Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_011841904.1 RSPH17029_RS14265 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_000015985.1:WP_011841904.1 Length = 445 Score = 285 bits (729), Expect = 2e-81 Identities = 175/400 (43%), Positives = 236/400 (59%), Gaps = 10/400 (2%) Query: 13 LPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHI--AKSHLFD 70 LP I G+ +AGV+ D+ LI +A G+ + VFT + AA V AK Sbjct: 50 LPAIGGVEFSAVEAGVRYQNRKDVMLIRLAPGTAMAGVFTRSSTRAACVLDCQAKIGAAS 109 Query: 71 EDGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADK 130 E G A+++N+GN+NA TGA G AV A +G +V STGVI EPLP ++ Sbjct: 110 EAGA-AIIVNSGNSNAFTGAVGVEAVEAVTRGVAEALGLPVERVFSSSTGVIGEPLPYER 168 Query: 131 IIAALPKMQPAFWNEA----ARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHP 186 I A +P + +A ARA+MTTDT PK AS + G+ ++ GIAKGSGMI P Sbjct: 169 ITAQIPALVEGLSGDAIEMAARAMMTTDTFPKGASATVE-GEGGPIQIAGIAKGSGMIAP 227 Query: 187 NMATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEI 246 +MATML +I TDAK+ QP+LQ M + TFN ITVD DTST+D+ ++ ATG + +E+ Sbjct: 228 DMATMLVYIFTDAKIPQPLLQKMLSRQVEATFNAITVDSDTSTSDALLLAATGTSPAAEL 287 Query: 247 DNIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARS 306 N + L + L+LAQ +VRDGEGA+KF+ VRV A + ++A + A A A S Sbjct: 288 -NGRSKAGRDFEAALGQVMLDLAQQVVRDGEGASKFVEVRVTGAASAEDAHKVAMAIANS 346 Query: 307 PLVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQA 366 PLVKTA DPN G+ + A+G + A D D + + DILVAE G R+ Y E G A Sbjct: 347 PLVKTAIAGEDPNWGRIVMAVGKSGAA-ADRDKLSIRFGDILVAEKGWRSPDYREEDGAA 405 Query: 367 VMSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 M + E+ V + L G + TV+TCDL+H Y+ INADYRS Sbjct: 406 YMKQAELVVAVDLGLGTDSRTVWTCDLTHRYIDINADYRS 445 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: 339 Number of extensions: 18 Number of successful extensions: 6 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: 445 Length adjustment: 32 Effective length of query: 374 Effective length of database: 413 Effective search space: 154462 Effective search space used: 154462 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: 51 (24.3 bits)
This GapMind analysis is from Apr 16 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