Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_077280034.1 B1C78_RS15285 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_002000365.1:WP_077280034.1 Length = 403 Score = 371 bits (953), Expect = e-107 Identities = 219/410 (53%), Positives = 268/410 (65%), Gaps = 11/410 (2%) Query: 1 MAVNLTEKTAEQLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAP 60 M +NLTE T E LP + G+ L A AG++ DL L+ VA S V AVFT N FCAAP Sbjct: 1 MPINLTEPT-ELLP-VPGVRLGVAAAGIRYRDRADLVLMEVAVRSNVAAVFTQNAFCAAP 58 Query: 61 VHIAKSHLFDEDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTG 120 V +A+ HL GVR L+IN+GNANAGTG +G DA A CA A +G + QV+PFSTG Sbjct: 59 VIVAREHLA-AGGVRYLLINSGNANAGTGDRGLKDARASCAHVAEILGGQAEQVLPFSTG 117 Query: 121 VILEPLPADKIIAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATG 176 VI E LP ++ A+P + W +A RAIMTTDTV K SR + TV TG Sbjct: 118 VIGEHLPVPRVREAMPGLAAGLAADNWMDAMRAIMTTDTVGKGISRRVTLSGG-TVTLTG 176 Query: 177 IAKGSGMIHPNMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVII 236 IAKGSGMI P+MATML F+ATDA V LQ M +E+FN ITVDGDTSTND+ V+ Sbjct: 177 IAKGSGMIRPDMATMLAFLATDAVVPAGDLQEMLNAAVEESFNCITVDGDTSTNDACVLA 236 Query: 237 ATGKNSQSEIDNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEA 296 ATG + ++ R+A + +C LAQAIVRDGEGATKFIT+ V +T DEA Sbjct: 237 ATGASGVRVAEDDDRRRFAAALQAVCDF---LAQAIVRDGEGATKFITLHVTGGQTPDEA 293 Query: 297 RQAAYAAARSPLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRA 356 R+ A A A SPLVKTA FASDPN G+ LAA+G A VA LD V + + D+L+ E GGRA Sbjct: 294 RRVADAVAHSPLVKTALFASDPNWGRILAAVGRAGVAGLDVSRVRIEIGDVLIVEGGGRA 353 Query: 357 ASYTEAQGQAVMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 A+YTE G+ VM + EI + I L RG++ A VYTCDLS+ YV INA+YRS Sbjct: 354 AAYTEEAGRQVMDQAEIPIYIHLGRGRSEARVYTCDLSYDYVRINAEYRS 403 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: 423 Number of extensions: 20 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: 403 Length adjustment: 31 Effective length of query: 375 Effective length of database: 372 Effective search space: 139500 Effective search space used: 139500 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