGASRFFLLTDVPGVLSKDKQLLSDLDPGR-IAALKADGTISGGMI 255 Query: 248 LKLEEIKRLLDDLPLSSSVSITR-PSELARELFTHAGSGTLIRR 290 K+E +D ++ + R P + E+FT G+GTL+ R Sbjct: 256 PKVETCVAAVDAGVDAAVILDGRVPHSMLLEIFTPQGAGTLVHR 299 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: 262 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: 441 Length of database: 299 Length adjustment: 29 Effective length of query: 412 Effective length of database: 270 Effective search space: 111240 Effective search space used: 111240 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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