Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate AZOBR_RS02855 AZOBR_RS02855 N-acetylglutamate synthase
Query= CharProtDB::CH_000559 (406 letters) >FitnessBrowser__azobra:AZOBR_RS02855 Length = 412 Score = 294 bits (753), Expect = 3e-84 Identities = 173/400 (43%), Positives = 232/400 (58%), Gaps = 9/400 (2%) Query: 13 LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDED 72 LP + G+ + TA +G++ G DL L + G+TV V T + C+APV + L Sbjct: 16 LPPVAGVRIATANSGIRYKGRDDLMLAVLDEGTTVAGVLTKSLTCSAPVIWCRDSL-PRG 74 Query: 73 GVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKII 132 RA+V+N GNANA TG G A AAA+ GC ++V STGVI PL AD I Sbjct: 75 SARAVVVNAGNANAFTGKAGDATVQATVEAAAKIAGCATDEVYVASTGVIGIPLAADAIA 134 Query: 133 AALPKMQPAFWNEAA------RAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186 LP M PA +++A RAIMTTDT K ++R+ +G TV +G AKGSGMI P Sbjct: 135 KVLPGMVPALKDDSAALEAGARAIMTTDTFAKGSTRQVAIGGT-TVTISGFAKGSGMIAP 193 Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246 +MATMLGF+ TDA ++ P LQ M E + +FN ITVDGDTST+D+ ++ ATGK + + Sbjct: 194 DMATMLGFLFTDAAIAAPALQSMLSEFTERSFNAITVDGDTSTSDTLLLFATGKAGNAPV 253 Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306 + P A ++ L + L+LA IVRDGEGATKF+++ + A+ A++ A A S Sbjct: 254 TDAQAPELAAFRKALEEVMLDLALQIVRDGEGATKFVSITLVGAENDVAAKRIALTVANS 313 Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366 PLVKTA D N G+ +AAIG A D DL+++ + L+ G Y EA A Sbjct: 314 PLVKTALAGEDANWGRIVAAIGRAG-ERADRDLIKITIGGTLICAEGMEVPGYDEAPVAA 372 Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 M EI V I L G + V+TCDL+HGY+ IN YRS Sbjct: 373 HMKGQEIDVHIDLGIGTGKSRVWTCDLTHGYIDINGSYRS 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: 388 Number of extensions: 19 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: 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 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