Align amino-acid N-acetyltransferase (EC 2.3.1.1); acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate AZOBR_RS03285 AZOBR_RS03285 acetylglutamate kinase
Query= BRENDA::Q0ASS9 (441 letters) >FitnessBrowser__azobra:AZOBR_RS03285 Length = 299 Score = 117 bits (293), Expect = 5e-31 Identities = 95/297 (31%), Positives = 143/297 (48%), Gaps = 30/297 (10%) Query: 16 LSHMRDGKEIREYLHRFSGIDQERFAVIKVGGAVIQDD--LPGLASALAFLQTVGLTPVV 73 L+ R E Y+ R++G R VIK GG + DD A + L+ VG+ PVV Sbjct: 10 LAKARTLSEALPYMRRYAG----RTFVIKYGGHAMGDDSLAEKFARDIVLLKQVGINPVV 65 Query: 74 VHGGGPQLDAALEAADIPTERVDGLRVTRDEAIPIIRDTLT-QANLALVDAIRDAGGRAA 132 VHGGGPQ+ L+ I + +DGLRVT E + ++ L N +V AI +AGGRA Sbjct: 66 VHGGGPQIGQMLQRLAIKSSFIDGLRVTDKETVEVVEMVLAGSINKQIVAAINNAGGRAV 125 Query: 133 AVPRGVFEADIVDADK-----------------LGRVGEPRHIHLDLVGSAARAGQAAIL 175 + + ++ A K LG VGEP ++ ++ S A++ ++ Sbjct: 126 GLSGK--DGSLITARKLRRTQRDPDSNIEKVLDLGFVGEPYQVNPQIITSLAQSDIIPVI 183 Query: 176 ACLGETPDGTLVNINADVAVRALVHALQPYKVVFLTGTGGLLDEDGDILSSINLATDFGD 235 A +G +G NINAD A A+ AL + LT G+LD++ +++ ++L D Sbjct: 184 APIGFDRNGDTYNINADTAAGAVASALGATRFFLLTDVAGVLDKNKELVPRMSL--DQAR 241 Query: 236 LMQAD-WVNGGMRLKLEE-IKRLLDDLPLSSSVSITRPSELARELFTHAGSGTLIRR 290 AD GGM K+E I + + + + P L E+FT G+GTLI R Sbjct: 242 AAIADGTATGGMIPKIETCIDAVEQGVDAAVILDGRVPHALLLEIFTEGGAGTLIGR 298 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: 294 Number of extensions: 16 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 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