Secondary structure and disorder prediction

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Sequence		M	T	M	N	I	T	S	K	Q	M	E	I	T	P	A	I	R	Q	H	V	A	D	R	L	A	K	L	E	K	W	Q	T	H	L	I	N	P	H	I	I	L	S	K	E	P	Q	G	F	V	A	D	A	T	I	N	T	P	N	G	V
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.
Sequence		L	V	A	S	G	K	H	E	D	M	Y	T	A	I	N	E	L	I	N	K	L	E	R	Q	L	N	K	L	Q	H	K	G	E	A	R	R	A	A	T	S	V	K	D	A	N	F	V	E	E	V	E	E	E
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 1l4s chain A Region: 3 - 113 Aligned: 111 Modelled: 111 Confidence: 100.0% Identity: 100% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 1imu chain A Region: 1 - 104 Aligned: 104 Modelled: 104 Confidence: 100.0% Identity: 64% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 2rql chain A Region: 1 - 95 Aligned: 95 Modelled: 95 Confidence: 100.0% Identity: 38% PDB header:translation Chain: A: PDB Molecule:probable sigma-54 modulation protein; PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf Phyre2 PDB 3tqm chain D Region: 1 - 91 Aligned: 91 Modelled: 90 Confidence: 99.9% Identity: 26% PDB header:protein binding Chain: D: PDB Molecule:ribosome-associated factor y; PDBTitle: structure of an ribosomal subunit interface protein from coxiella2 burnetii Phyre2 PDB 2ywq chain A domain 1 Region: 3 - 89 Aligned: 86 Modelled: 87 Confidence: 99.9% Identity: 27% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 1uil chain A Region: 48 - 88 Aligned: 41 Modelled: 41 Confidence: 25.1% Identity: 27% Fold: dsRBD-like Superfamily: dsRNA-binding domain-like Family: Double-stranded RNA-binding domain (dsRBD) Phyre2 PDB 3kxe chain D Region: 9 - 25 Aligned: 17 Modelled: 17 Confidence: 23.0% Identity: 6% PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex Phyre2 PDB 1by0 chain A Region: 78 - 93 Aligned: 16 Modelled: 16 Confidence: 16.6% Identity: 44% PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen Phyre2 PDB 1i7n chain A Region: 7 - 85 Aligned: 75 Modelled: 79 Confidence: 15.7% Identity: 12% PDB header:neuropeptide Chain: A: PDB Molecule:synapsin ii; PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain Phyre2 PDB 2kxo chain A Region: 2 - 59 Aligned: 58 Modelled: 58 Confidence: 13.7% Identity: 24% PDB header:cell cycle Chain: A: PDB Molecule:cell division topological specificity factor; PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae Phyre2 PDB 1o6d chain A Region: 1 - 32 Aligned: 31 Modelled: 32 Confidence: 12.7% Identity: 10% Fold: alpha/beta knot Superfamily: alpha/beta knot Family: YbeA-like Phyre2 PDB 3f6h chain A Region: 49 - 81 Aligned: 33 Modelled: 33 Confidence: 12.5% Identity: 12% PDB header:transferase Chain: A: PDB Molecule:alpha-isopropylmalate synthase; PDBTitle: crystal structure of the regulatory domain of licms in2 complexed with isoleucine - type iii Phyre2 PDB 2yh5 chain A Region: 38 - 82 Aligned: 43 Modelled: 45 Confidence: 12.1% Identity: 12% PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc Phyre2 PDB 2e9x chain D domain 1 Region: 16 - 30 Aligned: 15 Modelled: 15 Confidence: 12.1% Identity: 33% Fold: GINS helical bundle-like Superfamily: GINS helical bundle-like Family: SLD5 N-terminal domain-like Phyre2 PDB 1lr0 chain A Region: 11 - 85 Aligned: 67 Modelled: 75 Confidence: 10.2% Identity: 7% Fold: TolA/TonB C-terminal domain Superfamily: TolA/TonB C-terminal domain Family: TolA Phyre2 PDB 1hk8 chain A Region: 52 - 98 Aligned: 47 Modelled: 47 Confidence: 10.2% Identity: 17% PDB header:oxidoreductase Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase; PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp Phyre2 PDB 1hk8 chain A Region: 52 - 98 Aligned: 47 Modelled: 47 Confidence: 10.2% Identity: 17% Fold: PFL-like glycyl radical enzymes Superfamily: PFL-like glycyl radical enzymes Family: Class III anaerobic ribonucleotide reductase NRDD subunit Phyre2 PDB 2i52 chain A domain 1 Region: 9 - 64 Aligned: 56 Modelled: 56 Confidence: 9.5% Identity: 13% Fold: MK0786-like Superfamily: MK0786-like Family: MK0786-like Phyre2 PDB 3rd6 chain A Region: 34 - 85 Aligned: 52 Modelled: 52 Confidence: 9.0% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mll3558 protein; PDBTitle: crystal structure of mll3558 protein from rhizobium loti. northeast2 structural genomics consortium target id mlr403 Phyre2 PDB 3r9j chain D Region: 11 - 57 Aligned: 47 Modelled: 47 Confidence: 8.9% Identity: 11% PDB header:cell cycle,hydrolase/cell cycle Chain: D: PDB Molecule:cell division topological specificity factor; PDBTitle: 4.3a resolution structure of a mind-mine(i24n) protein complex Phyre2 1 d1l4sa_ 2 d1imua_ 3 c2rqlA_ 4 c3tqmD_ 5 d2ywqa1 6 d1uila_ 7 c3kxeD_ 8 c1by0A_ 9 c1i7nA_ 10 c2kxoA_ 11 d1o6da_ 12 c3f6hA_ 13 c2yh5A_ 14 d2e9xd1 15 d1lr0a_ 16 c1hk8A_ 17 d1hk8a_ 18 d2i52a1 19 c3rd6A_ 20 c3r9jD_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 d1l4sa_ 100.0 100 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 2 d1imua_ 100.0 64 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 3 c2rqlA_ 100.0 38 PDB header:translation Chain: A: PDB Molecule:probable sigma-54 modulation protein; PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf 4 c3tqmD_ 99.9 26 PDB header:protein binding Chain: D: PDB Molecule:ribosome-associated factor y; PDBTitle: structure of an ribosomal subunit interface protein from coxiella2 burnetii 5 d2ywqa1 99.9 27 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 6 d1uila_ 25.1 27 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 7 c3kxeD_ 23.0 6 PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 8 c1by0A_ 16.6 44 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 9 c1i7nA_ 15.7 12 PDB header:neuropeptide Chain: A: PDB Molecule:synapsin ii; PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain 10 c2kxoA_ 13.7 24 PDB header:cell cycle Chain: A: PDB Molecule:cell division topological specificity factor; PDBTitle: solution nmr structure of the cell division regulator mine protein2 from neisseria gonorrhoeae 11 d1o6da_ 12.7 10 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 12 c3f6hA_ 12.5 12 PDB header:transferase Chain: A: PDB Molecule:alpha-isopropylmalate synthase; PDBTitle: crystal structure of the regulatory domain of licms in2 complexed with isoleucine - type iii 13 c2yh5A_ 12.1 12 PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc 14 d2e9xd1 12.1 33 Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:SLD5 N-terminal domain-like 15 d1lr0a_ 10.2 7 Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TolA 16 c1hk8A_ 10.2 17 PDB header:oxidoreductase Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase; PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp 17 d1hk8a_ 10.2 17 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:Class III anaerobic ribonucleotide reductase NRDD subunit 18 d2i52a1 9.5 13 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 19 c3rd6A_ 9.0 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mll3558 protein; PDBTitle: crystal structure of mll3558 protein from rhizobium loti. northeast2 structural genomics consortium target id mlr403 20 c3r9jD_ 8.9 11 PDB header:cell cycle,hydrolase/cell cycle Chain: D: PDB Molecule:cell division topological specificity factor; PDBTitle: 4.3a resolution structure of a mind-mine(i24n) protein complex 21 c1pk8D_ not modelled 8.3 10 PDB header:membrane protein Chain: D: PDB Molecule:rat synapsin i; PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp 22 c3q2oB_ not modelled 7.9 10 PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase 23 c1hf9B_ not modelled 7.8 13 PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 24 c3zqbB_ not modelled 7.3 19 PDB header:cell invasion Chain: B: PDB Molecule:protein prgi, cell invasion protein sipd; PDBTitle: prgi-sipd from salmonella typhimurium 25 d1sr9a3 not modelled 6.9 13 Fold:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Superfamily:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Family:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain 26 c1mx0D_ not modelled 6.5 17 PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit 27 d1kr4a_ not modelled 6.5 13 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 28 c2kpoA_ not modelled 6.3 5 PDB header:de novo protein Chain: A: PDB Molecule:rossmann 2x2 fold protein; PDBTitle: solution nmr structure of de novo designed rossmann 2x2 fold protein,2 northeast structural genomics consortium target or16 29 d2r85a2 not modelled 6.0 6 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like 30 d1ghha_ not modelled 6.0 10 Fold:DNA damage-inducible protein DinI Superfamily:DNA damage-inducible protein DinI Family:DNA damage-inducible protein DinI 31 c2l9pA_ not modelled 5.7 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of q5hli9 from staphylococcus epidermidis,2 northeast structural genomics consortium target ser147 32 d1gsoa3 not modelled 5.6 9 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 33 c2l5gB_ not modelled 5.3 29 PDB header:transcription regulator Chain: B: PDB Molecule:putative uncharacterized protein ncor2; PDBTitle: co-ordinates and 1h, 13c and 15n chemical shift assignments for the2 complex of gps2 53-90 and smrt 167-207 34 c2q9qF_ not modelled 5.2 33 PDB header:replication Chain: F: PDB Molecule:gins complex subunit 4; PDBTitle: the crystal structure of full length human gins complex 35 d1vkza1 not modelled 5.2 19 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-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