Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate GFF3407 PGA1_c34600 arginine biosynthesis bifunctional protein ArgJ
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__Phaeo:GFF3407 Length = 409 Score = 274 bits (701), Expect = 3e-78 Identities = 168/403 (41%), Positives = 235/403 (58%), Gaps = 16/403 (3%) Query: 12 QLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDE 71 +LP I G+ +A AGVK TD+ L + GS V VFT + +APV ++ L Sbjct: 15 KLPQIAGVRFASAAAGVKYKNRTDVMLAVMDPGSAVAGVFTRSATRSAPVLDCQAKLASN 74 Query: 72 DGVRA----LVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLP 127 D A +++N+GN+NA TG G+ + A G +V STGVI EPLP Sbjct: 75 DNHTAHGAAILVNSGNSNAFTGHYGQTSVAEITRTVADITGIPAARVFTASTGVIGEPLP 134 Query: 128 ADKIIAALPKMQPAFW----NEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGM 183 D+I++ + + +AA AIMTTDT K A +VG + TV GIAKGSGM Sbjct: 135 HDRIVSQIATLNDGLVATAIEDAAEAIMTTDTFAKGAGATIEVGGK-TVSIAGIAKGSGM 193 Query: 184 IHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQ 243 I P+MATML +I TDA+++Q LQ++ +I D TFN ITVD DTST+DS ++ A+G Sbjct: 194 IAPDMATMLVYIFTDAQIAQNDLQVLLSQICDRTFNCITVDSDTSTSDSLMLCASG---A 250 Query: 244 SEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAA 303 S ID + +A E ++ L+L+ +VRDGEGATKF+ ++V A +A+ + Sbjct: 251 SGIDVTGNTDFALALE---NVMLDLSHQVVRDGEGATKFVEIQVTGAMNDHDAKVHGLSI 307 Query: 304 ARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQ 363 A SPLVKTA DPN G+ + AIG + A D D + + ++LVAE G + Y E Sbjct: 308 ANSPLVKTAIAGEDPNWGRVVMAIGKSGAA-ADRDKLSISFGEVLVAEKGWVSPDYKETD 366 Query: 364 GQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 G A M+K EI +++ L + +TV+TCDL+H Y+SINADYRS Sbjct: 367 GAAEMAKPEIVIKVDLGLAEGKSTVWTCDLTHQYISINADYRS 409 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: 379 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: 409 Length adjustment: 31 Effective length of query: 375 Effective length of database: 378 Effective search space: 141750 Effective search space used: 141750 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 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