1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	A	G	L	R	P	S	I	G	I	V	G	D	A	L	D	N	A	L	C	E	T	T	T	G	P	H	R	T	E	C	S	H	G	S	P	F	R	S	G	P	I	R	T	L	A	D	L	E	D	I	A	S	A	W	V	E	H	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?				?	?		?																									?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		C	H	T	Q	Q	G	V	R	I	P	G	R	L	Q	P	A
Secondary structure
SS confidence
Disorder								?	?	?	?	?	?	?	?	?	?
Disorder confidence

Confidence Key High(9)                     Low (0)

? Disordered ( 28%) Alpha helix ( 71%) Beta strand ( 0%)

Rank Aligned region

PDB 3f9k chain V Region: 4 - 76 Aligned: 64 Modelled: 73 Confidence: 98.0% Identity: 11% PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd Phyre2 PDB 1bco chain A domain 2 Region: 4 - 75 Aligned: 71 Modelled: 72 Confidence: 98.0% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 5cz1 chain B Region: 4 - 76 Aligned: 65 Modelled: 73 Confidence: 97.7% Identity: 11% PDB header:hydrolase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain of mmtv integrase Phyre2 PDB 3nf9 chain A Region: 4 - 71 Aligned: 60 Modelled: 68 Confidence: 96.9% Identity: 8% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design Phyre2 PDB 1asu chain A Region: 4 - 68 Aligned: 65 Modelled: 65 Confidence: 96.4% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 4mq3 chain A Region: 4 - 64 Aligned: 53 Modelled: 61 Confidence: 96.2% Identity: 19% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: the 1.1 angstrom structure of catalytic core domain of fiv integrase Phyre2 PDB 1c0m chain A domain 2 Region: 4 - 76 Aligned: 71 Modelled: 73 Confidence: 96.1% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3kks chain B Region: 4 - 76 Aligned: 63 Modelled: 73 Confidence: 95.9% Identity: 14% PDB header:dna binding protein Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii Phyre2 PDB 1bco chain A Region: 4 - 75 Aligned: 66 Modelled: 72 Confidence: 95.6% Identity: 14% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 5u1c chain A Region: 4 - 71 Aligned: 60 Modelled: 68 Confidence: 95.4% Identity: 8% PDB header:viral protein Chain: A: PDB Molecule:hiv-1 integrase, sso7d chimera; PDBTitle: structure of tetrameric hiv-1 strand transfer complex intasome Phyre2 PDB 1hyv chain A Region: 10 - 76 Aligned: 55 Modelled: 67 Confidence: 95.4% Identity: 9% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1exq chain A Region: 4 - 76 Aligned: 57 Modelled: 59 Confidence: 95.0% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1k6y chain B Region: 5 - 76 Aligned: 63 Modelled: 72 Confidence: 94.5% Identity: 10% PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase Phyre2 PDB 3jca chain E Region: 4 - 69 Aligned: 64 Modelled: 66 Confidence: 94.4% Identity: 19% PDB header:viral protein Chain: E: PDB Molecule:integrase; PDBTitle: core model of the mouse mammary tumor virus intasome Phyre2 PDB 1ex4 chain A Region: 2 - 76 Aligned: 66 Modelled: 75 Confidence: 94.2% Identity: 8% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain Phyre2 PDB 1c0m chain A Region: 4 - 76 Aligned: 71 Modelled: 73 Confidence: 94.1% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 5m0r chain F Region: 4 - 75 Aligned: 62 Modelled: 72 Confidence: 94.0% Identity: 16% PDB header:hydrolase Chain: F: PDB Molecule:integrase; PDBTitle: cryo-em reconstruction of the maedi-visna virus (mvv) strand transfer2 complex Phyre2 PDB 1c6v chain A Region: 15 - 76 Aligned: 53 Modelled: 62 Confidence: 93.3% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3l2t chain B Region: 2 - 75 Aligned: 65 Modelled: 74 Confidence: 92.5% Identity: 9% PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir) Phyre2 PDB 3hpg chain C Region: 4 - 75 Aligned: 62 Modelled: 72 Confidence: 90.1% Identity: 18% PDB header:transferase Chain: C: PDB Molecule:integrase; PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces Phyre2 1 c3f9kV_ 2 d1bcoa2 3 c5cz1B_ 4 c3nf9A_ 5 d1asua_ 6 c4mq3A_ 7 d1c0ma2 8 c3kksB_ 9 c1bcoA_ 10 c5u1cA_ 11 d1hyva_ 12 d1exqa_ 13 c1k6yB_ 14 c3jcaE_ 15 c1ex4A_ 16 c1c0mA_ 17 c5m0rF_ 18 d1c6va_ 19 c3l2tB_ 20 c3hpgC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75