Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate GFF201 PGA1_c02050 acetylglutamate kinase ArgB
Query= BRENDA::Q0ASS9 (441 letters) >FitnessBrowser__Phaeo:GFF201 Length = 286 Score = 105 bits (261), Expect = 2e-27 Identities = 79/270 (29%), Positives = 133/270 (49%), Gaps = 15/270 (5%) Query: 28 YLHRFSGIDQERFAVIKVGGAVIQDD--LPGLASALAFLQTVGLTPVVVHGGGPQLDAAL 85 YL R+ G V+K+GG + D + A + L+ VG+ PV+VHGGGP ++A L Sbjct: 23 YLQRYDGA----IVVVKLGGHAMGSDEAMETFARDIVLLRQVGVNPVIVHGGGPMINAML 78 Query: 86 EAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAAAVPRGVFEADIV 144 E I ++ V+G RVT + ++ L+ N +V AI GG A V +A+++ Sbjct: 79 EKLQIKSDFVNGKRVTDAATMEVVEMVLSGVVNKRIVQAINRQGG--AGVGLSGKDANLI 136 Query: 145 DADK----LGRVGEPRHIHLDLVGSAARAGQAAILACLGETPDGTLVNINADVAVRALVH 200 + LG VG P + ++ ++A +G PDG NIN D A A+ Sbjct: 137 TCTQADPDLGFVGTPSQMDPSVLHHLFEQDMIPVIAPIGAGPDGETFNINGDTAAGAIAS 196 Query: 201 ALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGDLMQADWVNGGMRLKLE-EIKRLLDD 259 AL+ +++ LT G+ + G++++ + A D + + + GGM K E + + Sbjct: 197 ALKADRLLLLTDVSGVKNGAGEVVTELK-AADVEAMTRDGVIIGGMIPKTETALAAVRSG 255 Query: 260 LPLSSSVSITRPSELARELFTHAGSGTLIR 289 + + V P+ + ELFT G+G++IR Sbjct: 256 VRACTIVDGRVPNAVLLELFTDHGAGSMIR 285 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: 280 Number of extensions: 13 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: 286 Length adjustment: 29 Effective length of query: 412 Effective length of database: 257 Effective search space: 105884 Effective search space used: 105884 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 09 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