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Table 4 Simplification of Table 3 by removal of slightly overlapping mIMRs

From: Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins

Rank mIMR prot len DNA positions AA positions Structure or function
1 #1-gag MA 95 0270-aa..ca-0364 091-RI..DT-122 MA-H5 related to viral entry
2 #2-gag CA 87 0742-gg..tg-0828 248-GW..RM-276 CA-H7 longest constituent of viral core
3 #3-gag p1 85 1256-aa..aa-1340 419-EG..GN-447 end NC, p1 to p1-p6 cleavage site
4 #6-gag NC 81 1171-aa..ga-1251 391-KC..CG-417 1st cys-his box; EF1α binding
5 #7-gag p2 80 1065-ac..ca-1144 356-PG..GN-382 p2, critical to budding
6 #10-gag CA 76 0812-at..ta-0887 271-NK..DY-296 major homology region
7 #11-gag CA 75 0920-ag..ga-0994 307-EQ..KT-332 endocytosis signal 1; CA-H9 helix
8 #14-gag CA 69 0985-ga..ag-1053 329-DC..QG-351 endocytosis signal 2; CA-H10 helix
9 #15-gag CA 64 0543-ca..aa-0606 181-PQ..LK-202 CA-H3-H4 helices, part of viral core
10 #17-gag NC 64 1362-gc..ag-1425 455-PT..QK-475 L-domain (budding); Tsg101
      455-PT..QK-475 docking; ubiquitin-gag conjugate
11 #1-NC NC 59 1209-aa..aa-1267 404-NC..QM-423 2cd cys-his box; end NC
12 #2-NC NC 47 1153-aa..ca-1199 385-NQ..GH-400 EF1α binding
  1. MIMRs that begin and end within two amino acids of a larger mIMR have been removed. Although the distribution of mIMRs is nearly continuous throughout gag, the functional and/or structural association of each is discrete, as indicated by the structure-function notation in the right hand column of this table, which is described in greater detail in Additional File 1.