Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	L	H	D	Y	Y	K	D	E	V	V	K	K	L	M	T	E	F	N	Y	N	S	V	M	Q	V	P	R	V	E	K	I	T	L	N	M	G	V	G	E	A	I	A	D	K	K	L	L	D	N	A	A	A	D	L	A	A	I
Secondary structure
SS confidence
Disorder		?	?	?																																						?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	G	Q	K	P	L	I	T	K	A	R	K	S	V	A	G	F	K	I	R	Q	G	Y	P	I	G	C	K	V	T	L	R	G	E	R	M	W	E	F	F	E	R	L	I	T	I	A	V	P	R	I	R	D	F	R	G	L	S	A	K
Secondary structure
SS confidence
Disorder						?				?		?	?	?	?	?	?	?	?	?		?																																	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.
Sequence		S	F	D	G	R	G	N	Y	S	M	G	V	R	E	Q	I	I	F	P	E	I	D	Y	D	K	V	D	R	V	R	G	L	D	I	T	I	T	T	T	A	K	S	D	E	E	G	R	A	L	L	A	A	F	D	F	P	F	R	K
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 1iq4 chain A Region: 1 - 179 Aligned: 179 Modelled: 179 Confidence: 100.0% Identity: 61% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 1mji chain A Region: 3 - 179 Aligned: 177 Modelled: 177 Confidence: 100.0% Identity: 56% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 2zjr chain D domain 1 Region: 3 - 179 Aligned: 177 Modelled: 177 Confidence: 100.0% Identity: 60% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 3bbo chain H Region: 3 - 177 Aligned: 175 Modelled: 175 Confidence: 100.0% Identity: 49% 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 2gyc chain D domain 1 Region: 3 - 179 Aligned: 177 Modelled: 177 Confidence: 100.0% Identity: 100% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 4a1c chain D Region: 21 - 167 Aligned: 137 Modelled: 147 Confidence: 100.0% Identity: 26% PDB header:ribosome Chain: D: PDB Molecule:60s ribosomal protein l11; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4. Phyre2 PDB 1s1i chain J Region: 24 - 159 Aligned: 126 Modelled: 136 Confidence: 100.0% Identity: 34% PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l11; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. Phyre2 PDB 1vqo chain D domain 1 Region: 24 - 138 Aligned: 99 Modelled: 107 Confidence: 100.0% Identity: 42% Fold: RL5-like Superfamily: RL5-like Family: Ribosomal protein L5 Phyre2 PDB 2rf4 chain B Region: 91 - 119 Aligned: 29 Modelled: 29 Confidence: 38.8% Identity: 38% PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 Phyre2 PDB 3d37 chain A domain 1 Region: 93 - 131 Aligned: 30 Modelled: 39 Confidence: 17.9% Identity: 27% Fold: Phage tail proteins Superfamily: Phage tail proteins Family: Baseplate protein-like Phyre2 PDB 2jvf chain A Region: 153 - 173 Aligned: 21 Modelled: 21 Confidence: 17.5% Identity: 33% 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 3hxx chain A Region: 116 - 176 Aligned: 60 Modelled: 61 Confidence: 17.5% Identity: 22% PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp Phyre2 PDB 1qys chain A Region: 153 - 173 Aligned: 21 Modelled: 21 Confidence: 17.1% Identity: 24% PDB header:de novo protein Chain: A: PDB Molecule:top7; PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold Phyre2 PDB 1yfs chain B Region: 116 - 176 Aligned: 59 Modelled: 61 Confidence: 12.8% Identity: 25% PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine Phyre2 PDB 1riq chain A domain 2 Region: 116 - 176 Aligned: 59 Modelled: 61 Confidence: 10.0% Identity: 24% Fold: Class II aaRS and biotin synthetases Superfamily: Class II aaRS and biotin synthetases Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain Phyre2 PDB 2x6v chain B Region: 86 - 133 Aligned: 44 Modelled: 48 Confidence: 9.2% Identity: 23% PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form Phyre2 PDB 1vjq chain B Region: 140 - 177 Aligned: 38 Modelled: 38 Confidence: 8.6% Identity: 24% PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. Phyre2 PDB 3c25 chain A Region: 109 - 128 Aligned: 20 Modelled: 20 Confidence: 6.4% Identity: 30% PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna Phyre2 PDB 2xzn chain H Region: 147 - 169 Aligned: 23 Modelled: 23 Confidence: 6.2% Identity: 26% PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 Phyre2 PDB 1xtz chain A Region: 151 - 178 Aligned: 25 Modelled: 28 Confidence: 5.6% Identity: 12% PDB header:isomerase Chain: A: PDB Molecule:ribose-5-phosphate isomerase; PDBTitle: crystal structure of the s. cerevisiae d-ribose-5-phosphate isomerase:2 comparison with the archeal and bacterial enzymes Phyre2 1 d1iq4a_ 2 d1mjia_ 3 d2zjrd1 4 c3bboH_ 5 d2gycd1 6 c4a1cD_ 7 c1s1iJ_ 8 d1vqod1 9 c2rf4B_ 10 d3d37a1 11 c2jvfA_ 12 c3hxxA_ 13 c1qysA_ 14 c1yfsB_ 15 d1riqa2 16 c2x6vB_ 17 c1vjqB_ 18 c3c25A_ 19 c2xznH_ 20 c1xtzA_ 21 22

Detailed template information

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

1 d1iq4a_ 100.0 61 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 2 d1mjia_ 100.0 56 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 3 d2zjrd1 100.0 60 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 4 c3bboH_ 100.0 49 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 5 d2gycd1 100.0 100 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 6 c4a1cD_ 100.0 26 PDB header:ribosome Chain: D: PDB Molecule:60s ribosomal protein l11; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4. 7 c1s1iJ_ 100.0 34 PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l11; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 8 d1vqod1 100.0 42 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 9 c2rf4B_ 38.8 38 PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 10 d3d37a1 17.9 27 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:Baseplate protein-like 11 c2jvfA_ 17.5 33 PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein 12 c3hxxA_ 17.5 22 PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp 13 c1qysA_ 17.1 24 PDB header:de novo protein Chain: A: PDB Molecule:top7; PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold 14 c1yfsB_ 12.8 25 PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine 15 d1riqa2 10.0 24 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 16 c2x6vB_ 9.2 23 PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form 17 c1vjqB_ 8.6 24 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. 18 c3c25A_ 6.4 30 PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna 19 c2xznH_ 6.2 26 PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 20 c1xtzA_ 5.6 12 PDB header:isomerase Chain: A: PDB Molecule:ribose-5-phosphate isomerase; PDBTitle: crystal structure of the s. cerevisiae d-ribose-5-phosphate isomerase:2 comparison with the archeal and bacterial enzymes 21 c2ejxA_ not modelled 5.5 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:st0812; PDBTitle: crystal structure of the hypothetical protein st0812 from2 sulfolobus tokodaii 22 d1nt2b_ not modelled 5.4 25 Fold:Nop domain Superfamily:Nop domain Family:Nop domain

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