Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Q	S	I	C	S	T	G	L	R	W	L	W	L	V	V	V	V	L	I	I	D	L	G	S	K	Y	L	I	L	Q	N	F	A	L	G	D	T	V	P	L	F	P	S	L	N	L	H	Y	A	R	N	Y	G	A	A	F	S	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	A	D	S	G	G	W	Q	R	W	F	F	A	G	I	A	I	G	I	S	V	I	L	A	V	M	M	Y	R	S	K	A	T	Q	K	L	N	N	I	A	Y	A	L	I	I	G	G	A	L	G	N	L	F	D	R	L	W	H	G	F
Secondary structure
SS confidence
Disorder					?	?																											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.
Sequence		V	V	D	M	I	D	F	Y	V	G	D	W	H	F	A	T	F	N	L	A	D	T	A	I	C	V	G	A	A	L	I	V	L	E	G	F	L	P	S	R	A	K	K	Q
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 3hzq chain A Region: 93 - 164 Aligned: 72 Modelled: 72 Confidence: 26.1% Identity: 18% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state Phyre2 PDB 2vap chain A domain 1 Region: 106 - 129 Aligned: 24 Modelled: 24 Confidence: 15.3% Identity: 25% Fold: Tubulin nucleotide-binding domain-like Superfamily: Tubulin nucleotide-binding domain-like Family: Tubulin, GTPase domain Phyre2 PDB 1ft8 chain E Region: 27 - 60 Aligned: 34 Modelled: 34 Confidence: 10.7% Identity: 18% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Non-canonical RBD domain Phyre2 PDB 1ear chain A domain 1 Region: 109 - 131 Aligned: 23 Modelled: 23 Confidence: 9.5% Identity: 22% Fold: Urease metallochaperone UreE, N-terminal domain Superfamily: Urease metallochaperone UreE, N-terminal domain Family: Urease metallochaperone UreE, N-terminal domain Phyre2 PDB 2d5b chain A domain 1 Region: 105 - 117 Aligned: 13 Modelled: 13 Confidence: 8.5% Identity: 38% Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Phyre2 PDB 1w5f chain A domain 1 Region: 106 - 129 Aligned: 24 Modelled: 24 Confidence: 7.6% Identity: 25% Fold: Tubulin nucleotide-binding domain-like Superfamily: Tubulin nucleotide-binding domain-like Family: Tubulin, GTPase domain Phyre2 PDB 2oar chain A domain 1 Region: 92 - 164 Aligned: 73 Modelled: 73 Confidence: 7.3% Identity: 18% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 1s7b chain A Region: 78 - 110 Aligned: 33 Modelled: 33 Confidence: 7.0% Identity: 18% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 1 c3hzqA_ 2 d2vapa1 3 d1ft8e_ 4 d1eara1 5 d2d5ba1 6 d1w5fa1 7 d2oara1 8 d1s7ba_

Detailed template information

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

1 c3hzqA_ 26.1 18 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 2 d2vapa1 15.3 25 Fold:Tubulin nucleotide-binding domain-like Superfamily:Tubulin nucleotide-binding domain-like Family:Tubulin, GTPase domain 3 d1ft8e_ 10.7 18 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD domain 4 d1eara1 9.5 22 Fold:Urease metallochaperone UreE, N-terminal domain Superfamily:Urease metallochaperone UreE, N-terminal domain Family:Urease metallochaperone UreE, N-terminal domain 5 d2d5ba1 8.5 38 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 6 d1w5fa1 7.6 25 Fold:Tubulin nucleotide-binding domain-like Superfamily:Tubulin nucleotide-binding domain-like Family:Tubulin, GTPase domain 7 d2oara1 7.3 18 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 8 d1s7ba_ 7.0 18 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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