1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		V	R	P	A	T	P	L	I	C	A	F	G	D	K	H	K	H	T	Y	G	V	T	P	I	C	R	A	L	A	V	H	G	V	Q	I	A	S	R	T	Y	F	A	D	R	A	A	A	P	S	K	R	A	L	W	D	T	T	I	T	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?																									?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	L	A	G	Y	Y	E	P	D	A	E	G	K	R	P	P	E	C	L	Y	G	S	L	K	M	W	A	H	L	Q	R	Q	G	F	R	W	P	S	A	T	V	K	T	I	M	R	A	N	G	W	R	G	V	P	L	A	A	H	I	T
Secondary structure
SS confidence
Disorder											?	?	?	?	?	?	?																																		?			?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		H	H	R	T	R	P	G	R	G	P	G	P	R	P	G	G	S	A	M	A	G	F	S	N	E	P	A	G	S	G	R	L	H	L	R	A	D	D	V	E	F	R	L	H	R	V	R	G	R	R	L	R	R	C	D	R	G	L	G	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?					?	?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.
Sequence		L	A	D	Q	R	R	S	V	R	R	T	R	I	T	P	R	P	S	R	L	T
Secondary structure
SS confidence
Disorder				?	?	?	?		?	?	?	?	?		?	?	?	?	?	?	?	?
Disorder confidence

Confidence Key High(9)                     Low (0)

? Disordered ( 30%) Alpha helix ( 59%) Beta strand ( 2%)

Rank Aligned region

PDB 4fcy chain A Region: 4 - 197 Aligned: 178 Modelled: 194 Confidence: 97.1% Identity: 14% PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposase; PDBTitle: crystal structure of the bacteriophage mu transpososome Phyre2 PDB 1u78 chain A Region: 12 - 109 Aligned: 81 Modelled: 98 Confidence: 95.3% Identity: 7% PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna Phyre2 PDB 1pdn chain C Region: 4 - 104 Aligned: 88 Modelled: 101 Confidence: 94.7% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A Region: 4 - 111 Aligned: 95 Modelled: 108 Confidence: 94.4% Identity: 14% PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions Phyre2 PDB 1c0m chain A Region: 129 - 162 Aligned: 34 Modelled: 34 Confidence: 88.8% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 3hef chain B Region: 8 - 68 Aligned: 53 Modelled: 61 Confidence: 87.2% Identity: 17% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small subunit Phyre2 PDB 1asu chain A Region: 128 - 162 Aligned: 35 Modelled: 35 Confidence: 85.8% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 2ahq chain A Region: 56 - 109 Aligned: 49 Modelled: 54 Confidence: 84.6% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: solution structure of the c-terminal rpon domain of sigma-2 54 from aquifex aeolicus Phyre2 PDB 1c0m chain A domain 2 Region: 127 - 162 Aligned: 36 Modelled: 36 Confidence: 84.0% Identity: 19% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 6gh5 chain M Region: 14 - 110 Aligned: 92 Modelled: 97 Confidence: 83.1% Identity: 14% PDB header:transcription Chain: M: PDB Molecule:rna polymerase sigma-54 factor,rna polymerase sigma-54 PDBTitle: cryo-em structure of bacterial rna polymerase-sigma54 holoenzyme2 transcription open complex Phyre2 PDB 5nwt chain M Region: 56 - 110 Aligned: 50 Modelled: 55 Confidence: 82.1% Identity: 22% PDB header:transferase Chain: M: PDB Molecule:rna polymerase sigma-54 factor,rna polymerase sigma-54 PDBTitle: crystal structure of escherichia coli rna polymerase - sigma542 holoenzyme complex Phyre2 PDB 1aoy chain A Region: 52 - 114 Aligned: 55 Modelled: 63 Confidence: 81.8% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Arginine repressor (ArgR), N-terminal DNA-binding domain Phyre2 PDB 5unk chain A Region: 82 - 117 Aligned: 36 Modelled: 36 Confidence: 81.5% Identity: 17% PDB header:dna binding protein Chain: A: PDB Molecule:sleeping beauty transposase; PDBTitle: nmr structure of the red subdomain of the sleeping beauty transposase Phyre2 PDB 5byh chain M Region: 56 - 110 Aligned: 50 Modelled: 55 Confidence: 81.0% Identity: 22% PDB header:transferase Chain: M: PDB Molecule:rna polymerase sigma-54 factor; PDBTitle: crystal structure of escherichia coli rna polymerase - sigma542 holoenzyme complex Phyre2 PDB 1rzs chain A Region: 20 - 60 Aligned: 36 Modelled: 41 Confidence: 80.9% Identity: 22% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2mt3 chain A Region: 56 - 118 Aligned: 58 Modelled: 63 Confidence: 80.6% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-54 factor; PDBTitle: structure of -24 dna binding domain of sigma 54 from e.coli Phyre2 PDB 2o8k chain A Region: 56 - 110 Aligned: 50 Modelled: 55 Confidence: 80.3% Identity: 24% PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element Phyre2 PDB 5cz1 chain B Region: 133 - 162 Aligned: 30 Modelled: 30 Confidence: 79.2% Identity: 3% PDB header:hydrolase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain of mmtv integrase Phyre2 PDB 5ui5 chain I Region: 55 - 117 Aligned: 54 Modelled: 63 Confidence: 77.3% Identity: 19% PDB header:transcription/dna Chain: I: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: crystal structure of aquifex aeolicus sigman bound to promoter dna Phyre2 PDB 3v4g chain A Region: 56 - 114 Aligned: 51 Modelled: 59 Confidence: 75.3% Identity: 12% PDB header:dna binding protein Chain: A: PDB Molecule:arginine repressor; PDBTitle: 1.60 angstrom resolution crystal structure of an arginine repressor2 from vibrio vulnificus cmcp6 Phyre2 1 c4fcyA_ 2 c1u78A_ 3 d1pdnc_ 4 c6paxA_ 5 c1c0mA_ 6 c3hefB_ 7 d1asua_ 8 c2ahqA_ 9 d1c0ma2 10 c6gh5M_ 11 c5nwtM_ 12 d1aoya_ 13 c5unkA_ 14 c5byhM_ 15 d1rzsa_ 16 c2mt3A_ 17 c2o8kA_ 18 c5cz1B_ 19 c5ui5I_ 20 c3v4gA_ 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 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111