Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_011606301.1 FRAAL_RS22705 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::P9WPZ3 (404 letters) >NCBI__GCF_000058485.1:WP_011606301.1 Length = 386 Score = 421 bits (1081), Expect = e-122 Identities = 235/393 (59%), Positives = 276/393 (70%), Gaps = 13/393 (3%) Query: 16 VTAPAGFRAAGVAAGIKASGALDLALVFNEGPDYAAAGVFTRNQVKAAPVLWTQQVLTTG 75 VTAP GFRAAGVAAG+K SG D+ALV N+GP AAAGVFTRN+++AAPVLWT+Q L G Sbjct: 3 VTAPKGFRAAGVAAGLKPSGRPDIALVVNDGPSDAAAGVFTRNRIQAAPVLWTRQTLADG 62 Query: 76 RLRAVILNSGGANACTGPAGFADTHATAEAVAAALSDWGTETGAIEVAVCSTGLIGDRLP 135 RLRAV+LNSGGANACTGP GFADTHATAE VAA L GA +VAVCSTGLIG RLP Sbjct: 63 RLRAVVLNSGGANACTGPGGFADTHATAEHVAAGLG-----LGAGDVAVCSTGLIGVRLP 117 Query: 136 MDKLLAGVAHVVHEMHGGLVGGDEAAHAIMTTDNVPKQVALHHH--DNWTVGGMAKGAGM 193 MD LLAGV V ++ GGD+AA AI TTD V K TVG M KGA M Sbjct: 118 MDILLAGVTRAVADLAD--TGGDDAAEAIRTTDTVAKTAVRTSTATPGVTVGAMGKGAAM 175 Query: 194 LAPSLATMLCVLTTDAAAEPAALERALRRAAAATFDRLDIDGSCSTNDTVLLLSSGASEI 253 LAPSLATML V+TTDA A+ A L+R +R+A+ TF+R+D DG STNDTVLLL+SG++ + Sbjct: 176 LAPSLATMLVVVTTDAVADAATLDRVVRQASRVTFERVDSDGCLSTNDTVLLLASGSAGV 235 Query: 254 PPAQADLDEAVLRVCDDLCAQLQADAEGVTKRVTVTVTGAATEDDALVAARQIARDSLVK 313 +A+L E V VC DL Q+ DAEG TK + +TVTGAA+E DAL R +AR++L+K Sbjct: 236 TLPEAELTELVAAVCADLAQQMLDDAEGSTKTIAITVTGAASEADALEVGRSVARNNLLK 295 Query: 314 TALFGSDPNWGRVLAAVGMAPITLDPDRISVSFNGAAVCVHGVGAPGARE--VDLSDADI 371 AL+G DPNWGRVLAAVG +PD++ VS NG VC GAPG VDLSD I Sbjct: 296 CALYGKDPNWGRVLAAVGTTQAAFEPDQLDVSMNGVQVC--RAGAPGEDRDLVDLSDRRI 353 Query: 372 DITVDLGVGDGQARIRTTDLSHAYVEENSAYSS 404 DI VDL G + I T DL+ YV ENSAYS+ Sbjct: 354 DILVDLHAGGEELTIWTNDLTDGYVYENSAYST 386 Lambda K H 0.317 0.131 0.380 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: 492 Number of extensions: 14 Number of successful extensions: 4 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: 404 Length of database: 386 Length adjustment: 31 Effective length of query: 373 Effective length of database: 355 Effective search space: 132415 Effective search space used: 132415 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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