Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate WP_012048893.1 SWIT_RS13595 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ
Query= BRENDA::Q92MJ1 (413 letters) >NCBI__GCF_000016765.1:WP_012048893.1 Length = 407 Score = 424 bits (1089), Expect = e-123 Identities = 232/408 (56%), Positives = 279/408 (68%), Gaps = 4/408 (0%) Query: 6 SPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVD 65 SPLAP F ++P + G R+A A AG K +R D+ FD VAGV T S+CPS V+ Sbjct: 4 SPLAPAAFPDLPPIAGARVAVARAGYKRWDRADLTYAAFDEGTVVAGVTTTSRCPSPEVE 63 Query: 66 HCRQNLPGGIARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGVIG 125 CR LP G ARA+VVN+GN+NAFTG +GR A A A+GC ++VF+ASTGVIG Sbjct: 64 WCRAALPLGQARALVVNAGNSNAFTGNRGRAAVEAITARVAGAIGCRPSDVFVASTGVIG 123 Query: 126 EPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIAKG 185 PL K +D + A + W EAA IMTTDT+ K A SA +GG +V + GI KG Sbjct: 124 VPLPIDKAEAGIDAVLR-APEASWEEAAATIMTTDTFAKAARASAMVGGARVELVGIVKG 182 Query: 186 AGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFATGA 245 +GMIAPDMATML FV TDA IAP LQA+L +F+ +TVD DTSTSDT++ FATG Sbjct: 183 SGMIAPDMATMLGFVFTDAAIAPELLQAMLNRANARSFSCITVDGDTSTSDTVLAFATGK 242 Query: 246 AAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAAAK 305 A G A++E DP D AAL+ + +LA VVRDGEGA K + VTVEGAE+DA+A Sbjct: 243 A---GHARLETMDDPGADALEAALNAVCLELAQLVVRDGEGASKFIAVTVEGAESDASAH 299 Query: 306 RIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGERDPA 365 RIALSIANSPLVKTA+AGEDANWGRVVMAVGK+GE AERDRL+I FG +VA G Sbjct: 300 RIALSIANSPLVKTAIAGEDANWGRVVMAVGKAGEPAERDRLSIRFGATQVATGGLAVEG 359 Query: 366 YSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 Y EA A ++G I I VDIGLG+GRATV+TCDLT Y+ IN DYRS Sbjct: 360 YDEAPVAAHLKGREIEIGVDIGLGNGRATVWTCDLTHGYISINADYRS 407 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: 414 Number of extensions: 11 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: 407 Length adjustment: 31 Effective length of query: 382 Effective length of database: 376 Effective search space: 143632 Effective search space used: 143632 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 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