Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate Ac3H11_4758 Glutamate N-acetyltransferase (EC 2.3.1.35) / N-acetylglutamate synthase (EC 2.3.1.1)
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4758 Length = 412 Score = 443 bits (1139), Expect = e-129 Identities = 233/413 (56%), Positives = 291/413 (70%), Gaps = 8/413 (1%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 M VNL A L I G+ + A+AGV+K DLT+ + G++V VFT NRFCAAP Sbjct: 1 MPVNLVAPVAADLYPIAGVRIGVAEAGVRKANRKDLTVFLLDEGASVAGVFTQNRFCAAP 60 Query: 61 VHIAKSHLFDEDG---VRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPF 117 V I++ HL + +RA+VINTGNANAGTGA G A + C A ARQ+ P Q++PF Sbjct: 61 VQISREHLSQQQAGQPIRAMVINTGNANAGTGADGLARARSTCVALARQLSVAPEQILPF 120 Query: 118 STGVILEPLPADKIIAALPKM----QPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVR 173 STGVI+EPLP D+I A LP QP W AA IMTTDT+PKA S + ++G TV Sbjct: 121 STGVIMEPLPNDRIEAGLPAAIADAQPGHWARAAEGIMTTDTLPKAFSAQAQIGGA-TVS 179 Query: 174 ATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSF 233 TGI+KG+GMI PNMATMLGF+ATDA V+ V+Q + +E+AD +FN +T+DGDTSTNDSF Sbjct: 180 ITGISKGAGMIRPNMATMLGFLATDACVAPAVMQQLARELADGSFNRVTIDGDTSTNDSF 239 Query: 234 VIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTC 293 V++AT K + + I ++ LK + +++ +LAQAIVRDGEGATKFITVRVE KT Sbjct: 240 VVVATNKAAHAPITSLDSAEGQALKAAMLAVSQKLAQAIVRDGEGATKFITVRVEGGKTG 299 Query: 294 DEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHG 353 DE R+ AYA A SPLVKTAFFASDPNLG+ LAA+GYA + DLD +++YLDD+ VA G Sbjct: 300 DECRKVAYAIAHSPLVKTAFFASDPNLGRILAAVGYAGIDDLDQTGIDLYLDDVHVAVQG 359 Query: 354 GRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 GR +Y E GQ VM + EITVR+ L RG AA TV+TCD SH YV+INADYRS Sbjct: 360 GRNPAYREEDGQRVMKQAEITVRVLLGRGNAADTVWTCDFSHEYVTINADYRS 412 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: 453 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: 406 Length of database: 412 Length adjustment: 31 Effective length of query: 375 Effective length of database: 381 Effective search space: 142875 Effective search space used: 142875 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