Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate HSERO_RS01730 HSERO_RS01730 N-acetylglutamate synthase
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__HerbieS:HSERO_RS01730 Length = 411 Score = 421 bits (1082), Expect = e-122 Identities = 229/413 (55%), Positives = 287/413 (69%), Gaps = 9/413 (2%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 MAVN L + GI L A+AGV+K D+ ++ +A +TV VFT NRFCAAP Sbjct: 1 MAVNSPIPVPSDLKAVAGIELGHAEAGVRKANRKDVLVMKLAETATVAGVFTKNRFCAAP 60 Query: 61 VHIAKSHLFDEDG---VRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPF 117 V I +++L +RALVINTGNANAGTG +G A +VCAA A+Q+G + Q++PF Sbjct: 61 VQICQANLAQLSAGKPIRALVINTGNANAGTGEEGLQRAKSVCAALAQQMGVEAQQILPF 120 Query: 118 STGVILEPLPADKIIAALPK----MQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVR 173 STGVILEPLPAD+IIA LP+ ++ W AA +IMTTDT PKAASR +G + V Sbjct: 121 STGVILEPLPADRIIAGLPQAIGNLKADNWFNAAESIMTTDTQPKAASRTLTIGGKQVVM 180 Query: 174 ATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSF 233 TGI+KG+GMI PNMATMLGF+A DAK+ Q +L + ++ AD +FN IT+DGDTSTNDSF Sbjct: 181 -TGISKGAGMIKPNMATMLGFLAFDAKLPQALLNQLVKDAADHSFNCITIDGDTSTNDSF 239 Query: 234 VIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTC 293 +++ATG + EI + Y QL + L+ LA IVRDGEGATKFI V VE+ K+ Sbjct: 240 ILMATGAG-ELEITSADSEEYQQLAAAVTDLSQHLAHQIVRDGEGATKFIEVAVEDGKSV 298 Query: 294 DEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHG 353 +E RQ AY+ SPLVKTAFFASDPNLG+ LAAIGYA + DLD + ++LDD+ VA+ G Sbjct: 299 EECRQIAYSIGHSPLVKTAFFASDPNLGRILAAIGYAGIDDLDVSKINLWLDDVWVAKDG 358 Query: 354 GRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 GR Y E GQ VM K EI VR+KL RG A A+++TCDLSH YVSINADYRS Sbjct: 359 GRNPDYREEDGQRVMKKAEIVVRVKLARGAAKASIWTCDLSHDYVSINADYRS 411 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: 381 Number of extensions: 10 Number of successful extensions: 5 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: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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