Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	N	L	I	K	V	V	K	M	K	P	Y	F	A	A	L	M	L	S	V	S	V	L	P	A	Y	A	G	P	L	G	T	A	D	K	A	D	L	P	Q	S	N	V	S	S	P	M	M	A	Q	S	L	R	Q	P	D	L	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																	?		?	?								?	?	?	?		?	?	?	?		?	?	?	?									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.
Sequence		P	I	S	T	D	R	K	T	E	C	F	R	L	Y	T	P	D	R	K	P	G	V	N	C	V	P	D	G	S	T	G	H
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 1zup chain A domain 1 Region: 65 - 80 Aligned: 16 Modelled: 16 Confidence: 51.0% Identity: 38% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: TM1739-like Phyre2 PDB 2jln chain A Region: 51 - 68 Aligned: 18 Modelled: 18 Confidence: 38.1% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 3mcu chain F Region: 28 - 66 Aligned: 39 Modelled: 39 Confidence: 14.6% Identity: 26% PDB header:oxidoreductase Chain: F: PDB Molecule:dipicolinate synthase, b chain; PDBTitle: crystal structure of the dipicolinate synthase chain b from2 bacillus cereus. northeast structural genomics consortium3 target bcr215. Phyre2 PDB 1zc1 chain A Region: 21 - 70 Aligned: 44 Modelled: 50 Confidence: 11.9% Identity: 30% PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites Phyre2 PDB 2yuj chain A Region: 21 - 70 Aligned: 44 Modelled: 50 Confidence: 10.9% Identity: 36% PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 Phyre2 PDB 3pvc chain A Region: 53 - 87 Aligned: 35 Modelled: 35 Confidence: 8.9% Identity: 26% PDB header:oxidoreductase, transferase Chain: A: PDB Molecule:trna 5-methylaminomethyl-2-thiouridine biosynthesis PDBTitle: crystal structure of apo mnmc from yersinia pestis Phyre2 PDB 3lqk chain A Region: 28 - 62 Aligned: 35 Modelled: 35 Confidence: 8.9% Identity: 29% PDB header:oxidoreductase Chain: A: PDB Molecule:dipicolinate synthase subunit b; PDBTitle: crystal structure of dipicolinate synthase subunit b from bacillus2 halodurans c Phyre2 PDB 2l14 chain B Region: 40 - 61 Aligned: 22 Modelled: 22 Confidence: 6.7% Identity: 41% PDB header:protein binding Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of cbp nuclear coactivator binding domain in complex with2 p53 tad Phyre2 PDB 1q3j chain A Region: 79 - 92 Aligned: 14 Modelled: 14 Confidence: 6.5% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Gurmarin-like Family: Antifungal peptide Phyre2 PDB 1c99 chain A Region: 55 - 61 Aligned: 7 Modelled: 7 Confidence: 5.3% Identity: 86% Fold: Transmembrane helix hairpin Superfamily: F1F0 ATP synthase subunit C Family: F1F0 ATP synthase subunit C Phyre2 1 d1zupa1 2 c2jlnA_ 3 c3mcuF_ 4 c1zc1A_ 5 c2yujA_ 6 c3pvcA_ 7 c3lqkA_ 8 c2l14B_ 9 d1q3ja_ 10 d1c99a_

Detailed template information

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

1 d1zupa1 51.0 38 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:TM1739-like 2 c2jlnA_ 38.1 28 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 3 c3mcuF_ 14.6 26 PDB header:oxidoreductase Chain: F: PDB Molecule:dipicolinate synthase, b chain; PDBTitle: crystal structure of the dipicolinate synthase chain b from2 bacillus cereus. northeast structural genomics consortium3 target bcr215. 4 c1zc1A_ 11.9 30 PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites 5 c2yujA_ 10.9 36 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 6 c3pvcA_ 8.9 26 PDB header:oxidoreductase, transferase Chain: A: PDB Molecule:trna 5-methylaminomethyl-2-thiouridine biosynthesis PDBTitle: crystal structure of apo mnmc from yersinia pestis 7 c3lqkA_ 8.9 29 PDB header:oxidoreductase Chain: A: PDB Molecule:dipicolinate synthase subunit b; PDBTitle: crystal structure of dipicolinate synthase subunit b from bacillus2 halodurans c 8 c2l14B_ 6.7 41 PDB header:protein binding Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: structure of cbp nuclear coactivator binding domain in complex with2 p53 tad 9 d1q3ja_ 6.5 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Gurmarin-like Family:Antifungal peptide 10 d1c99a_ 5.3 86 Fold:Transmembrane helix hairpin Superfamily:F1F0 ATP synthase subunit C Family:F1F0 ATP synthase subunit C

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

---

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