Secondary structure and disorder prediction

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Sequence		M	Q	L	N	I	T	G	N	N	V	E	I	T	E	A	L	R	E	F	V	T	A	K	F	A	K	L	E	Q	Y	F	D	R	I	N	Q	V	Y	V	V	L	K	V	E	K	V	T	H	T	S	D	A	T	L	H	V	N	G	G	E
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.
Sequence		I	H	A	S	A	E	G	Q	D	M	Y	A	A	I	D	G	L	I	D	K	L	A	R	Q	L	T	K	H	K	D	K	L	K	Q	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 2rql chain A Region: 1 - 95 Aligned: 95 Modelled: 95 Confidence: 100.0% Identity: 100% 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 1imu chain A Region: 1 - 95 Aligned: 95 Modelled: 95 Confidence: 100.0% Identity: 34% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 3tqm chain D Region: 1 - 91 Aligned: 91 Modelled: 90 Confidence: 99.9% Identity: 33% 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 1l4s chain A Region: 3 - 95 Aligned: 93 Modelled: 93 Confidence: 99.9% Identity: 38% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 2ywq chain A domain 1 Region: 3 - 89 Aligned: 86 Modelled: 87 Confidence: 99.9% Identity: 33% Fold: Ribosome binding protein Y (YfiA homologue) Superfamily: Ribosome binding protein Y (YfiA homologue) Family: Ribosome binding protein Y (YfiA homologue) Phyre2 PDB 1sr9 chain A domain 3 Region: 33 - 81 Aligned: 49 Modelled: 49 Confidence: 24.2% Identity: 22% Fold: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Superfamily: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Family: 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Phyre2 PDB 3f6h chain A Region: 49 - 81 Aligned: 33 Modelled: 33 Confidence: 23.6% Identity: 21% 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 1uil chain A Region: 48 - 88 Aligned: 41 Modelled: 41 Confidence: 21.7% Identity: 24% 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: 19.9% Identity: 18% 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 1i7n chain A Region: 7 - 85 Aligned: 75 Modelled: 77 Confidence: 19.7% Identity: 13% 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: 19.2% Identity: 10% 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 1by0 chain A Region: 78 - 94 Aligned: 17 Modelled: 17 Confidence: 18.9% Identity: 41% 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 1pk8 chain D Region: 10 - 81 Aligned: 68 Modelled: 72 Confidence: 18.0% Identity: 9% PDB header:membrane protein Chain: D: PDB Molecule:rat synapsin i; PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp Phyre2 PDB 2yh5 chain A Region: 38 - 82 Aligned: 43 Modelled: 45 Confidence: 17.6% Identity: 12% PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc Phyre2 PDB 2cly chain C domain 1 Region: 10 - 32 Aligned: 23 Modelled: 23 Confidence: 16.6% Identity: 17% Fold: Mitochondrial ATP synthase coupling factor 6 Superfamily: Mitochondrial ATP synthase coupling factor 6 Family: Mitochondrial ATP synthase coupling factor 6 Phyre2 PDB 2r85 chain A domain 2 Region: 11 - 59 Aligned: 49 Modelled: 49 Confidence: 12.3% Identity: 8% Fold: ATP-grasp Superfamily: Glutathione synthetase ATP-binding domain-like Family: PurP ATP-binding domain-like Phyre2 PDB 2hkj chain A domain 2 Region: 65 - 94 Aligned: 30 Modelled: 30 Confidence: 12.2% Identity: 23% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: DNA gyrase/MutL, second domain Phyre2 PDB 1vzs chain A Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 11.0% Identity: 20% Fold: Mitochondrial ATP synthase coupling factor 6 Superfamily: Mitochondrial ATP synthase coupling factor 6 Family: Mitochondrial ATP synthase coupling factor 6 Phyre2 PDB 3r9j chain D Region: 11 - 57 Aligned: 47 Modelled: 47 Confidence: 11.0% Identity: 9% 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 PDB 1mx0 chain D Region: 65 - 94 Aligned: 30 Modelled: 30 Confidence: 10.8% Identity: 23% PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit Phyre2 1 c2rqlA_ 2 d1imua_ 3 c3tqmD_ 4 d1l4sa_ 5 d2ywqa1 6 d1sr9a3 7 c3f6hA_ 8 d1uila_ 9 c3kxeD_ 10 c1i7nA_ 11 c2kxoA_ 12 c1by0A_ 13 c1pk8D_ 14 c2yh5A_ 15 d2clyc1 16 d2r85a2 17 d2hkja2 18 d1vzsa_ 19 c3r9jD_ 20 c1mx0D_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49

Detailed template information

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

1 c2rqlA_ 100.0 100 PDB header:translation Chain: A: PDB Molecule:probable sigma-54 modulation protein; PDBTitle: solution structure of the e. coli ribosome hibernation2 promoting factor hpf 2 d1imua_ 100.0 34 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 3 c3tqmD_ 99.9 33 PDB header:protein binding Chain: D: PDB Molecule:ribosome-associated factor y; PDBTitle: structure of an ribosomal subunit interface protein from coxiella2 burnetii 4 d1l4sa_ 99.9 38 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 5 d2ywqa1 99.9 33 Fold:Ribosome binding protein Y (YfiA homologue) Superfamily:Ribosome binding protein Y (YfiA homologue) Family:Ribosome binding protein Y (YfiA homologue) 6 d1sr9a3 24.2 22 Fold:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Superfamily:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Family:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain 7 c3f6hA_ 23.6 21 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 8 d1uila_ 21.7 24 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 9 c3kxeD_ 19.9 18 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 10 c1i7nA_ 19.7 13 PDB header:neuropeptide Chain: A: PDB Molecule:synapsin ii; PDBTitle: crystal structure analysis of the c domain of synapsin ii2 from rat brain 11 c2kxoA_ 19.2 10 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 12 c1by0A_ 18.9 41 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 13 c1pk8D_ 18.0 9 PDB header:membrane protein Chain: D: PDB Molecule:rat synapsin i; PDBTitle: crystal structure of rat synapsin i c domain complexed to2 ca.atp 14 c2yh5A_ 17.6 12 PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc 15 d2clyc1 16.6 17 Fold:Mitochondrial ATP synthase coupling factor 6 Superfamily:Mitochondrial ATP synthase coupling factor 6 Family:Mitochondrial ATP synthase coupling factor 6 16 d2r85a2 12.3 8 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like 17 d2hkja2 12.2 23 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 18 d1vzsa_ 11.0 20 Fold:Mitochondrial ATP synthase coupling factor 6 Superfamily:Mitochondrial ATP synthase coupling factor 6 Family:Mitochondrial ATP synthase coupling factor 6 19 c3r9jD_ 11.0 9 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 20 c1mx0D_ 10.8 23 PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit 21 c2p0aA_ not modelled 10.2 17 PDB header:neuropeptide Chain: A: PDB Molecule:synapsin-3; PDBTitle: the crystal structure of human synapsin iii (syn3) in complex with2 amppnp 22 d2e9xd1 not modelled 9.8 20 Fold:GINS helical bundle-like Superfamily:GINS helical bundle-like Family:SLD5 N-terminal domain-like 23 c3r23B_ not modelled 9.7 18 PDB header:ligase Chain: B: PDB Molecule:d-alanine--d-alanine ligase; PDBTitle: crystal structure of d-alanine--d-alanine ligase from bacillus2 anthracis 24 d1hk8a_ not modelled 9.6 16 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:Class III anaerobic ribonucleotide reductase NRDD subunit 25 c1hk8A_ not modelled 9.6 16 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 26 c3l2iB_ not modelled 9.2 15 PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: 1.85 angstrom crystal structure of the 3-dehydroquinate dehydratase2 (arod) from salmonella typhimurium lt2. 27 d1o6da_ not modelled 8.9 10 Fold:alpha/beta knot Superfamily:alpha/beta knot Family:YbeA-like 28 c3ehuA_ not modelled 8.3 19 PDB header:membrane protein Chain: A: PDB Molecule:fusion protein of crfr1 extracellular domain and mbp; PDBTitle: crystal structure of the extracellular domain of human corticotropin2 releasing factor receptor type 1 (crfr1) in complex with crf 29 d1sfla_ not modelled 8.2 24 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 30 d1gsoa3 not modelled 8.2 5 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 31 d2i52a1 not modelled 8.1 5 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 32 c3q2oB_ not modelled 7.6 15 PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase 33 c3rd6A_ not modelled 7.5 13 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 34 c1hf9B_ not modelled 7.4 31 PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 35 d1lr0a_ not modelled 7.4 12 Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TolA 36 c2yr1B_ not modelled 6.7 21 PDB header:lyase Chain: B: PDB Molecule:3-dehydroquinate dehydratase; PDBTitle: crystal structure of 3-dehydroquinate dehydratase from geobacillus2 kaustophilus hta426 37 d2r7ka2 not modelled 6.5 12 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:PurP ATP-binding domain-like 38 d1xppa_ not modelled 6.1 13 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL 39 c1q0vA_ not modelled 6.0 19 PDB header:transport binding Chain: A: PDB Molecule:hydrophilic protein; has cysteine rich putative PDBTitle: solution structure of tandem uims of vps27 40 d1ehia2 not modelled 6.0 12 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:ATP-binding domain of peptide synthetases 41 c3e5nA_ not modelled 5.9 18 PDB header:ligase Chain: A: PDB Molecule:d-alanine-d-alanine ligase a; PDBTitle: crystal strucutre of d-alanine-d-alanine ligase from2 xanthomonas oryzae pv. oryzae kacc10331 42 c2l5gB_ not modelled 5.9 30 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 43 c1a92B_ not modelled 5.9 35 PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen 44 c2l9pA_ not modelled 5.7 11 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 45 c1g6uB_ not modelled 5.7 23 PDB header:de novo protein Chain: B: PDB Molecule:domain swapped dimer; PDBTitle: crystal structure of a domain swapped dimer 46 c1ulzA_ not modelled 5.7 10 PDB header:ligase Chain: A: PDB Molecule:pyruvate carboxylase n-terminal domain; PDBTitle: crystal structure of the biotin carboxylase subunit of pyruvate2 carboxylase 47 d1ghha_ not modelled 5.6 12 Fold:DNA damage-inducible protein DinI Superfamily:DNA damage-inducible protein DinI Family:DNA damage-inducible protein DinI 48 c3oqvA_ not modelled 5.4 11 PDB header:protein binding Chain: A: PDB Molecule:albc; PDBTitle: albc, a cyclodipeptide synthase from streptomyces noursei 49 c2q2eB_ not modelled 5.3 27 PDB header:isomerase Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b; PDBTitle: crystal structure of the topoisomerase vi holoenzyme from2 methanosarcina mazei

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