Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_013834765.1 THICY_RS01060 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000214825.1:WP_013834765.1 Length = 407 Score = 370 bits (951), Expect = e-107 Identities = 205/404 (50%), Positives = 260/404 (64%), Gaps = 9/404 (2%) Query: 10 AEQLPDID---GIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKS 66 A +LPDI G+ L A +KK G TDL +I A S A FTTN CAAPVH+AK Sbjct: 6 AYELPDIHPVAGVYLGATAAKIKKNGKTDLVVIEFAPESVTAATFTTNACCAAPVHVAKK 65 Query: 67 HLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPL 126 HL RAL+IN+GNANA TG G +A C A ++GC+P +++PFSTGVI EPL Sbjct: 66 HLAKTQP-RALLINSGNANAATGESGFANAKQTCQWLADELGCEPEEILPFSTGVIGEPL 124 Query: 127 PADKI----IAALPKMQPAFWNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSG 182 P +KI +AA+ W A IMTTD VPK SR + D H + TG+AKGSG Sbjct: 125 PMNKIQLGLVAAVADRAIDHWPHAMAGIMTTDIVPKMVSRVVSI-DGHDITITGMAKGSG 183 Query: 183 MIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNS 242 MIHPNMATMLGF+ATDAK+++ +LQ + ++FN ITVDGDTSTND+ + AT + Sbjct: 184 MIHPNMATMLGFVATDAKITEELLQACLSQAVKKSFNRITVDGDTSTNDACTLTATQQAD 243 Query: 243 QSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYA 302 I + Y + + ELAQ IVRDGEGATKFI+V V + E + A+A Sbjct: 244 MPSITDAESTAYKAFAVEIERVMTELAQMIVRDGEGATKFISVEVNGGLSEAECLKVAHA 303 Query: 303 AARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEA 362 A SPLVKTA FASDPN G+ LAA+G A V LD + +E++L D+ + GGRAA YTE Sbjct: 304 VALSPLVKTAMFASDPNWGRILAAVGRAGVEQLDINRLEIFLGDVCIVRDGGRAADYTED 363 Query: 363 QGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 QGQ VM ++I+VRI+L+RGQ + TV+TCD S+ YV INA+YRS Sbjct: 364 QGQKVMKAEDISVRIELNRGQHSETVWTCDFSYDYVKINAEYRS 407 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: 385 Number of extensions: 11 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: 407 Length adjustment: 31 Effective length of query: 375 Effective length of database: 376 Effective search space: 141000 Effective search space used: 141000 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