Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	Q	N	S	V	T	L	D	S	A	G	A	I	T	R	Y	F	A	K	A	N	L	H	T	Q	Q	E	T	L	G	E	I	V	T	E	I	L	K	D	G	R	N	L	S	R	K	S	L	C	A	K	L	L	C	R	L	E	H	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?															?																																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.
Sequence		T	G	E	E	E	Q	K	H	Y	N	A	L	I	G	L	L	F	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 2oxl chain A Region: 27 - 75 Aligned: 49 Modelled: 49 Confidence: 97.4% Identity: 20% PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance Phyre2 PDB 3c6a chain A Region: 2 - 58 Aligned: 57 Modelled: 57 Confidence: 41.0% Identity: 23% PDB header:viral protein Chain: A: PDB Molecule:terminase large subunit; PDBTitle: crystal structure of the rb49 gp17 nuclease domain Phyre2 PDB 1stz chain A domain 1 Region: 24 - 53 Aligned: 30 Modelled: 30 Confidence: 36.5% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Heat-inducible transcription repressor HrcA, N-terminal domain Phyre2 PDB 1j2j chain B Region: 51 - 73 Aligned: 23 Modelled: 23 Confidence: 27.1% Identity: 35% Fold: Spectrin repeat-like Superfamily: GAT-like domain Family: GAT domain Phyre2 PDB 2l82 chain A Region: 21 - 42 Aligned: 22 Modelled: 22 Confidence: 16.7% Identity: 36% PDB header:de novo protein Chain: A: PDB Molecule:designed protein or32; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or32 Phyre2 PDB 1jhf chain A domain 1 Region: 24 - 53 Aligned: 30 Modelled: 30 Confidence: 15.1% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: LexA repressor, N-terminal DNA-binding domain Phyre2 PDB 2dzl chain A Region: 11 - 26 Aligned: 16 Modelled: 16 Confidence: 13.0% Identity: 19% PDB header:structural genomics unknown function Chain: A: PDB Molecule:protein fam100b; PDBTitle: solution structure of the uba domain in human protein2 fam100b Phyre2 PDB 1bcg chain A Region: 1 - 12 Aligned: 12 Modelled: 12 Confidence: 9.8% Identity: 42% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Long-chain scorpion toxins Phyre2 PDB 3p3d chain A Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 9.5% Identity: 19% PDB header:nuclear protein Chain: A: PDB Molecule:nucleoporin 53; PDBTitle: crystal structure of the nup53 rrm domain from pichia guilliermondii Phyre2 PDB 1wwh chain B Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 6.9% Identity: 31% PDB header:protein transport Chain: B: PDB Molecule:nucleoporin 35; PDBTitle: crystal structure of the mppn domain of mouse nup35 Phyre2 PDB 1wwh chain A domain 1 Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 6.7% Identity: 31% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 3mgj chain A Region: 27 - 44 Aligned: 18 Modelled: 18 Confidence: 6.3% Identity: 22% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mj1480; PDBTitle: crystal structure of the saccharop_dh_n domain of mj14802 protein from methanococcus jannaschii. northeast structural3 genomics consortium target mjr83a. Phyre2 PDB 1x3a chain A domain 1 Region: 15 - 30 Aligned: 16 Modelled: 16 Confidence: 5.7% Identity: 31% Fold: BSD domain-like Superfamily: BSD domain-like Family: BSD domain Phyre2 PDB 1au7 chain B Region: 2 - 29 Aligned: 28 Modelled: 28 Confidence: 5.6% Identity: 18% PDB header:transcription/dna Chain: B: PDB Molecule:protein pit-1; PDBTitle: pit-1 mutant/dna complex Phyre2 PDB 1zav chain A domain 1 Region: 21 - 46 Aligned: 26 Modelled: 26 Confidence: 5.5% Identity: 19% Fold: Ferredoxin-like Superfamily: Ribosomal protein L10-like Family: Ribosomal protein L10-like Phyre2 PDB 3bxj chain B Region: 13 - 62 Aligned: 50 Modelled: 50 Confidence: 5.5% Identity: 20% PDB header:signaling protein Chain: B: PDB Molecule:ras gtpase-activating protein syngap; PDBTitle: crystal structure of the c2-gap fragment of syngap Phyre2 PDB 3idw chain A Region: 5 - 40 Aligned: 34 Modelled: 36 Confidence: 5.3% Identity: 18% PDB header:endocytosis Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1; PDBTitle: crystal structure of sla1 homology domain 2 Phyre2 1 c2oxlA_ 2 c3c6aA_ 3 d1stza1 4 d1j2jb_ 5 c2l82A_ 6 d1jhfa1 7 c2dzlA_ 8 d1bcga_ 9 c3p3dA_ 10 c1wwhB_ 11 d1wwha1 12 c3mgjA_ 13 d1x3aa1 14 c1au7B_ 15 d1zava1 16 c3bxjB_ 17 c3idwA_

Detailed template information

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

1 c2oxlA_ 97.4 20 PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance 2 c3c6aA_ 41.0 23 PDB header:viral protein Chain: A: PDB Molecule:terminase large subunit; PDBTitle: crystal structure of the rb49 gp17 nuclease domain 3 d1stza1 36.5 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain 4 d1j2jb_ 27.1 35 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 5 c2l82A_ 16.7 36 PDB header:de novo protein Chain: A: PDB Molecule:designed protein or32; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or32 6 d1jhfa1 15.1 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 7 c2dzlA_ 13.0 19 PDB header:structural genomics unknown function Chain: A: PDB Molecule:protein fam100b; PDBTitle: solution structure of the uba domain in human protein2 fam100b 8 d1bcga_ 9.8 42 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Long-chain scorpion toxins 9 c3p3dA_ 9.5 19 PDB header:nuclear protein Chain: A: PDB Molecule:nucleoporin 53; PDBTitle: crystal structure of the nup53 rrm domain from pichia guilliermondii 10 c1wwhB_ 6.9 31 PDB header:protein transport Chain: B: PDB Molecule:nucleoporin 35; PDBTitle: crystal structure of the mppn domain of mouse nup35 11 d1wwha1 6.7 31 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 12 c3mgjA_ 6.3 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mj1480; PDBTitle: crystal structure of the saccharop_dh_n domain of mj14802 protein from methanococcus jannaschii. northeast structural3 genomics consortium target mjr83a. 13 d1x3aa1 5.7 31 Fold:BSD domain-like Superfamily:BSD domain-like Family:BSD domain 14 c1au7B_ 5.6 18 PDB header:transcription/dna Chain: B: PDB Molecule:protein pit-1; PDBTitle: pit-1 mutant/dna complex 15 d1zava1 5.5 19 Fold:Ferredoxin-like Superfamily:Ribosomal protein L10-like Family:Ribosomal protein L10-like 16 c3bxjB_ 5.5 20 PDB header:signaling protein Chain: B: PDB Molecule:ras gtpase-activating protein syngap; PDBTitle: crystal structure of the c2-gap fragment of syngap 17 c3idwA_ 5.3 18 PDB header:endocytosis Chain: A: PDB Molecule:actin cytoskeleton-regulatory complex protein sla1; PDBTitle: crystal structure of sla1 homology domain 2

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