Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate BPHYT_RS17185 BPHYT_RS17185 N-acetylglutamate synthase
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS17185 Length = 413 Score = 443 bits (1139), Expect = e-129 Identities = 235/414 (56%), Positives = 291/414 (70%), Gaps = 9/414 (2%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 MAVN QL + G++L A+A ++KP D+ +I+V G+TVG VFT NRFCAAP Sbjct: 1 MAVNFPSIDPAQLHPVAGVSLGWAEANIRKPNRKDVLVISVGDGATVGGVFTQNRFCAAP 60 Query: 61 VHIAKSHL----FDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMP 116 V + + +L VRALVINTGNANAGTG G + A CA AR P QV+P Sbjct: 61 VTVCRENLDRVRAGGKPVRALVINTGNANAGTGEPGLVAARETCAELARLADITPEQVLP 120 Query: 117 FSTGVILEPLPADKIIAALP----KMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTV 172 FSTGVILEPLP D++ A LP + A W +AA+AIMTTDT+PKA SR+ + + HTV Sbjct: 121 FSTGVILEPLPVDRLKAGLPAALANRKEANWYDAAQAIMTTDTLPKATSRQVTI-EGHTV 179 Query: 173 RATGIAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDS 232 TGI+KG+GMI PNMATMLGF+A DA V+QPVL + + +AD +FN IT+DGDTSTNDS Sbjct: 180 TLTGISKGAGMIKPNMATMLGFLAFDAAVAQPVLDALVKHVADRSFNCITIDGDTSTNDS 239 Query: 233 FVIIATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKT 292 F++IA+GK+S I + P YA L++ + +A LAQ IVRDGEGATKF+TV+VE + Sbjct: 240 FILIASGKSSLPAITSTDSPAYAALRDAVTEVAQTLAQLIVRDGEGATKFMTVQVEGGSS 299 Query: 293 CDEARQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEH 352 E RQ AYA SPLVKTAF+ASDPNLG+ LAAIGYA V DLD +++YLDD+LVA Sbjct: 300 VGECRQIAYAIGHSPLVKTAFYASDPNLGRILAAIGYAGVDDLDVGKIDLYLDDVLVATA 359 Query: 353 GGRAASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 GGR +Y E GQ VM K EI +R+ L RG A AT++TCDLSH YVSINADYRS Sbjct: 360 GGRNPAYREEDGQRVMKKSEIGIRVVLGRGDAQATIWTCDLSHDYVSINADYRS 413 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: 449 Number of extensions: 12 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: 413 Length adjustment: 31 Effective length of query: 375 Effective length of database: 382 Effective search space: 143250 Effective search space used: 143250 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