Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	M	T	N	A	Q	R	L	I	L	S	N	Q	Y	K	M	M	T	M	L	D	P	A	N	A	E	R	Y	R	R	L	Q	T	I	I	E	R	G	Y	G	L	Q	M	R	E	L	D	R	E	F	G	E	L	K	E	E	T	C	R
Secondary structure
SS confidence
Disorder		?	?	?	?																			?		?																								?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	I	I	D	I	M	E	M	Y	H	A	L	H	V	S	W	S	N	L	Q	D	Q	Q	S	I	D	E	R	R	V	T	F	L	G	F	D	A	A	T	E	A	R	Y	L	G	Y	V	R	F	M	V	N	V	E	G	R	Y	T	H	F
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?						?		?	?	?																	?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.
Sequence		D	A	G	T	H	G	F	N	A	Q	T	P	M	W	E	K	Y	Q	R	M	L	N	V	W	H	A	C	P	R	Q	Y	H	L	S	A	N	E	I	N	Q	I	I	N	A
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 1wpb chain A Region: 1 - 164 Aligned: 164 Modelled: 164 Confidence: 100.0% Identity: 100% Fold: YfbU-like Superfamily: YfbU-like Family: YfbU-like Phyre2 PDB 1zar chain A domain 1 Region: 31 - 96 Aligned: 60 Modelled: 66 Confidence: 32.5% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Rio2 serine protein kinase N-terminal domain Phyre2 PDB 2bcg chain G domain 2 Region: 62 - 73 Aligned: 12 Modelled: 12 Confidence: 32.4% Identity: 17% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: GDI-like N domain Phyre2 PDB 2cfx chain A domain 1 Region: 1 - 40 Aligned: 40 Modelled: 40 Confidence: 22.3% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 3ayh chain A Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 20.6% Identity: 36% PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase iii subunit rpc9; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii Phyre2 PDB 2ckz chain C Region: 1 - 15 Aligned: 15 Modelled: 15 Confidence: 20.2% Identity: 27% PDB header:transferase Chain: C: PDB Molecule:dna-directed rna polymerase iii 18 kd PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25. Phyre2 PDB 1kso chain A Region: 131 - 162 Aligned: 32 Modelled: 32 Confidence: 16.4% Identity: 9% Fold: EF Hand-like Superfamily: EF-hand Family: S100 proteins Phyre2 PDB 3c1v chain A domain 1 Region: 131 - 162 Aligned: 32 Modelled: 32 Confidence: 15.6% Identity: 16% Fold: EF Hand-like Superfamily: EF-hand Family: S100 proteins Phyre2 PDB 1vq0 chain A domain 2 Region: 147 - 163 Aligned: 17 Modelled: 17 Confidence: 15.4% Identity: 24% Fold: HSP33 redox switch-like Superfamily: HSP33 redox switch-like Family: HSP33 redox switch-like Phyre2 PDB 2op5 chain A domain 1 Region: 14 - 46 Aligned: 33 Modelled: 33 Confidence: 14.3% Identity: 24% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Marine metagenome family DABB1 Phyre2 PDB 1psr chain A Region: 129 - 162 Aligned: 34 Modelled: 34 Confidence: 14.0% Identity: 12% Fold: EF Hand-like Superfamily: EF-hand Family: S100 proteins Phyre2 PDB 3mk4 chain A Region: 96 - 162 Aligned: 53 Modelled: 67 Confidence: 12.9% Identity: 15% PDB header:protein transport Chain: A: PDB Molecule:peroxisomal biogenesis factor 3; PDBTitle: x-ray structure of human pex3 in complex with a pex19 derived peptide Phyre2 PDB 1nsh chain A Region: 129 - 162 Aligned: 34 Modelled: 34 Confidence: 12.3% Identity: 18% Fold: EF Hand-like Superfamily: EF-hand Family: S100 proteins Phyre2 PDB 1xjh chain A Region: 147 - 163 Aligned: 17 Modelled: 17 Confidence: 11.9% Identity: 35% Fold: HSP33 redox switch-like Superfamily: HSP33 redox switch-like Family: HSP33 redox switch-like Phyre2 PDB 1vzy chain A domain 2 Region: 147 - 163 Aligned: 17 Modelled: 17 Confidence: 10.8% Identity: 18% Fold: HSP33 redox switch-like Superfamily: HSP33 redox switch-like Family: HSP33 redox switch-like Phyre2 PDB 1xk4 chain C domain 1 Region: 131 - 162 Aligned: 32 Modelled: 32 Confidence: 8.8% Identity: 16% Fold: EF Hand-like Superfamily: EF-hand Family: S100 proteins Phyre2 PDB 2l4w chain A Region: 131 - 155 Aligned: 25 Modelled: 25 Confidence: 8.7% Identity: 36% PDB header:protein transport Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of the xanthomonas virb7 Phyre2 PDB 1gsa chain A domain 1 Region: 18 - 51 Aligned: 34 Modelled: 34 Confidence: 8.1% Identity: 18% Fold: PreATP-grasp domain Superfamily: PreATP-grasp domain Family: Prokaryotic glutathione synthetase, N-terminal domain Phyre2 PDB 2fok chain A domain 2 Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 7.5% Identity: 42% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Restriction endonuclease FokI, N-terminal (recognition) domain Phyre2 PDB 1irj chain G Region: 131 - 162 Aligned: 32 Modelled: 32 Confidence: 7.3% Identity: 16% PDB header:metal binding protein Chain: G: PDB Molecule:migration inhibitory factor-related protein 14; PDBTitle: crystal structure of the mrp14 complexed with chaps Phyre2 1 d1wpba_ 2 d1zara1 3 d2bcgg2 4 d2cfxa1 5 c3ayhA_ 6 c2ckzC_ 7 d1ksoa_ 8 d3c1va1 9 d1vq0a2 10 d2op5a1 11 d1psra_ 12 c3mk4A_ 13 d1nsha_ 14 d1xjha_ 15 d1vzya2 16 d1xk4c1 17 c2l4wA_ 18 d1gsaa1 19 d2foka2 20 c1irjG_ 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 d1wpba_ 100.0 100 Fold:YfbU-like Superfamily:YfbU-like Family:YfbU-like 2 d1zara1 32.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Rio2 serine protein kinase N-terminal domain 3 d2bcgg2 32.4 17 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:GDI-like N domain 4 d2cfxa1 22.3 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 5 c3ayhA_ 20.6 36 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase iii subunit rpc9; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii 6 c2ckzC_ 20.2 27 PDB header:transferase Chain: C: PDB Molecule:dna-directed rna polymerase iii 18 kd PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25. 7 d1ksoa_ 16.4 9 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 8 d3c1va1 15.6 16 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 9 d1vq0a2 15.4 24 Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like 10 d2op5a1 14.3 24 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Marine metagenome family DABB1 11 d1psra_ 14.0 12 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 12 c3mk4A_ 12.9 15 PDB header:protein transport Chain: A: PDB Molecule:peroxisomal biogenesis factor 3; PDBTitle: x-ray structure of human pex3 in complex with a pex19 derived peptide 13 d1nsha_ 12.3 18 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 14 d1xjha_ 11.9 35 Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like 15 d1vzya2 10.8 18 Fold:HSP33 redox switch-like Superfamily:HSP33 redox switch-like Family:HSP33 redox switch-like 16 d1xk4c1 8.8 16 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 17 c2l4wA_ 8.7 36 PDB header:protein transport Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of the xanthomonas virb7 18 d1gsaa1 8.1 18 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:Prokaryotic glutathione synthetase, N-terminal domain 19 d2foka2 7.5 42 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 20 c1irjG_ 7.3 16 PDB header:metal binding protein Chain: G: PDB Molecule:migration inhibitory factor-related protein 14; PDBTitle: crystal structure of the mrp14 complexed with chaps 21 d1qlsa_ not modelled 7.3 12 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 22 d1rr7a_ not modelled 7.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 23 c1rr7A_ not modelled 7.1 16 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 24 d2aq0a1 not modelled 7.0 15 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 25 c2kaxA_ not modelled 6.7 25 PDB header:metal binding protein Chain: A: PDB Molecule:protein s100-a5; PDBTitle: solution structure and dynamics of s100a5 in the apo and2 ca2+ -bound states 26 d1hmca_ not modelled 6.3 17 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 27 c1ontA_ not modelled 6.2 31 PDB header:antagonist Chain: A: PDB Molecule:conantokin-t; PDBTitle: nmda receptor antagonist, conantokin-t, nmr, 17 structures 28 c2i6hA_ not modelled 6.2 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein atu0120; PDBTitle: structure of protein of unknown function atu0120 from agrobacterium2 tumefaciens 29 d2i6ha1 not modelled 6.2 21 Fold:alpha-alpha superhelix Superfamily:TPR-like Family:Atu0120-like 30 c1vzyA_ not modelled 6.0 18 PDB header:chaperone Chain: A: PDB Molecule:33 kda chaperonin; PDBTitle: crystal structure of the bacillus subtilis hsp33 31 c2rgiA_ not modelled 5.9 16 PDB header:metal binding protein Chain: A: PDB Molecule:protein s100-a2; PDBTitle: crystal structure of ca2+-free s100a2 at 1.6 a resolution 32 d1k8ua_ not modelled 5.9 22 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins 33 d1dqna_ not modelled 5.8 23 Fold:PRTase-like Superfamily:PRTase-like Family:Phosphoribosyltransferases (PRTases) 34 d1mxsa_ not modelled 5.5 15 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 35 d1e8aa_ not modelled 5.2 28 Fold:EF Hand-like Superfamily:EF-hand Family:S100 proteins

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