Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	Q	N	P	I	H	L	R	L	E	R	L	E	S	W	Q	H	V	T	F	M	A	C	L	C	E	R	M	Y	P	N	Y	A	M	F	C	Q	Q	T	G	F	G	D	G	Q	I	Y	R	R	I	L	D	L	I	W	E	T	L	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?								?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	K	D	A	K	V	N	F	D	S	Q	L	E	K	F	E	E	A	I	P	S	A	D	D	F	D	L	Y	G	V	Y	P	A	I	D	A	C	V	A	L	S	E	L	V	H	S	R	L	S	G	E	T	L	E	H	A	V	E	V	S
Secondary structure
SS confidence
Disorder					?	?																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	T	S	I	T	T	V	A	M	L	E	M	T	Q	A	G	R	E	M	S	D	E	E	L	K	E	N	P	A	V	E	Q	E	W	D	I	Q	W	E	I	F	R	L	L	A	E	C	E	E	R	D	I	E	L	I	K	G	L	R	A
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?																										?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.
Sequence		D	L	R	E	A	G	E	S	N	I	G	I	I	F	Q	Q
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 3f7c chain A Region: 2 - 195 Aligned: 193 Modelled: 194 Confidence: 100.0% Identity: 30% PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function (duf416); PDBTitle: crystal structure of a duf416 family protein (maqu_0942) from2 marinobacter aquaeolei vt8 at 2.00 a resolution Phyre2 PDB 2q9r chain A Region: 6 - 194 Aligned: 188 Modelled: 189 Confidence: 100.0% Identity: 37% PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a duf416 family protein (sbal_3149) from2 shewanella baltica os155 at 1.91 a resolution Phyre2 PDB 1pul chain A domain 1 Region: 32 - 102 Aligned: 71 Modelled: 71 Confidence: 64.3% Identity: 14% Fold: EF Hand-like Superfamily: EF-hand Family: p25-alpha Phyre2 PDB 2dpy chain A Region: 89 - 183 Aligned: 91 Modelled: 95 Confidence: 44.4% Identity: 14% PDB header:hydrolase Chain: A: PDB Molecule:flagellum-specific atp synthase; PDBTitle: crystal structure of the flagellar type iii atpase flii Phyre2 PDB 1z9h chain A domain 1 Region: 80 - 106 Aligned: 27 Modelled: 27 Confidence: 32.8% Identity: 26% Fold: GST C-terminal domain-like Superfamily: GST C-terminal domain-like Family: Glutathione S-transferase (GST), C-terminal domain Phyre2 PDB 3lj4 chain I Region: 11 - 35 Aligned: 25 Modelled: 25 Confidence: 29.0% Identity: 28% PDB header:viral protein Chain: I: PDB Molecule:portal protein; PDBTitle: bacteriophage p22 portal protein bound to middle tail factor gp4. this2 file contain the first biological assembly Phyre2 PDB 1szi chain A Region: 95 - 171 Aligned: 76 Modelled: 77 Confidence: 22.9% Identity: 14% Fold: Four-helical up-and-down bundle Superfamily: Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Family: Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Phyre2 PDB 1m98 chain A domain 1 Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 21.0% Identity: 15% Fold: Orange carotenoid protein, N-terminal domain Superfamily: Orange carotenoid protein, N-terminal domain Family: Orange carotenoid protein, N-terminal domain Phyre2 PDB 3t98 chain A Region: 170 - 192 Aligned: 23 Modelled: 23 Confidence: 19.2% Identity: 30% PDB header:protein transport Chain: A: PDB Molecule:nuclear pore complex protein nup54; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup54/nup58 Phyre2 PDB 1m98 chain A Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 15.8% Identity: 15% PDB header:unknown function Chain: A: PDB Molecule:orange carotenoid protein; PDBTitle: crystal structure of orange carotenoid protein Phyre2 PDB 1iyj chain B domain 1 Region: 14 - 32 Aligned: 19 Modelled: 19 Confidence: 13.6% Identity: 11% Fold: BRCA2 helical domain Superfamily: BRCA2 helical domain Family: BRCA2 helical domain Phyre2 PDB 1fnn chain A domain 1 Region: 7 - 55 Aligned: 48 Modelled: 49 Confidence: 13.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Helicase DNA-binding domain Phyre2 PDB 2an7 chain A Region: 2 - 32 Aligned: 31 Modelled: 31 Confidence: 12.7% Identity: 26% PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard Phyre2 PDB 2obl chain A Region: 89 - 183 Aligned: 91 Modelled: 95 Confidence: 12.0% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:escn; PDBTitle: structural and biochemical analysis of a prototypical atpase from the2 type iii secretion system of pathogenic bacteria Phyre2 PDB 2r4g chain A Region: 14 - 75 Aligned: 54 Modelled: 62 Confidence: 11.9% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: the high resolution structure of the rna-binding domain of telomerase Phyre2 PDB 2bjc chain A domain 1 Region: 112 - 157 Aligned: 44 Modelled: 46 Confidence: 11.1% Identity: 20% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1zoq chain C domain 1 Region: 157 - 177 Aligned: 21 Modelled: 21 Confidence: 9.7% Identity: 19% Fold: Nuclear receptor coactivator interlocking domain Superfamily: Nuclear receptor coactivator interlocking domain Family: Nuclear receptor coactivator interlocking domain Phyre2 PDB 1miu chain A domain 1 Region: 14 - 32 Aligned: 19 Modelled: 19 Confidence: 9.7% Identity: 11% Fold: BRCA2 helical domain Superfamily: BRCA2 helical domain Family: BRCA2 helical domain Phyre2 PDB 1wlm chain A domain 1 Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 9.2% Identity: 23% Fold: EF Hand-like Superfamily: EF-hand Family: p25-alpha Phyre2 PDB 1fx0 chain B Region: 89 - 152 Aligned: 61 Modelled: 64 Confidence: 8.5% Identity: 23% PDB header:hydrolase Chain: B: PDB Molecule:atp synthase beta chain; PDBTitle: crystal structure of the chloroplast f1-atpase from spinach Phyre2 1 c3f7cA_ 2 c2q9rA_ 3 d1pula1 4 c2dpyA_ 5 d1z9ha1 6 c3lj4i_ 7 d1szia_ 8 d1m98a1 9 c3t98A_ 10 c1m98A_ 11 d1iyjb1 12 d1fnna1 13 c2an7A_ 14 c2oblA_ 15 c2r4gA_ 16 d2bjca1 17 d1zoqc1 18 d1miua1 19 d1wlma1 20 c1fx0B_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 c3f7cA_ 100.0 30 PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function (duf416); PDBTitle: crystal structure of a duf416 family protein (maqu_0942) from2 marinobacter aquaeolei vt8 at 2.00 a resolution 2 c2q9rA_ 100.0 37 PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a duf416 family protein (sbal_3149) from2 shewanella baltica os155 at 1.91 a resolution 3 d1pula1 64.3 14 Fold:EF Hand-like Superfamily:EF-hand Family:p25-alpha 4 c2dpyA_ 44.4 14 PDB header:hydrolase Chain: A: PDB Molecule:flagellum-specific atp synthase; PDBTitle: crystal structure of the flagellar type iii atpase flii 5 d1z9ha1 32.8 26 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain 6 c3lj4i_ 29.0 28 PDB header:viral protein Chain: I: PDB Molecule:portal protein; PDBTitle: bacteriophage p22 portal protein bound to middle tail factor gp4. this2 file contain the first biological assembly 7 d1szia_ 22.9 14 Fold:Four-helical up-and-down bundle Superfamily:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain Family:Mannose-6-phosphate receptor binding protein 1 (Tip47), C-terminal domain 8 d1m98a1 21.0 15 Fold:Orange carotenoid protein, N-terminal domain Superfamily:Orange carotenoid protein, N-terminal domain Family:Orange carotenoid protein, N-terminal domain 9 c3t98A_ 19.2 30 PDB header:protein transport Chain: A: PDB Molecule:nuclear pore complex protein nup54; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup54/nup58 10 c1m98A_ 15.8 15 PDB header:unknown function Chain: A: PDB Molecule:orange carotenoid protein; PDBTitle: crystal structure of orange carotenoid protein 11 d1iyjb1 13.6 11 Fold:BRCA2 helical domain Superfamily:BRCA2 helical domain Family:BRCA2 helical domain 12 d1fnna1 13.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 13 c2an7A_ 12.7 26 PDB header:dna binding protein Chain: A: PDB Molecule:protein pard; PDBTitle: solution structure of the bacterial antidote pard 14 c2oblA_ 12.0 12 PDB header:hydrolase Chain: A: PDB Molecule:escn; PDBTitle: structural and biochemical analysis of a prototypical atpase from the2 type iii secretion system of pathogenic bacteria 15 c2r4gA_ 11.9 13 PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: the high resolution structure of the rna-binding domain of telomerase 16 d2bjca1 11.1 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 17 d1zoqc1 9.7 19 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking domain 18 d1miua1 9.7 11 Fold:BRCA2 helical domain Superfamily:BRCA2 helical domain Family:BRCA2 helical domain 19 d1wlma1 9.2 23 Fold:EF Hand-like Superfamily:EF-hand Family:p25-alpha 20 c1fx0B_ 8.5 23 PDB header:hydrolase Chain: B: PDB Molecule:atp synthase beta chain; PDBTitle: crystal structure of the chloroplast f1-atpase from spinach 21 c3ovkD_ not modelled 7.6 14 PDB header:hydrolase Chain: D: PDB Molecule:aminopeptidase p, xaa-pro dipeptidase; PDBTitle: crystal structure of an xxa-pro aminopeptidase from streptococcus2 pyogenes 22 c2h12C_ not modelled 7.3 22 PDB header:transferase Chain: C: PDB Molecule:citrate synthase; PDBTitle: structure of acetobacter aceti citrate synthase complexed2 with oxaloacetate and carboxymethyldethia coenzyme a (cmx) 23 c2o8kA_ not modelled 7.1 21 PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element 24 c2qe7C_ not modelled 6.9 16 PDB header:hydrolase Chain: C: PDB Molecule:atp synthase subunit alpha; PDBTitle: crystal structure of the f1-atpase from the thermoalkaliphilic2 bacterium bacillus sp. ta2.a1 25 c2jrfA_ not modelled 6.9 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tubulin polymerization-promoting protein family PDBTitle: solution nmr structure of tubulin polymerization-promoting2 protein family member 3 from homo sapiens. northeast3 structural genomics target hr387. 26 d2cx6a1 not modelled 6.7 32 Fold:Barstar-like Superfamily:Barstar-related Family:Barstar-related 27 c1mjeA_ not modelled 6.7 11 PDB header:gene regulation/antitumor protein/dna Chain: A: PDB Molecule:breast cancer 2; PDBTitle: structure of a brca2-dss1-ssdna complex 28 c1iyjB_ not modelled 6.6 11 PDB header:gene regulation/antitumor protein Chain: B: PDB Molecule:breast cancer susceptibility; PDBTitle: structure of a brca2-dss1 complex 29 d1or7a1 not modelled 6.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 30 c3a8qB_ not modelled 6.4 27 PDB header:signaling protein Chain: B: PDB Molecule:t-lymphoma invasion and metastasis-inducing PDBTitle: low-resolution crystal structure of the tiam2 phccex domain 31 d1k28a3 not modelled 6.4 18 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Phage lysozyme 32 d1dd3a2 not modelled 6.3 30 Fold:ClpS-like Superfamily:ClpS-like Family:Ribosomal protein L7/12, C-terminal domain 33 c1miuA_ not modelled 6.2 11 PDB header:gene regulation/antitumor protein Chain: A: PDB Molecule:breast cancer type 2 susceptibility protein; PDBTitle: structure of a brca2-dss1 complex 34 d1zq1a1 not modelled 5.8 57 Fold:Sm-like fold Superfamily:GatD N-terminal domain-like Family:GatD N-terminal domain-like 35 c2yufA_ not modelled 5.7 22 PDB header:transcription Chain: A: PDB Molecule:ngfi-a-binding protein 1; PDBTitle: solution structure of the ncd2 domain in human2 transcriptional repressor nab1 protein 36 c3lhfC_ not modelled 5.6 15 PDB header:recombination Chain: C: PDB Molecule:serine recombinase; PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a 37 c3a5dM_ not modelled 5.5 23 PDB header:hydrolase Chain: M: PDB Molecule:v-type atp synthase beta chain; PDBTitle: inter-subunit interaction and quaternary rearrangement2 defined by the central stalk of prokaryotic v1-atpase 38 d1gx5a_ not modelled 5.1 19 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase

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