Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_059149857.1 V474_RS01890 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_001046635.1:WP_059149857.1 Length = 408 Score = 369 bits (948), Expect = e-107 Identities = 210/413 (50%), Positives = 268/413 (64%), Gaps = 5/413 (1%) Query: 1 MSGSVSPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCP 60 M+ VSPLA F +PA+ GV AG K R D+ + F+ +VAGVFT++ C Sbjct: 1 MAYPVSPLA-SPFPALPAIAGVTPHVVRAGYKDWGRCDLTYVTFEAGTAVAGVFTKNLCC 59 Query: 61 SAPVDHCRQNLPGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLAS 120 S+ V+ R N+ G ARA+VVN+GN+NAFTG +GREA + A +G +VF++S Sbjct: 60 SSEVELGRDNIVQGRARALVVNAGNSNAFTGYRGREAVEQIMDQVAAHIGAPREQVFVSS 119 Query: 121 TGVIGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAIN 180 TGVIG PL K ++K A +A W +AA I TTDT+ K A +A IG KV I+ Sbjct: 120 TGVIGVPLPKDKAREGVEK-ALTAQPCTWEDAANTIATTDTFAKGAAATAMIGDTKVTIS 178 Query: 181 GIAKGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLML 240 I KG+GMIAPDMATML ++ TDA + PA LQA L A TF+ +TVDSDTSTSDT++ Sbjct: 179 AIIKGSGMIAPDMATMLGYLFTDAAVEPAFLQACLSAANLRTFSCITVDSDTSTSDTVLA 238 Query: 241 FATGAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAEN 300 FATG A G A + F AA+ D+ R LA VVRDGEGA+K + V V GA + Sbjct: 239 FATGKA---GNAPLTSFQSDGAHAFAAAVHDVCRQLAHLVVRDGEGAQKFIAVAVTGAVS 295 Query: 301 DAAAKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEG 360 D +A+++ ++IANSPLVKTA+AGEDANWGRVVMAVGK+GE A+RD+L+I FG A EG Sbjct: 296 DESARKVGMAIANSPLVKTAIAGEDANWGRVVMAVGKAGEPADRDKLSIGFGGTWAAREG 355 Query: 361 ERDPAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 Y EA A ++G I I VD+GLG G ATV+TCDLT Y+ IN DYRS Sbjct: 356 VPLADYDEAPVAAHLKGHDISIEVDLGLGDGSATVWTCDLTHGYISINADYRS 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: 393 Number of extensions: 9 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: 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 Jul 26 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