Align glutamate N-acetyltransferase (EC 2.3.1.35) (characterized)
to candidate 3610184 Dshi_3565 arginine biosynthesis bifunctional protein ArgJ (RefSeq)
Query= BRENDA::Q92MJ1 (413 letters) >FitnessBrowser__Dino:3610184 Length = 407 Score = 392 bits (1007), Expect = e-113 Identities = 228/410 (55%), Positives = 268/410 (65%), Gaps = 11/410 (2%) Query: 6 SPLAPKTFAEMPALRGVRMATAAAGIKYKNRTDVLMMLFDRPASVAGVFTRSKCPSAPVD 65 SPLAP F ++P + GV ATA AG++Y R DV++ L + +AGVFTRS SA V Sbjct: 7 SPLAPAAFPDLPVISGVSFATAEAGVRYAGRRDVMLALCAPGSVLAGVFTRSATRSANVC 66 Query: 66 HCRQNLPGG--IARAVVVNSGNANAFTGKKGREATRLTAEAAAKAVGCSEAEVFLASTGV 123 C+ + G A+VVNSGN+NAFTGK G E+ ++A A +G A VF +STGV Sbjct: 67 DCQAKIDGDGPEGAAIVVNSGNSNAFTGKAGDESVAAISDAVAGVLGLPAARVFTSSTGV 126 Query: 124 IGEPLDATKFAGVLDKLAASATQDFWFEAAKAIMTTDTYPKVATRSAEIGGVKVAINGIA 183 IGE L + L LAA+ EAA+AIMTTDT+PK A I G V I GIA Sbjct: 127 IGERLPHDRITAKLADLAAALDPAGIAEAAEAIMTTDTFPKGAGAEIVIDGKPVRIAGIA 186 Query: 184 KGAGMIAPDMATMLSFVVTDADIAPAALQALLQAGVEPTFNSVTVDSDTSTSDTLMLFAT 243 KG+GMIAPDMATML ++ TDA I A LQALL TFN +TVDSDTSTSDTL+L AT Sbjct: 187 KGSGMIAPDMATMLVYIFTDAAIPRADLQALLSRLTNRTFNCITVDSDTSTSDTLLLAAT 246 Query: 244 GAAAGDGQAKVEDAADPRLDGFRAALDDLLRDLALQVVRDGEGARKMVEVTVEGAENDAA 303 GA+ D F AL ++ DLA QVVRDGEGA K V V V GA DA Sbjct: 247 GASGVDVTGST---------AFEVALHGVMLDLAHQVVRDGEGATKFVTVRVTGACTDAD 297 Query: 304 AKRIALSIANSPLVKTAVAGEDANWGRVVMAVGKSGEMAERDRLAIWFGDIRVAVEGERD 363 A+ ALSIANSPLVKTA+AGED NWGRVVMAVGKSG A+RDRL I FGDI VA G Sbjct: 298 ARTHALSIANSPLVKTAIAGEDPNWGRVVMAVGKSGAEADRDRLTIRFGDILVAENGWVA 357 Query: 364 PAYSEAAATAVMQGETIPIRVDIGLGSGRATVYTCDLTKEYVEINGDYRS 413 P+Y+EAA A MQ E I + VD+GLG+G ATV+TCDLTK Y+EIN DYRS Sbjct: 358 PSYTEAAGAAYMQREEIEVAVDLGLGTGAATVWTCDLTKRYIEINADYRS 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: 459 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 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