Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	K	L	A	F	P	R	E	L	R	L	L	T	P	S	Q	F	T	F	V	F	Q	Q	P	Q	R	A	G	T	P	Q	I	T	I	L	G	R	L	N	S	L	G	H	P	R	I	G	L	T	V	A	K	K	N	V	R	R	A	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.
Sequence		E	R	N	R	I	K	R	L	T	R	E	S	F	R	L	R	Q	H	E	L	P	A	M	D	F	V	V	V	A	K	K	G	V	A	D	L	D	N	R	A	L	S	E	A	L	E	K	L	W	R	R	H	C	R	L	A	R	G	S
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 2ljp chain A Region: 1 - 119 Aligned: 119 Modelled: 119 Confidence: 100.0% Identity: 100% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease p protein component; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for e.coli2 ribonuclease p protein Phyre2 PDB 1d6t chain A Region: 4 - 112 Aligned: 108 Modelled: 109 Confidence: 100.0% Identity: 24% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: RNase P protein Phyre2 PDB 1a6f chain A Region: 6 - 112 Aligned: 106 Modelled: 107 Confidence: 100.0% Identity: 28% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: RNase P protein Phyre2 PDB 1nz0 chain A Region: 10 - 112 Aligned: 102 Modelled: 103 Confidence: 100.0% Identity: 29% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: RNase P protein Phyre2 PDB 2c4r chain L Region: 51 - 113 Aligned: 48 Modelled: 49 Confidence: 38.5% Identity: 10% PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e Phyre2 PDB 1q6o chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 15.9% Identity: 0% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: Decarboxylase Phyre2 PDB 2y94 chain C Region: 89 - 109 Aligned: 21 Modelled: 21 Confidence: 11.7% Identity: 14% PDB header:transferase Chain: C: PDB Molecule:5'-amp-activated protein kinase catalytic subunit alpha-1; PDBTitle: structure of an active form of mammalian ampk Phyre2 PDB 3oqv chain A Region: 63 - 110 Aligned: 47 Modelled: 48 Confidence: 11.0% Identity: 13% PDB header:protein binding Chain: A: PDB Molecule:albc; PDBTitle: albc, a cyclodipeptide synthase from streptomyces noursei Phyre2 PDB 1qjh chain A Region: 80 - 111 Aligned: 32 Modelled: 32 Confidence: 10.1% Identity: 6% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 3bvj chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 9.7% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:uridine 5'-monophosphate synthase; PDBTitle: crystal structure of human orotidine 5'-monophosphate decarboxylase2 complexed with xmp Phyre2 PDB 1tte chain A Region: 63 - 85 Aligned: 23 Modelled: 23 Confidence: 9.4% Identity: 17% PDB header:ligase Chain: A: PDB Molecule:ubiquitin-conjugating enzyme e2-24 kda; PDBTitle: the structure of a class ii ubiquitin-conjugating enzyme,2 ubc1. Phyre2 PDB 2kjw chain A Region: 83 - 111 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 7% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 Phyre2 PDB 2qcn chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 8.5% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:uridine 5'-monophosphate synthase; PDBTitle: covalent complex of the orotidine-5'-monophosphate decarboxylase2 domain of human ump synthase with 6-iodo-ump Phyre2 PDB 2j5a chain A domain 1 Region: 76 - 111 Aligned: 36 Modelled: 36 Confidence: 8.1% Identity: 11% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 1lou chain A Region: 80 - 111 Aligned: 32 Modelled: 32 Confidence: 7.7% Identity: 6% Fold: Ferredoxin-like Superfamily: Ribosomal protein S6 Family: Ribosomal protein S6 Phyre2 PDB 3bbn chain F Region: 80 - 109 Aligned: 30 Modelled: 30 Confidence: 6.6% Identity: 17% PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 1vsr chain A Region: 64 - 87 Aligned: 24 Modelled: 24 Confidence: 6.5% Identity: 42% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Very short patch repair (VSR) endonuclease Phyre2 PDB 2fsu chain A domain 1 Region: 71 - 97 Aligned: 27 Modelled: 27 Confidence: 6.4% Identity: 15% Fold: PLP-dependent transferase-like Superfamily: PhnH-like Family: PhnH-like Phyre2 PDB 2fsu chain A Region: 71 - 97 Aligned: 27 Modelled: 27 Confidence: 6.4% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein phnh; PDBTitle: crystal structure of the phnh protein from escherichia coli Phyre2 PDB 2ayv chain A domain 1 Region: 64 - 87 Aligned: 24 Modelled: 24 Confidence: 5.4% Identity: 17% Fold: UBC-like Superfamily: UBC-like Family: UBC-related Phyre2 1 c2ljpA_ 2 d1d6ta_ 3 d1a6fa_ 4 d1nz0a_ 5 c2c4rL_ 6 d1q6oa_ 7 c2y94C_ 8 c3oqvA_ 9 d1qjha_ 10 c3bvjA_ 11 c1tteA_ 12 c2kjwA_ 13 c2qcnA_ 14 d2j5aa1 15 d1loua_ 16 c3bbnF_ 17 d1vsra_ 18 d2fsua1 19 c2fsuA_ 20 d2ayva1 21 22

Detailed template information

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

1 c2ljpA_ 100.0 100 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease p protein component; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for e.coli2 ribonuclease p protein 2 d1d6ta_ 100.0 24 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 3 d1a6fa_ 100.0 28 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 4 d1nz0a_ 100.0 29 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 5 c2c4rL_ 38.5 10 PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e 6 d1q6oa_ 15.9 0 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Decarboxylase 7 c2y94C_ 11.7 14 PDB header:transferase Chain: C: PDB Molecule:5'-amp-activated protein kinase catalytic subunit alpha-1; PDBTitle: structure of an active form of mammalian ampk 8 c3oqvA_ 11.0 13 PDB header:protein binding Chain: A: PDB Molecule:albc; PDBTitle: albc, a cyclodipeptide synthase from streptomyces noursei 9 d1qjha_ 10.1 6 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 10 c3bvjA_ 9.7 16 PDB header:lyase Chain: A: PDB Molecule:uridine 5'-monophosphate synthase; PDBTitle: crystal structure of human orotidine 5'-monophosphate decarboxylase2 complexed with xmp 11 c1tteA_ 9.4 17 PDB header:ligase Chain: A: PDB Molecule:ubiquitin-conjugating enzyme e2-24 kda; PDBTitle: the structure of a class ii ubiquitin-conjugating enzyme,2 ubc1. 12 c2kjwA_ 8.6 7 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 13 c2qcnA_ 8.5 16 PDB header:lyase Chain: A: PDB Molecule:uridine 5'-monophosphate synthase; PDBTitle: covalent complex of the orotidine-5'-monophosphate decarboxylase2 domain of human ump synthase with 6-iodo-ump 14 d2j5aa1 8.1 11 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 15 d1loua_ 7.7 6 Fold:Ferredoxin-like Superfamily:Ribosomal protein S6 Family:Ribosomal protein S6 16 c3bbnF_ 6.6 17 PDB header:ribosome Chain: F: PDB Molecule:ribosomal protein s6; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 17 d1vsra_ 6.5 42 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Very short patch repair (VSR) endonuclease 18 d2fsua1 6.4 15 Fold:PLP-dependent transferase-like Superfamily:PhnH-like Family:PhnH-like 19 c2fsuA_ 6.4 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein phnh; PDBTitle: crystal structure of the phnh protein from escherichia coli 20 d2ayva1 5.4 17 Fold:UBC-like Superfamily:UBC-like Family:UBC-related 21 d2jfga2 not modelled 5.3 14 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 22 c3exsB_ not modelled 5.1 6 PDB header:lyase Chain: B: PDB Molecule:rmpd (hexulose-6-phosphate synthase); PDBTitle: crystal structure of kgpdc from streptococcus mutans in2 complex with d-r5p

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