Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	N	N	M	S	S	R	Q	A	C	H	A	A	R	Y	V	V	A	R	V	L	R	G	L	F	W	C	L	K	Y	T	V	I	L	P	L	A	T	M	A	L	M	A	L	F	V	L	W	K	D	N	T	T	P	G	K	L	L	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	E	I	N	F	V	R	Q	T	A	P	A	G	Q	F	P	V	S	E	C	W	F	S	S	S	D	S	S	G	R	S	E	I	Q	G	I	C	H	Y	R	A	A	D	A	A	D	Y	V	R	E	T	D	R	S	L	M	Q	L	V	T
Secondary structure
SS confidence
Disorder									?	?		?	?	?							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	L	W	A	T	L	A	L	M	Y	V	S	L	A	A	I	T	G	K	Y	P	V	R	P	G	K	M	K	C	I	R	V	V	T	A	D	E	H	L	K	E	V	Y	T	E	D	A	S	L	P	G	K	I	R	K	C	P	V	Y	L
Secondary structure
SS confidence
Disorder																																																	?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.
Sequence		P	D	D	R	T	N	R	N	N	G	D	K	N	E	H	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 2v4j chain E Region: 57 - 118 Aligned: 61 Modelled: 62 Confidence: 36.6% Identity: 18% PDB header:oxidoreductase Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration Phyre2 PDB 3c07 chain A domain 2 Region: 37 - 65 Aligned: 29 Modelled: 27 Confidence: 31.2% Identity: 17% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 2jso chain A Region: 145 - 188 Aligned: 44 Modelled: 44 Confidence: 18.8% Identity: 23% PDB header:signaling protein Chain: A: PDB Molecule:polymyxin resistance protein pmrd; PDBTitle: antimicrobial resistance protein Phyre2 PDB 2rqx chain A Region: 145 - 188 Aligned: 44 Modelled: 44 Confidence: 13.1% Identity: 23% PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae Phyre2 PDB 1oed chain A Region: 29 - 58 Aligned: 30 Modelled: 30 Confidence: 12.2% Identity: 17% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 1qjw chain A Region: 49 - 113 Aligned: 56 Modelled: 56 Confidence: 9.7% Identity: 21% Fold: 7-stranded beta/alpha barrel Superfamily: Glycosyl hydrolases family 6, cellulases Family: Glycosyl hydrolases family 6, cellulases Phyre2 PDB 1oed chain E Region: 29 - 59 Aligned: 31 Modelled: 31 Confidence: 8.5% Identity: 13% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 3kdp chain G Region: 127 - 138 Aligned: 12 Modelled: 12 Confidence: 7.2% Identity: 42% PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 3kdp chain H Region: 127 - 138 Aligned: 12 Modelled: 12 Confidence: 7.2% Identity: 42% PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump Phyre2 PDB 2bid chain A Region: 57 - 101 Aligned: 44 Modelled: 45 Confidence: 7.0% Identity: 11% Fold: Toxins' membrane translocation domains Superfamily: Bcl-2 inhibitors of programmed cell death Family: Bcl-2 inhibitors of programmed cell death Phyre2 PDB 1doa chain B Region: 142 - 169 Aligned: 22 Modelled: 28 Confidence: 6.6% Identity: 32% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: RhoGDI-like Phyre2 PDB 2k58 chain B Region: 34 - 50 Aligned: 17 Modelled: 17 Confidence: 6.6% Identity: 24% PDB header:transport protein Chain: B: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of the first transmembrane domain of the2 neuronal acetylcholine receptor beta 2 subunit Phyre2 PDB 3hei chain I Region: 74 - 88 Aligned: 15 Modelled: 15 Confidence: 6.5% Identity: 40% PDB header:transferase/signaling protein Chain: I: PDB Molecule:ephrin type-a receptor 2; PDBTitle: ligand recognition by a-class eph receptors: crystal structures of the2 epha2 ligand-binding domain and the epha2/ephrin-a1 complex Phyre2 PDB 1oey chain J Region: 57 - 78 Aligned: 20 Modelled: 19 Confidence: 5.8% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 2gp4 chain A domain 2 Region: 51 - 60 Aligned: 10 Modelled: 10 Confidence: 5.7% Identity: 40% Fold: IlvD/EDD N-terminal domain-like Superfamily: IlvD/EDD N-terminal domain-like Family: lvD/EDD N-terminal domain-like Phyre2 PDB 2bod chain X domain 1 Region: 49 - 113 Aligned: 46 Modelled: 46 Confidence: 5.3% Identity: 35% Fold: 7-stranded beta/alpha barrel Superfamily: Glycosyl hydrolases family 6, cellulases Family: Glycosyl hydrolases family 6, cellulases Phyre2 PDB 1dys chain A Region: 49 - 116 Aligned: 63 Modelled: 68 Confidence: 5.3% Identity: 24% Fold: 7-stranded beta/alpha barrel Superfamily: Glycosyl hydrolases family 6, cellulases Family: Glycosyl hydrolases family 6, cellulases Phyre2 PDB 2ytu chain A Region: 21 - 30 Aligned: 10 Modelled: 10 Confidence: 5.2% Identity: 40% PDB header:signaling protein Chain: A: PDB Molecule:friend leukemia integration 1 transcription PDBTitle: solution structure of the sam_pnt-domain of the human2 friend leukemiaintegration 1 transcription factor Phyre2 PDB 3bz6 chain A domain 2 Region: 36 - 58 Aligned: 22 Modelled: 23 Confidence: 5.2% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PSPTO2686-like Phyre2 PDB 2kw3 chain C Region: 137 - 144 Aligned: 8 Modelled: 8 Confidence: 5.2% Identity: 50% PDB header:dna binding protein Chain: C: PDB Molecule:regulatory factor x-associated protein; PDBTitle: heterotrimeric interaction between rfx5 and rfxap Phyre2 1 c2v4jE_ 2 d3c07a2 3 c2jsoA_ 4 c2rqxA_ 5 d1oeda_ 6 d1qjwa_ 7 d1oede_ 8 c3kdpG_ 9 c3kdpH_ 10 d2bida_ 11 d1doab_ 12 c2k58B_ 13 c3heiI_ 14 d1oeyj_ 15 d2gp4a2 16 d2bodx1 17 d1dysa_ 18 c2ytuA_ 19 d3bz6a2 20 c2kw3C_ 21

Detailed template information

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

1 c2v4jE_ 36.6 18 PDB header:oxidoreductase Chain: E: PDB Molecule:sulfite reductase, dissimilatory-type subunit PDBTitle: the crystal structure of desulfovibrio vulgaris2 dissimilatory sulfite reductase bound to dsrc provides3 novel insights into the mechanism of sulfate respiration 2 d3c07a2 31.2 17 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 3 c2jsoA_ 18.8 23 PDB header:signaling protein Chain: A: PDB Molecule:polymyxin resistance protein pmrd; PDBTitle: antimicrobial resistance protein 4 c2rqxA_ 13.1 23 PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae 5 d1oeda_ 12.2 17 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 6 d1qjwa_ 9.7 21 Fold:7-stranded beta/alpha barrel Superfamily:Glycosyl hydrolases family 6, cellulases Family:Glycosyl hydrolases family 6, cellulases 7 d1oede_ 8.5 13 Fold:Neurotransmitter-gated ion-channel transmembrane pore Superfamily:Neurotransmitter-gated ion-channel transmembrane pore Family:Neurotransmitter-gated ion-channel transmembrane pore 8 c3kdpG_ 7.2 42 PDB header:hydrolase Chain: G: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 9 c3kdpH_ 7.2 42 PDB header:hydrolase Chain: H: PDB Molecule:na+/k+ atpase gamma subunit transcript variant a; PDBTitle: crystal structure of the sodium-potassium pump 10 d2bida_ 7.0 11 Fold:Toxins' membrane translocation domains Superfamily:Bcl-2 inhibitors of programmed cell death Family:Bcl-2 inhibitors of programmed cell death 11 d1doab_ 6.6 32 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 12 c2k58B_ 6.6 24 PDB header:transport protein Chain: B: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of the first transmembrane domain of the2 neuronal acetylcholine receptor beta 2 subunit 13 c3heiI_ 6.5 40 PDB header:transferase/signaling protein Chain: I: PDB Molecule:ephrin type-a receptor 2; PDBTitle: ligand recognition by a-class eph receptors: crystal structures of the2 epha2 ligand-binding domain and the epha2/ephrin-a1 complex 14 d1oeyj_ 5.8 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 15 d2gp4a2 5.7 40 Fold:IlvD/EDD N-terminal domain-like Superfamily:IlvD/EDD N-terminal domain-like Family:lvD/EDD N-terminal domain-like 16 d2bodx1 5.3 35 Fold:7-stranded beta/alpha barrel Superfamily:Glycosyl hydrolases family 6, cellulases Family:Glycosyl hydrolases family 6, cellulases 17 d1dysa_ 5.3 24 Fold:7-stranded beta/alpha barrel Superfamily:Glycosyl hydrolases family 6, cellulases Family:Glycosyl hydrolases family 6, cellulases 18 c2ytuA_ 5.2 40 PDB header:signaling protein Chain: A: PDB Molecule:friend leukemia integration 1 transcription PDBTitle: solution structure of the sam_pnt-domain of the human2 friend leukemiaintegration 1 transcription factor 19 d3bz6a2 5.2 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PSPTO2686-like 20 c2kw3C_ 5.2 50 PDB header:dna binding protein Chain: C: PDB Molecule:regulatory factor x-associated protein; PDBTitle: heterotrimeric interaction between rfx5 and rfxap 21 c3nctC_ not modelled 5.1 33 PDB header:dna binding protein, chaperone Chain: C: PDB Molecule:protein psib; PDBTitle: x-ray crystal structure of the bacterial conjugation factor psib, a2 negative regulator of reca

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