Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	Y	D	S	E	F	G	S	H	V	S	L	Y	R	D	R	I	K	Q	V	I	D	D	S	L	N	E	H	L	N	S	M	I	L	R	V	D	L	H	D	P	I	D	T	E	N	M	D	N	P	F	F	Q	P	R	V	D	S	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																							?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	I	S	R	F	T	S	A	L	K	A	K	L	K	H	D	K	H	I	K	T	Q	R	K	D	W	P	D	S	R	H	S	T	L	R	Y	A	W	V	R	E	Y	T	K	N	R	K	R	H	Y	H	L	I	L	C	F	N	Q	D	A
Secondary structure
SS confidence
Disorder																					?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	Y	H	L	G	D	Y	D	L	N	R	N	T	L	R	T	M	I	T	T	A	W	Y	S	A	L	G	I	P	I	D	S	S	G	K	L	V	N	Y	P	P	N	G	K	Y	L	L	N	R	K	R	D	N	F	E	Q	T	Y	S	D
Secondary structure
SS confidence
Disorder								?		?																				?																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.
Sequence		L	M	N	R	V	D	Y	M	T	K	V	R	T	K	I	V	G	D	G	D	R	N	F	G	C	S	R	G
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: 31 - 120 Aligned: 61 Modelled: 72 Confidence: 74.1% Identity: 16% 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 3dkx chain A Region: 103 - 118 Aligned: 16 Modelled: 16 Confidence: 69.9% Identity: 31% 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: 102 - 118 Aligned: 17 Modelled: 17 Confidence: 61.1% Identity: 24% 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 2ns6 chain A Region: 33 - 114 Aligned: 55 Modelled: 67 Confidence: 25.7% Identity: 18% 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 2nzc chain A domain 1 Region: 22 - 75 Aligned: 48 Modelled: 54 Confidence: 17.4% Identity: 17% Fold: Ferredoxin-like Superfamily: ACT-like Family: TM1266-like Phyre2 PDB 2hw0 chain A Region: 89 - 120 Aligned: 32 Modelled: 32 Confidence: 11.5% Identity: 9% 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 2hwt chain A Region: 89 - 120 Aligned: 32 Modelled: 32 Confidence: 10.2% Identity: 9% 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 1m55 chain A Region: 86 - 178 Aligned: 85 Modelled: 93 Confidence: 10.2% Identity: 11% Fold: Origin of replication-binding domain, RBD-like Superfamily: Origin of replication-binding domain, RBD-like Family: Replication protein Rep, nuclease domain Phyre2 PDB 3max chain B Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 9.9% Identity: 26% 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 PDB 2h1x chain B Region: 104 - 117 Aligned: 14 Modelled: 14 Confidence: 9.9% 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 1f86 chain A Region: 101 - 117 Aligned: 17 Modelled: 17 Confidence: 9.8% Identity: 12% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 3ew8 chain A Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 9.6% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:histone deacetylase 8; PDBTitle: crystal structure analysis of human hdac8 d101l variant Phyre2 PDB 3ugs chain B Region: 111 - 150 Aligned: 31 Modelled: 40 Confidence: 9.1% Identity: 19% PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni Phyre2 PDB 1t64 chain A Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 9.0% Identity: 19% Fold: Arginase/deacetylase Superfamily: Arginase/deacetylase Family: Histone deacetylase, HDAC Phyre2 PDB 1tta chain A Region: 101 - 117 Aligned: 17 Modelled: 17 Confidence: 9.0% Identity: 12% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 2elz chain A Region: 199 - 208 Aligned: 10 Modelled: 10 Confidence: 8.9% Identity: 40% PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 224; PDBTitle: solution structure of the 17th zf-c2h2 domain from human2 zinc finger protein 224 Phyre2 PDB 2b7t chain A domain 1 Region: 94 - 148 Aligned: 53 Modelled: 55 Confidence: 8.5% Identity: 11% Fold: dsRBD-like Superfamily: dsRNA-binding domain-like Family: Double-stranded RNA-binding domain (dsRBD) Phyre2 PDB 1tfp chain A Region: 101 - 117 Aligned: 17 Modelled: 17 Confidence: 8.1% Identity: 18% Fold: Prealbumin-like Superfamily: Transthyretin (synonym: prealbumin) Family: Transthyretin (synonym: prealbumin) Phyre2 PDB 2h0e chain A Region: 104 - 116 Aligned: 13 Modelled: 13 Confidence: 7.9% Identity: 31% 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: 104 - 117 Aligned: 14 Modelled: 14 Confidence: 7.8% Identity: 29% PDB header:hydrolase Chain: C: PDB Molecule:transthyretin-like protein; PDBTitle: transthyretin-like protein from salmonella dublin Phyre2 1 d1l5ia_ 2 c3dkxA_ 3 c2x3gA_ 4 c2ns6A_ 5 d2nzca1 6 c2hw0A_ 7 c2hwtA_ 8 d1m55a_ 9 c3maxB_ 10 c2h1xB_ 11 d1f86a_ 12 c3ew8A_ 13 c3ugsB_ 14 d1t64a_ 15 d1ttaa_ 16 c2elzA_ 17 d2b7ta1 18 d1tfpa_ 19 c2h0eA_ 20 c2gpzC_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 d1l5ia_ 74.1 16 Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:DNA-binding domain of REP protein 2 c3dkxA_ 69.9 31 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 3 c2x3gA_ 61.1 24 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 4 c2ns6A_ 25.7 18 PDB header:hydrolase Chain: A: PDB Molecule:mobilization protein a; PDBTitle: crystal structure of the minimal relaxase domain of moba2 from plasmid r1162 5 d2nzca1 17.4 17 Fold:Ferredoxin-like Superfamily:ACT-like Family:TM1266-like 6 c2hw0A_ 11.5 9 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 7 c2hwtA_ 10.2 9 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 8 d1m55a_ 10.2 11 Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:Replication protein Rep, nuclease domain 9 c3maxB_ 9.9 26 PDB header:hydrolase Chain: B: PDB Molecule:histone deacetylase 2; PDBTitle: crystal structure of human hdac2 complexed with an n-(2-aminophenyl)2 benzamide 10 c2h1xB_ 9.9 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 d1f86a_ 9.8 12 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 12 c3ew8A_ 9.6 19 PDB header:hydrolase Chain: A: PDB Molecule:histone deacetylase 8; PDBTitle: crystal structure analysis of human hdac8 d101l variant 13 c3ugsB_ 9.1 19 PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni 14 d1t64a_ 9.0 19 Fold:Arginase/deacetylase Superfamily:Arginase/deacetylase Family:Histone deacetylase, HDAC 15 d1ttaa_ 9.0 12 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 16 c2elzA_ 8.9 40 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 224; PDBTitle: solution structure of the 17th zf-c2h2 domain from human2 zinc finger protein 224 17 d2b7ta1 8.5 11 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 18 d1tfpa_ 8.1 18 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 19 c2h0eA_ 7.9 31 PDB header:hydrolase Chain: A: PDB Molecule:transthyretin-like protein pucm; PDBTitle: crystal structure of pucm in the absence of substrate 20 c2gpzC_ 7.8 29 PDB header:hydrolase Chain: C: PDB Molecule:transthyretin-like protein; PDBTitle: transthyretin-like protein from salmonella dublin 21 d2b7va1 not modelled 7.4 9 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 22 c2jepB_ not modelled 6.7 16 PDB header:hydrolase Chain: B: PDB Molecule:xyloglucanase; PDBTitle: native family 5 xyloglucanase from paenibacillus pabuli 23 d1oo2a_ not modelled 6.6 25 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 24 c2jttD_ not modelled 6.1 21 PDB header:calcium binding protein/antitumor protei Chain: D: PDB Molecule:calcyclin-binding protein; PDBTitle: solution structure of calcium loaded s100a6 bound to c-2 terminal siah-1 interacting protein 25 c2yttA_ not modelled 6.0 30 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 473; PDBTitle: solution structure of the c2h2 type zinc finger (region 204-2 236) of human zinc finger protein 473 26 c2entA_ not modelled 5.9 40 PDB header:transcription Chain: A: PDB Molecule:krueppel-like factor 15; PDBTitle: solution structure of the second c2h2-type zinc finger2 domain from human krueppel-like factor 15 27 d1luza_ not modelled 5.4 25 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 28 d1kgia_ not modelled 5.3 19 Fold:Prealbumin-like Superfamily:Transthyretin (synonym: prealbumin) Family:Transthyretin (synonym: prealbumin) 29 d1ohea1 not modelled 5.1 20 Fold:(Phosphotyrosine protein) phosphatases II Superfamily:(Phosphotyrosine protein) phosphatases II Family:Dual specificity phosphatase-like

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