Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		L	L	I	S	F	I	L	P	Q	K	W	T	S	A	A	V	V	T	P	P	E	P	V	Q	W	Q	E	L	E	K	S	F	T	K	L	R	V	L	D	L	D	I	K	I	D	R	T	E	A	F	N	L	F	I	K	K	F	Q	S	V
Secondary structure
SS confidence
Disorder		?	?				?	?						?						?	?	?														?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	L	L	E	E	Y	L	R	S	S	P	Y	V	M	D	Q	L	K	E	A	K	I	D	E	L	D	L	H	R	A	I	V	A	L	S	E	K	M	K	A	V	D	D	N	A	S	K	K	K	D	E	P	S	L	Y	T	S	W	T	L
Secondary structure
SS confidence
Disorder																				?	?	?	?	?														?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.
Sequence		S	F	T	A	P	T	S	E	E	A	Q	T	V	L	S	G	Y	I	D	Y	I	S	T	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 3b8m chain A domain 1 Region: 10 - 143 Aligned: 128 Modelled: 134 Confidence: 100.0% Identity: 98% Fold: Ferredoxin-like Superfamily: Bacterial polysaccharide co-polymerase-like Family: FepE-like Phyre2 PDB 3b8o chain A domain 1 Region: 10 - 143 Aligned: 122 Modelled: 128 Confidence: 100.0% Identity: 16% Fold: Ferredoxin-like Superfamily: Bacterial polysaccharide co-polymerase-like Family: FepE-like Phyre2 PDB 3b8p chain A domain 1 Region: 9 - 143 Aligned: 104 Modelled: 104 Confidence: 99.9% Identity: 24% Fold: Ferredoxin-like Superfamily: Bacterial polysaccharide co-polymerase-like Family: FepE-like Phyre2 PDB 1p5d chain X domain 4 Region: 118 - 144 Aligned: 27 Modelled: 27 Confidence: 21.2% Identity: 22% Fold: TBP-like Superfamily: Phosphoglucomutase, C-terminal domain Family: Phosphoglucomutase, C-terminal domain Phyre2 PDB 1mix chain A domain 2 Region: 119 - 141 Aligned: 23 Modelled: 23 Confidence: 17.2% Identity: 30% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Third domain of FERM Phyre2 PDB 1mji chain A Region: 117 - 137 Aligned: 21 Modelled: 21 Confidence: 11.2% Identity: 33% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 3bbo chain H Region: 117 - 137 Aligned: 21 Modelled: 21 Confidence: 10.0% Identity: 33% PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein l5; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2zjr chain D domain 1 Region: 117 - 137 Aligned: 21 Modelled: 21 Confidence: 10.0% Identity: 38% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 1mk7 chain B Region: 119 - 141 Aligned: 23 Modelled: 23 Confidence: 9.9% Identity: 30% PDB header:structural protein Chain: B: PDB Molecule:talin; PDBTitle: crystal structure of an integrin beta3-talin chimera Phyre2 PDB 1iq4 chain A Region: 117 - 137 Aligned: 21 Modelled: 21 Confidence: 8.2% Identity: 33% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 2k9i chain B Region: 3 - 11 Aligned: 9 Modelled: 9 Confidence: 7.7% Identity: 33% PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus Phyre2 PDB 2jvf chain A Region: 82 - 139 Aligned: 46 Modelled: 58 Confidence: 7.6% Identity: 17% PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein Phyre2 PDB 3g9w chain A Region: 119 - 141 Aligned: 23 Modelled: 23 Confidence: 7.2% Identity: 30% PDB header:cell adhesion Chain: A: PDB Molecule:talin-2; PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail Phyre2 PDB 1eik chain A Region: 126 - 137 Aligned: 12 Modelled: 12 Confidence: 7.1% Identity: 33% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 1dzf chain A domain 2 Region: 126 - 137 Aligned: 12 Modelled: 12 Confidence: 6.9% Identity: 33% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 2pmz chain V Region: 126 - 137 Aligned: 12 Modelled: 12 Confidence: 6.9% Identity: 25% PDB header:translation, transferase Chain: V: PDB Molecule:dna-directed rna polymerase subunit h; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 1hmj chain A Region: 126 - 137 Aligned: 12 Modelled: 12 Confidence: 6.3% Identity: 33% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 2a5y chain B domain 2 Region: 132 - 141 Aligned: 10 Modelled: 10 Confidence: 6.2% Identity: 40% Fold: DEATH domain Superfamily: DEATH domain Family: Caspase recruitment domain, CARD Phyre2 PDB 3n7n chain E Region: 41 - 55 Aligned: 15 Modelled: 15 Confidence: 6.1% Identity: 20% PDB header:replication Chain: E: PDB Molecule:monopolin complex subunit lrs4; PDBTitle: structure of csm1/lrs4 complex Phyre2 PDB 1uuj chain A Region: 6 - 13 Aligned: 8 Modelled: 8 Confidence: 6.0% Identity: 63% Fold: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Superfamily: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Family: Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Phyre2 1 d3b8ma1 2 d3b8oa1 3 d3b8pa1 4 d1p5dx4 5 d1mixa2 6 d1mjia_ 7 c3bboH_ 8 d2zjrd1 9 c1mk7B_ 10 d1iq4a_ 11 c2k9iB_ 12 c2jvfA_ 13 c3g9wA_ 14 d1eika_ 15 d1dzfa2 16 c2pmzV_ 17 d1hmja_ 18 d2a5yb2 19 c3n7nE_ 20 d1uuja_ 21

Detailed template information

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

1 d3b8ma1 100.0 98 Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like 2 d3b8oa1 100.0 16 Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like 3 d3b8pa1 99.9 24 Fold:Ferredoxin-like Superfamily:Bacterial polysaccharide co-polymerase-like Family:FepE-like 4 d1p5dx4 21.2 22 Fold:TBP-like Superfamily:Phosphoglucomutase, C-terminal domain Family:Phosphoglucomutase, C-terminal domain 5 d1mixa2 17.2 30 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Third domain of FERM 6 d1mjia_ 11.2 33 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 7 c3bboH_ 10.0 33 PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein l5; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 8 d2zjrd1 10.0 38 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 9 c1mk7B_ 9.9 30 PDB header:structural protein Chain: B: PDB Molecule:talin; PDBTitle: crystal structure of an integrin beta3-talin chimera 10 d1iq4a_ 8.2 33 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 11 c2k9iB_ 7.7 33 PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus 12 c2jvfA_ 7.6 17 PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein 13 c3g9wA_ 7.2 30 PDB header:cell adhesion Chain: A: PDB Molecule:talin-2; PDBTitle: crystal structure of talin2 f2-f3 in complex with the integrin beta1d2 cytoplasmic tail 14 d1eika_ 7.1 33 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 15 d1dzfa2 6.9 33 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 16 c2pmzV_ 6.9 25 PDB header:translation, transferase Chain: V: PDB Molecule:dna-directed rna polymerase subunit h; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 17 d1hmja_ 6.3 33 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 18 d2a5yb2 6.2 40 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 19 c3n7nE_ 6.1 20 PDB header:replication Chain: E: PDB Molecule:monopolin complex subunit lrs4; PDBTitle: structure of csm1/lrs4 complex 20 d1uuja_ 6.0 63 Fold:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Superfamily:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Family:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain 21 d2j6ba1 not modelled 5.5 15 Fold:STIV B116-like Superfamily:STIV B116-like Family:STIV B116-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