Secondary structure and disorder prediction

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

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1l5i chain A Region: 32 - 119 Aligned: 61 Modelled: 72 Confidence: 81.6% Identity: 30% Fold: Origin of replication-binding domain, RBD-like Superfamily: Origin of replication-binding domain, RBD-like Family: DNA-binding domain of REP protein Phyre2 PDB 2ns6 chain A Region: 34 - 113 Aligned: 55 Modelled: 55 Confidence: 73.8% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:mobilization protein a; PDBTitle: crystal structure of the minimal relaxase domain of moba2 from plasmid r1162 Phyre2 PDB 3dkx chain A Region: 102 - 117 Aligned: 16 Modelled: 16 Confidence: 71.5% Identity: 25% PDB header:replication Chain: A: PDB Molecule:replication protein repb; PDBTitle: crystal structure of the replication initiator protein2 encoded on plasmid pmv158 (repb), trigonal form, to 2.7 ang3 resolution Phyre2 PDB 2x3g chain A Region: 101 - 117 Aligned: 17 Modelled: 17 Confidence: 63.0% Identity: 41% PDB header:viral protein Chain: A: PDB Molecule:sirv1 hypothetical protein orf119; PDBTitle: crystal structure of the hypothetical protein orf119 from2 sulfolobus islandicus rod-shaped virus 1 Phyre2 PDB 2hwt chain A Region: 89 - 119 Aligned: 31 Modelled: 31 Confidence: 39.9% Identity: 16% PDB header:replication, hydrolase Chain: A: PDB Molecule:putative replicase-associated protein; PDBTitle: nmr solution structure of the master-rep protein nuclease2 domain (2-95) from the faba bean necrotic yellows virus Phyre2 PDB 2nzc chain A domain 1 Region: 21 - 76 Aligned: 50 Modelled: 56 Confidence: 16.9% Identity: 14% Fold: Ferredoxin-like Superfamily: ACT-like Family: TM1266-like Phyre2 PDB 1f86 chain A Region: 100 - 116 Aligned: 17 Modelled: 17 Confidence: 16.5% Identity: 29% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 1tta chain A Region: 100 - 116 Aligned: 17 Modelled: 17 Confidence: 15.4% Identity: 29% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 1tfp chain A Region: 100 - 116 Aligned: 17 Modelled: 17 Confidence: 12.5% Identity: 35% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 2h1x chain B Region: 103 - 116 Aligned: 14 Modelled: 14 Confidence: 10.7% Identity: 36% PDB header:hydrolase Chain: B: PDB Molecule:5-hydroxyisourate hydrolase (formerly known as PDBTitle: crystal structure of 5-hydroxyisourate hydrolase (formerly2 known as trp, transthyretin related protein) Phyre2 PDB 2h0e chain A Region: 103 - 116 Aligned: 14 Modelled: 14 Confidence: 10.4% Identity: 43% PDB header:hydrolase Chain: A: PDB Molecule:transthyretin-like protein pucm; PDBTitle: crystal structure of pucm in the absence of substrate Phyre2 PDB 2gpz chain C Region: 103 - 116 Aligned: 14 Modelled: 14 Confidence: 9.6% Identity: 36% PDB header:hydrolase Chain: C: PDB Molecule:transthyretin-like protein; PDBTitle: transthyretin-like protein from salmonella dublin Phyre2 PDB 4a69 chain A Region: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 9.3% Identity: 26% PDB header:transcription Chain: A: PDB Molecule:histone deacetylase 3,; PDBTitle: structure of hdac3 bound to corepressor and inositol tetraphosphate Phyre2 PDB 2ljh chain A Region: 93 - 125 Aligned: 33 Modelled: 33 Confidence: 9.2% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:double-stranded rna-specific editase adar; PDBTitle: nmr structure of double-stranded rna-specific editase adar Phyre2 PDB 2hw0 chain A Region: 88 - 119 Aligned: 32 Modelled: 32 Confidence: 8.8% Identity: 22% PDB header:hydrolase, replication Chain: A: PDB Molecule:replicase; PDBTitle: nmr solution structure of the nuclease domain from the2 replicator initiator protein from porcine circovirus pcv2 Phyre2 PDB 1oo2 chain A Region: 100 - 116 Aligned: 17 Modelled: 17 Confidence: 8.7% Identity: 29% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 1kgi chain A Region: 100 - 116 Aligned: 17 Modelled: 17 Confidence: 8.6% Identity: 35% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 1ohe chain A domain 1 Region: 4 - 36 Aligned: 33 Modelled: 33 Confidence: 8.3% Identity: 9% Fold: (Phosphotyrosine protein) phosphatases II Superfamily: (Phosphotyrosine protein) phosphatases II Family: Dual specificity phosphatase-like Phyre2 PDB 1luz chain A Region: 4 - 39 Aligned: 35 Modelled: 36 Confidence: 8.1% Identity: 17% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 3max chain B Region: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 7.7% Identity: 22% PDB header:hydrolase Chain: B: PDB Molecule:histone deacetylase 2; PDBTitle: crystal structure of human hdac2 complexed with an n-(2-aminophenyl)2 benzamide Phyre2 1 d1l5ia_ 2 c2ns6A_ 3 c3dkxA_ 4 c2x3gA_ 5 c2hwtA_ 6 d2nzca1 7 d1f86a_ 8 d1ttaa_ 9 d1tfpa_ 10 c2h1xB_ 11 c2h0eA_ 12 c2gpzC_ 13 c4a69A_ 14 c2ljhA_ 15 c2hw0A_ 16 d1oo2a_ 17 d1kgia_ 18 d1ohea1 19 d1luza_ 20 c3maxB_ 21 22 23 24 25 26 27 28

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 d1l5ia_ 81.6 30 Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:DNA-binding domain of REP protein 2 c2ns6A_ 73.8 15 PDB header:hydrolase Chain: A: PDB Molecule:mobilization protein a; PDBTitle: crystal structure of the minimal relaxase domain of moba2 from plasmid r1162 3 c3dkxA_ 71.5 25 PDB header:replication Chain: A: PDB Molecule:replication protein repb; PDBTitle: crystal structure of the replication initiator protein2 encoded on plasmid pmv158 (repb), trigonal form, to 2.7 ang3 resolution 4 c2x3gA_ 63.0 41 PDB header:viral protein Chain: A: PDB Molecule:sirv1 hypothetical protein orf119; PDBTitle: crystal structure of the hypothetical protein orf119 from2 sulfolobus islandicus rod-shaped virus 1 5 c2hwtA_ 39.9 16 PDB header:replication, hydrolase Chain: A: PDB Molecule:putative replicase-associated protein; PDBTitle: nmr solution structure of the master-rep protein nuclease2 domain (2-95) from the faba bean necrotic yellows virus 6 d2nzca1 16.9 14 Fold:Ferredoxin-like Superfamily:ACT-like Family:TM1266-like 7 d1f86a_ 16.5 29 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 8 d1ttaa_ 15.4 29 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 9 d1tfpa_ 12.5 35 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 10 c2h1xB_ 10.7 36 PDB header:hydrolase Chain: B: PDB Molecule:5-hydroxyisourate hydrolase (formerly known as PDBTitle: crystal structure of 5-hydroxyisourate hydrolase (formerly2 known as trp, transthyretin related protein) 11 c2h0eA_ 10.4 43 PDB header:hydrolase Chain: A: PDB Molecule:transthyretin-like protein pucm; PDBTitle: crystal structure of pucm in the absence of substrate 12 c2gpzC_ 9.6 36 PDB header:hydrolase Chain: C: PDB Molecule:transthyretin-like protein; PDBTitle: transthyretin-like protein from salmonella dublin 13 c4a69A_ 9.3 26 PDB header:transcription Chain: A: PDB Molecule:histone deacetylase 3,; PDBTitle: structure of hdac3 bound to corepressor and inositol tetraphosphate 14 c2ljhA_ 9.2 12 PDB header:hydrolase Chain: A: PDB Molecule:double-stranded rna-specific editase adar; PDBTitle: nmr structure of double-stranded rna-specific editase adar 15 c2hw0A_ 8.8 22 PDB header:hydrolase, replication Chain: A: PDB Molecule:replicase; PDBTitle: nmr solution structure of the nuclease domain from the2 replicator initiator protein from porcine circovirus pcv2 16 d1oo2a_ 8.7 29 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 17 d1kgia_ 8.6 35 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 18 d1ohea1 8.3 9 Fold:(Phosphotyrosine protein) phosphatases II Superfamily:(Phosphotyrosine protein) phosphatases II Family:Dual specificity phosphatase-like 19 d1luza_ 8.1 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 20 c3maxB_ 7.7 22 PDB header:hydrolase Chain: B: PDB Molecule:histone deacetylase 2; PDBTitle: crystal structure of human hdac2 complexed with an n-(2-aminophenyl)2 benzamide 21 c3ew8A_ not modelled 7.7 26 PDB header:hydrolase Chain: A: PDB Molecule:histone deacetylase 8; PDBTitle: crystal structure analysis of human hdac8 d101l variant 22 d1m55a_ not modelled 7.6 13 Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:Replication protein Rep, nuclease domain 23 d1t64a_ not modelled 7.1 26 Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Histone deacetylase, HDAC 24 c3qvaB_ not modelled 6.0 17 PDB header:hydrolase Chain: B: PDB Molecule:transthyretin-like protein; PDBTitle: structure of klebsiella pneumoniae 5-hydroxyisourate hydrolase 25 c1oheA_ not modelled 5.9 9 PDB header:hydrolase Chain: A: PDB Molecule:cdc14b2 phosphatase; PDBTitle: structure of cdc14b phosphatase with a peptide ligand 26 c3swfA_ not modelled 5.7 21 PDB header:transport protein Chain: A: PDB Molecule:cgmp-gated cation channel alpha-1; PDBTitle: cnga1 621-690 containing clz domain 27 c2jepB_ not modelled 5.4 8 PDB header:hydrolase Chain: B: PDB Molecule:xyloglucanase; PDBTitle: native family 5 xyloglucanase from paenibacillus pabuli 28 c3ugsB_ not modelled 5.3 3 PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0