Align glutamate N-acetyltransferase/amino-acid acetyltransferase; EC 2.3.1.35 2.3.1.1 (characterized)
to candidate WP_092992063.1 BLP65_RS02000 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= CharProtDB::CH_000559 (406 letters) >NCBI__GCF_900102855.1:WP_092992063.1 Length = 404 Score = 370 bits (951), Expect = e-107 Identities = 202/399 (50%), Positives = 263/399 (65%), Gaps = 8/399 (2%) Query: 12 QLPDIDGIALYTAQAGVKKPGHTDLTLIAVAAGSTVGAVFTTNRFCAAPVHIAKSHLFDE 71 +L + G+ L T AG+KKPG DL LI +A G+T AVFT N FCAAPV +A+ HL Sbjct: 10 KLHPVGGVRLGTTAAGIKKPGRPDLVLIELARGATASAVFTRNAFCAAPVILAREHLSAR 69 Query: 72 DGVRALVINTGNANAGTGAQGRIDALAVCAAAARQIGCKPNQVMPFSTGVILEPLPADKI 131 + L++NTGNANAGTG QG +DA C A A + GC+ V+PFSTGVI EPLP + Sbjct: 70 EP-SYLLVNTGNANAGTGRQGLVDAQTCCEAVASRGGCEAADVLPFSTGVIGEPLPVATL 128 Query: 132 IAALPKMQPAF----WNEAARAIMTTDTVPKAASREGKVGDQHTVRATGIAKGSGMIHPN 187 +P A W AA I+TTDTVPK +SR+ ++G + V TGI+KG+GMI P+ Sbjct: 129 TQGIPAAFSALVAEGWANAADGILTTDTVPKGSSRQVEIGGR-PVTITGISKGAGMIRPD 187 Query: 188 MATMLGFIATDAKVSQPVLQLMTQEIADETFNTITVDGDTSTNDSFVIIATGKNSQSEID 247 MATML FIATDA V + VL + + A +FN I+VDGDTSTND+ V++ATG + Sbjct: 188 MATMLAFIATDAVVERDVLDGLLKRAAGLSFNRISVDGDTSTNDACVLMATGASGVKPEP 247 Query: 248 NIADPRYAQLKELLCSLALELAQAIVRDGEGATKFITVRVENAKTCDEARQAAYAAARSP 307 D + L+ + ++ ELAQ IVRDGEGATKFI ++V + E AY A SP Sbjct: 248 GSDD--FETLETAVTAVCRELAQLIVRDGEGATKFIAIKVVKGRDQKECTDVAYTIAHSP 305 Query: 308 LVKTAFFASDPNLGKRLAAIGYADVADLDTDLVEMYLDDILVAEHGGRAASYTEAQGQAV 367 LVKTAFFASDPN G+ LAA+G A V DL+ V ++L+++ + GGRAA Y EA+GQ V Sbjct: 306 LVKTAFFASDPNWGRILAAVGRAGVPDLNLQAVTIHLNEVCIVSDGGRAADYEEARGQLV 365 Query: 368 MSKDEITVRIKLHRGQAAATVYTCDLSHGYVSINADYRS 406 M ++EIT+R+ L RG A ATV+TCD S+ YV INA+YR+ Sbjct: 366 MDQEEITIRVDLSRGSAEATVWTCDFSYDYVRINAEYRT 404 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: 402 Number of extensions: 17 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: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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 Jul 25 2024. The underlying query database was built on Jul 25 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