Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_073037615.1 BUB04_RS05200 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_900129305.1:WP_073037615.1 Length = 408 Score = 344 bits (882), Expect = 3e-99 Identities = 191/396 (48%), Positives = 256/396 (64%), Gaps = 6/396 (1%) Query: 21 GVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVDHCRQNLPG--GIARA 78 G R+A A +G++YK+R D +M+ D PAS AG+FTR++ +APV CR++L G ARA Sbjct: 16 GFRVAAARSGMRYKDRLDCALMVSDVPASAAGIFTRNRFCAAPVMVCREHLAASAGTARA 75 Query: 79 VVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIGEPLDATKFAGVLD 138 V+VN+G ANA TG +G E R +A A A+ +G A V +ASTGVIG + VL Sbjct: 76 VLVNAGIANACTGDEGLERARRSARAVARRLGVDPARVLVASTGVIGPQIREELLEAVLP 135 Query: 139 KLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIAKGAGMIAPDMATMLS 198 LA + W +AA+AIMTTDT PK A +GG +V + GIAKG+GMIAPDMATML+ Sbjct: 136 DLAEHLAPEGWEDAARAIMTTDTVPKTAWAKGILGGKEVTVGGIAKGSGMIAPDMATMLA 195 Query: 199 FVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATGAAAGDGQAKVEDAA 258 FV TDA ++P LQALL+ + TFN +TVD DTST+DT+++ A+GAA G ++D Sbjct: 196 FVATDAAVSPDVLQALLKEVSDRTFNRITVDGDTSTNDTVLVLASGAA---GNPSIQDPH 252 Query: 259 DPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAAKRIALSIANSPLVK 318 P F L+ + DLA Q+VRDGEGA K V V V GA A R+A ++ANSPLVK Sbjct: 253 GPDAHDFLNLLEAVCADLARQIVRDGEGATKFVTVRVRGARTRDRAARVARTVANSPLVK 312 Query: 319 TAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGE-RDPAYSEAAATAVMQG 377 TA+ G+DANWGRVV A G++G DR+++ FGD+ V G E A+AV++ Sbjct: 313 TALFGQDANWGRVVAAAGRAGVDFAPDRVSLRFGDVTVFENGRPLSGPELEEKASAVLRP 372 Query: 378 ETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 + + I +D+G G T YTCD + +YV+IN DYRS Sbjct: 373 KEVEIALDLGEGEEEDTYYTCDFSYDYVKINADYRS 408 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: 378 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: 413 Length of database: 408 Length adjustment: 31 Effective length of query: 382 Effective length of database: 377 Effective search space: 144014 Effective search space used: 144014 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 10 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