Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate 3610184 Dshi_3565 arginine biosynthesis bifunctional protein ArgJ (RefSeq)
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__Dino:3610184 Length = 407 Score = 288 bits (738), Expect = 2e-82 Identities = 183/400 (45%), Positives = 238/400 (59%), Gaps = 15/400 (3%) Query: 13 LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72 LP I G++ TA+AGV+ G D+ L A GS + VFT + +A V ++ + D D Sbjct: 17 LPVISGVSFATAEAGVRYAGRRDVMLALCAPGSVLAGVFTRSATRSANVCDCQAKI-DGD 75 Query: 73 GVR--ALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADK 130 G A+V+N+GN+NA TG G A+ A A +G +V STGVI E LP D+ Sbjct: 76 GPEGAAIVVNSGNSNAFTGKAGDESVAAISDAVAGVLGLPAARVFTSSTGVIGERLPHDR 135 Query: 131 IIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186 I A L + PA EAA AIMTTDT PK A E + D VR GIAKGSGMI P Sbjct: 136 ITAKLADLAAALDPAGIAEAAEAIMTTDTFPKGAGAEIVI-DGKPVRIAGIAKGSGMIAP 194 Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246 +MATML +I TDA + + LQ + + + TFN ITVD DTST+D+ ++ ATG + Sbjct: 195 DMATMLVYIFTDAAIPRADLQALLSRLTNRTFNCITVDSDTSTSDTLLLAATGASGVDVT 254 Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306 + A + L + L+LA +VRDGEGATKF+TVRV A T +AR A + A S Sbjct: 255 GSTA------FEVALHGVMLDLAHQVVRDGEGATKFVTVRVTGACTDADARTHALSIANS 308 Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366 PLVKTA DPN G+ + A+G + A+ D D + + DILVAE+G A SYTEA G A Sbjct: 309 PLVKTAIAGEDPNWGRVVMAVGKSG-AEADRDRLTIRFGDILVAENGWVAPSYTEAAGAA 367 Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 M ++EI V + L G AATV+TCDL+ Y+ INADYRS Sbjct: 368 YMQREEIEVAVDLGLGTGAATVWTCDLTKRYIEINADYRS 407 Lambda K H 0.317 0.130 0.367 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: 389 Number of extensions: 18 Number of successful extensions: 6 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: 406 Length of database: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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 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