Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_092058723.1 BQ4888_RS16595 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_900111775.1:WP_092058723.1 Length = 399 Score = 322 bits (824), Expect = 2e-92 Identities = 180/400 (45%), Positives = 254/400 (63%), Gaps = 6/400 (1%) Query: 15 EMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVDHCRQNLPGG 74 ++ + G R A AAG+K R D+ +++ D+PA AGVFT +K +APV C + G Sbjct: 5 DLHGVAGFRFAAGAAGLKKSGRLDLALIVADKPALCAGVFTTNKVVAAPVQICAPRIRQG 64 Query: 75 IARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIGEPLDATKFA 134 +A++VNSGNANA TG++GR+ AA A+G E V ++STGVIG PL KF Sbjct: 65 RCQAILVNSGNANACTGEQGRQDALRCGAIAAAALGIDEELVAVSSTGVIGAPLPMAKFE 124 Query: 135 GVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIAKGAGMIAPDMA 194 + KLAA +D E A AIMTTD++ K + E+ G I G+AKGAGMI P+MA Sbjct: 125 EAVPKLAAQLREDHADEVAAAIMTTDSFAKRYAVTGEVDGRPYRILGVAKGAGMIHPNMA 184 Query: 195 TMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATGAAAGDGQAKV 254 TML+F++TDA++ + L+ V+ +FN +TVD DTST+D ++L A+GAA G A + Sbjct: 185 TMLAFILTDAELEGGFVDTALRQSVDGSFNCITVDRDTSTNDMVLLLASGAA---GNAPI 241 Query: 255 EDAADPRLDG-FRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAAKRIALSIAN 313 AA + G F++ LD++L +LA +VRDGEGA K+V + V GA +DA A++ A S+A Sbjct: 242 --AAGSKAAGEFQSLLDEVLLELAKMIVRDGEGATKLVRIEVTGAASDAEARQAACSVAT 299 Query: 314 SPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGERDPAYSEAAATA 373 S LVKTA G+DANWGR++ AVG SG + +++ I FG++ V +G EA AT Sbjct: 300 SSLVKTAFFGQDANWGRIIAAVGYSGAQVDPEKVDIRFGEVPVVKDGLGTGKELEAKATE 359 Query: 374 VMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 V++ + +D+ GSGRA YT DLT +YV+IN DYRS Sbjct: 360 VLKTPEFTVFIDLKQGSGRAYYYTSDLTYDYVKINADYRS 399 Lambda K H 0.316 0.130 0.365 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: 375 Number of extensions: 16 Number of successful extensions: 3 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: 413 Length of database: 399 Length adjustment: 31 Effective length of query: 382 Effective length of database: 368 Effective search space: 140576 Effective search space used: 140576 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 (21.6 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