Only the N-terminal domain of the unbound HIV capsid is used.

NOTE THAT IN THE ALIGNMENTS BELOW, GAPS MOST LIKELY INDICATE
RESIDUES MISSING IN THE ELECTRON DENSITY.
Alignment: 1AK4_A against 2CPL_
Query= 
         (165 letters)

>2CPL_
          Length = 164

 Score =  343 bits (881), Expect = e-100
 Identities = 164/164 (100%), Positives = 164/164 (100%)

Query: 2   VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFM 61
           VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFM
Sbjct: 1   VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFM 60

Query: 62  CQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEW 121
           CQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEW
Sbjct: 61  CQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEW 120

Query: 122 LDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 165
           LDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Sbjct: 121 LDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE 164


Alignment: 1AK4_D against 1E6J_P
Query= 
         (145 letters)

>1E6J_P
          Length = 210

 Score =  275 bits (704), Expect = 2e-79
 Identities = 133/135 (98%), Positives = 135/135 (99%)

Query: 11  VHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLK 70
           VHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLK
Sbjct: 1   VHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLK 60

Query: 71  ETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIY 130
           ETINEEAAEWDR+HPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMT+NPPIPVGEIY
Sbjct: 61  ETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIY 120

Query: 131 KRWIILGLNKIVRMY 145
           KRWIILGLNKIVRMY
Sbjct: 121 KRWIILGLNKIVRMY 135



 Score = 14.6 bits (26), Expect = 0.95
 Identities = 5/8 (62%), Positives = 5/8 (62%)

Query: 112 QEQIGWMT 119
           QE   WMT
Sbjct: 169 QEVKNWMT 176