Secondary structure and disorder prediction

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Sequence		M	L	E	D	T	T	I	H	N	A	I	T	D	K	A	L	A	S	Y	F	R	S	S	G	N	L	L	E	E	E	S	A	V	L	G	Q	A	V	T	N	L	M	L	S	G	D	N	V	N	N	K	N	I	I	L	S	L	I	H	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?										?			?																	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.
Sequence		L	E	T	T	S	D	I	L	K	A	D	V	I	R	K	T	L	E	I	V	L	R	Y	T	A	D	D	M
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: 25 - 86 Aligned: 62 Modelled: 62 Confidence: 99.9% Identity: 98% 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 1stz chain B Region: 30 - 53 Aligned: 24 Modelled: 24 Confidence: 25.1% Identity: 17% PDB header:transcription Chain: B: PDB Molecule:heat-inducible transcription repressor hrca homolog; PDBTitle: crystal structure of a hypothetical protein at 2.2 a resolution Phyre2 PDB 1v92 chain A Region: 13 - 24 Aligned: 12 Modelled: 12 Confidence: 15.5% Identity: 42% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: TAP-C domain-like Phyre2 PDB 3ct5 chain A Region: 14 - 40 Aligned: 27 Modelled: 27 Confidence: 13.4% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:morphogenesis protein 1; PDBTitle: crystal and cryoem structural studies of a cell wall degrading enzyme2 in the bacteriophage phi29 tail Phyre2 PDB 2bn5 chain A Region: 13 - 31 Aligned: 19 Modelled: 19 Confidence: 11.2% Identity: 37% PDB header:nuclear protein Chain: A: PDB Molecule:psi; PDBTitle: p-element somatic inhibitor protein complex with u1-70k2 proline-rich peptide Phyre2 PDB 1stz chain A domain 1 Region: 32 - 53 Aligned: 22 Modelled: 22 Confidence: 10.7% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Heat-inducible transcription repressor HrcA, N-terminal domain Phyre2 PDB 3gxv chain A Region: 18 - 87 Aligned: 60 Modelled: 70 Confidence: 10.3% Identity: 20% PDB header:hydrolase/replication Chain: A: PDB Molecule:replicative dna helicase; PDBTitle: three-dimensional structure of n-terminal domain of dnab2 helicase from helicobacter pylori and its interactions with3 primase Phyre2 PDB 2j8a chain A Region: 4 - 25 Aligned: 22 Modelled: 22 Confidence: 9.8% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-4 PDBTitle: x-ray structure of the n-terminus rrm domain of set1 Phyre2 PDB 3eyy chain A Region: 13 - 80 Aligned: 61 Modelled: 68 Confidence: 9.5% Identity: 18% PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition Phyre2 PDB 1eiy chain A domain 1 Region: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 8.9% Identity: 22% Fold: Long alpha-hairpin Superfamily: tRNA-binding arm Family: Phenylalanyl-tRNA synthetase (PheRS) Phyre2 PDB 2izp chain B Region: 14 - 44 Aligned: 31 Modelled: 31 Confidence: 8.9% Identity: 16% PDB header:toxin Chain: B: PDB Molecule:putative membrane antigen; PDBTitle: bipd - an invasion prtein associated with the type-iii2 secretion system of burkholderia pseudomallei. Phyre2 PDB 2b3y chain A domain 2 Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 8.6% Identity: 29% Fold: Aconitase iron-sulfur domain Superfamily: Aconitase iron-sulfur domain Family: Aconitase iron-sulfur domain Phyre2 PDB 1ugp chain A Region: 20 - 76 Aligned: 56 Modelled: 57 Confidence: 8.0% Identity: 20% Fold: Nitrile hydratase alpha chain Superfamily: Nitrile hydratase alpha chain Family: Nitrile hydratase alpha chain Phyre2 PDB 1got chain G Region: 48 - 82 Aligned: 35 Modelled: 35 Confidence: 7.8% Identity: 11% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Transducin (heterotrimeric G protein), gamma chain Family: Transducin (heterotrimeric G protein), gamma chain Phyre2 PDB 3h8d chain E Region: 12 - 22 Aligned: 11 Modelled: 11 Confidence: 7.7% Identity: 45% PDB header:motor protein/signaling protein Chain: E: PDB Molecule:disabled homolog 2; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide Phyre2 PDB 3f1i chain H Region: 32 - 61 Aligned: 30 Modelled: 30 Confidence: 7.6% Identity: 20% PDB header:protein binding Chain: H: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: human escrt-0 core complex Phyre2 PDB 1aco chain A domain 2 Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 7.3% Identity: 29% Fold: Aconitase iron-sulfur domain Superfamily: Aconitase iron-sulfur domain Family: Aconitase iron-sulfur domain Phyre2 PDB 2dzl chain A Region: 13 - 24 Aligned: 12 Modelled: 12 Confidence: 6.9% Identity: 25% 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 1q5z chain A Region: 58 - 78 Aligned: 21 Modelled: 21 Confidence: 6.8% Identity: 38% Fold: Invasion protein A (SipA) , C-terminal actin binding domain Superfamily: Invasion protein A (SipA) , C-terminal actin binding domain Family: Invasion protein A (SipA) , C-terminal actin binding domain Phyre2 PDB 1q5z chain A Region: 58 - 78 Aligned: 21 Modelled: 21 Confidence: 6.8% Identity: 38% PDB header:cell invasion Chain: A: PDB Molecule:sipa; PDBTitle: crystal structure of the c-terminal actin binding domain of2 salmonella invasion protein a (sipa) Phyre2 1 c2oxlA_ 2 c1stzB_ 3 d1v92a_ 4 c3ct5A_ 5 c2bn5A_ 6 d1stza1 7 c3gxvA_ 8 c2j8aA_ 9 c3eyyA_ 10 d1eiya1 11 c2izpB_ 12 d2b3ya2 13 d1ugpa_ 14 d1gotg_ 15 c3h8dE_ 16 c3f1iH_ 17 d1acoa2 18 c2dzlA_ 19 d1q5za_ 20 c1q5zA_ 21 22 23 24 25 26 27

Detailed template information

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

1 c2oxlA_ 99.9 98 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 c1stzB_ 25.1 17 PDB header:transcription Chain: B: PDB Molecule:heat-inducible transcription repressor hrca homolog; PDBTitle: crystal structure of a hypothetical protein at 2.2 a resolution 3 d1v92a_ 15.5 42 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like 4 c3ct5A_ 13.4 19 PDB header:hydrolase Chain: A: PDB Molecule:morphogenesis protein 1; PDBTitle: crystal and cryoem structural studies of a cell wall degrading enzyme2 in the bacteriophage phi29 tail 5 c2bn5A_ 11.2 37 PDB header:nuclear protein Chain: A: PDB Molecule:psi; PDBTitle: p-element somatic inhibitor protein complex with u1-70k2 proline-rich peptide 6 d1stza1 10.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain 7 c3gxvA_ 10.3 20 PDB header:hydrolase/replication Chain: A: PDB Molecule:replicative dna helicase; PDBTitle: three-dimensional structure of n-terminal domain of dnab2 helicase from helicobacter pylori and its interactions with3 primase 8 c2j8aA_ 9.8 23 PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-4 PDBTitle: x-ray structure of the n-terminus rrm domain of set1 9 c3eyyA_ 9.5 18 PDB header:transport Chain: A: PDB Molecule:putative iron uptake regulatory protein; PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition 10 d1eiya1 8.9 22 Fold:Long alpha-hairpin Superfamily:tRNA-binding arm Family:Phenylalanyl-tRNA synthetase (PheRS) 11 c2izpB_ 8.9 16 PDB header:toxin Chain: B: PDB Molecule:putative membrane antigen; PDBTitle: bipd - an invasion prtein associated with the type-iii2 secretion system of burkholderia pseudomallei. 12 d2b3ya2 8.6 29 Fold:Aconitase iron-sulfur domain Superfamily:Aconitase iron-sulfur domain Family:Aconitase iron-sulfur domain 13 d1ugpa_ 8.0 20 Fold:Nitrile hydratase alpha chain Superfamily:Nitrile hydratase alpha chain Family:Nitrile hydratase alpha chain 14 d1gotg_ 7.8 11 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Transducin (heterotrimeric G protein), gamma chain Family:Transducin (heterotrimeric G protein), gamma chain 15 c3h8dE_ 7.7 45 PDB header:motor protein/signaling protein Chain: E: PDB Molecule:disabled homolog 2; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide 16 c3f1iH_ 7.6 20 PDB header:protein binding Chain: H: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: human escrt-0 core complex 17 d1acoa2 7.3 29 Fold:Aconitase iron-sulfur domain Superfamily:Aconitase iron-sulfur domain Family:Aconitase iron-sulfur domain 18 c2dzlA_ 6.9 25 PDB header:structural genomics unknown function Chain: A: PDB Molecule:protein fam100b; PDBTitle: solution structure of the uba domain in human protein2 fam100b 19 d1q5za_ 6.8 38 Fold:Invasion protein A (SipA) , C-terminal actin binding domain Superfamily:Invasion protein A (SipA) , C-terminal actin binding domain Family:Invasion protein A (SipA) , C-terminal actin binding domain 20 c1q5zA_ 6.8 38 PDB header:cell invasion Chain: A: PDB Molecule:sipa; PDBTitle: crystal structure of the c-terminal actin binding domain of2 salmonella invasion protein a (sipa) 21 d2iy5a1 not modelled 6.5 22 Fold:Long alpha-hairpin Superfamily:tRNA-binding arm Family:Phenylalanyl-tRNA synthetase (PheRS) 22 d1mzba_ not modelled 6.2 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FUR-like 23 c2b3yB_ not modelled 6.1 29 PDB header:lyase Chain: B: PDB Molecule:iron-responsive element binding protein 1; PDBTitle: structure of a monoclinic crystal form of human cytosolic aconitase2 (irp1) 24 c3csqC_ not modelled 5.7 18 PDB header:hydrolase Chain: C: PDB Molecule:morphogenesis protein 1; PDBTitle: crystal and cryoem structural studies of a cell wall2 degrading enzyme in the bacteriophage phi29 tail 25 c2o8sA_ not modelled 5.5 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:agr_c_984p; PDBTitle: x-ray crystal structure of protein agr_c_984 from agrobacterium2 tumefaciens. northeast structural genomics consortium target atr120. 26 d1l5ja3 not modelled 5.4 0 Fold:Aconitase iron-sulfur domain Superfamily:Aconitase iron-sulfur domain Family:Aconitase iron-sulfur domain 27 d2f76x1 not modelled 5.2 17 Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:Mason-Pfizer monkey virus matrix protein

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