Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	I	S	D	T	K	L	R	T	I	Y	G	K	P	Y	S	G	P	Q	E	V	A	D	A	D	G	L	S	V	R	I	S	P	K	G	V	I	Q	F	Q	Y	R	Y	R	W	H	G	K	P	N	R	L	G	L	G	R	Y	P	S
Secondary structure
SS confidence
Disorder		?	?	?	?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.
Sequence		L	S	L	K	D	A	R	Q	I	T	A	D	L	R	K	L	Y	F	S	G	T	D	P	R	T	Y	F	E	E	K	V	E	N	S	M	T	V	A	Q	C	L	D	Y	W	F	D	N	Y	V	S	T	T	L	R	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 3ju0 chain A Region: 2 - 93 Aligned: 90 Modelled: 92 Confidence: 99.9% Identity: 29% PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: structure of the arm-type binding domain of hai7 integrase Phyre2 PDB 3jtz chain A Region: 2 - 80 Aligned: 77 Modelled: 79 Confidence: 99.9% Identity: 39% PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: structure of the arm-type binding domain of hpi integrase Phyre2 PDB 1z1b chain A Region: 24 - 115 Aligned: 87 Modelled: 92 Confidence: 97.9% Identity: 21% PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site Phyre2 PDB 3igm chain A Region: 39 - 77 Aligned: 39 Modelled: 39 Confidence: 66.6% Identity: 8% PDB header:transcription/dna Chain: A: PDB Molecule:pf14_0633 protein; PDBTitle: a 2.2a crystal structure of the ap2 domain of pf14_0633 from p.2 falciparum, bound as a domain-swapped dimer to its cognate dna Phyre2 PDB 1kjk chain A Region: 30 - 81 Aligned: 44 Modelled: 52 Confidence: 49.4% Identity: 30% PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: solution structure of the lambda integrase amino-terminal2 domain Phyre2 PDB 1z1b chain A domain 1 Region: 30 - 81 Aligned: 44 Modelled: 52 Confidence: 49.4% Identity: 30% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: lambda integrase N-terminal domain Phyre2 PDB 1j6x chain A Region: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 20.6% Identity: 13% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 2zcy chain M Region: 21 - 77 Aligned: 56 Modelled: 57 Confidence: 19.9% Identity: 14% PDB header:hydrolase Chain: M: PDB Molecule:proteasome component pre4; PDBTitle: yeast 20s proteasome:syringolin a-complex Phyre2 PDB 3pcq chain M Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 17.2% Identity: 50% PDB header:photosynthesis Chain: M: PDB Molecule:photosystem i reaction center subunit xii; PDBTitle: femtosecond x-ray protein nanocrystallography Phyre2 PDB 1jb0 chain M Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 17.0% Identity: 50% PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 PDB 1jb0 chain M Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 17.0% Identity: 50% Fold: Single transmembrane helix Superfamily: Subunit XII of photosystem I reaction centre, PsaM Family: Subunit XII of photosystem I reaction centre, PsaM Phyre2 PDB 1ryp chain 2 Region: 21 - 77 Aligned: 56 Modelled: 57 Confidence: 17.0% Identity: 14% Fold: Ntn hydrolase-like Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family: Proteasome subunits Phyre2 PDB 1gcc chain A Region: 29 - 82 Aligned: 49 Modelled: 54 Confidence: 15.6% Identity: 24% Fold: DNA-binding domain Superfamily: DNA-binding domain Family: GCC-box binding domain Phyre2 PDB 1vje chain A Region: 56 - 76 Aligned: 21 Modelled: 21 Confidence: 15.4% Identity: 33% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 1j6w chain A Region: 56 - 76 Aligned: 21 Modelled: 21 Confidence: 14.9% Identity: 33% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 3byp chain A domain 1 Region: 59 - 79 Aligned: 21 Modelled: 21 Confidence: 13.9% Identity: 10% Fold: Alpha-lytic protease prodomain-like Superfamily: Cation efflux protein cytoplasmic domain-like Family: Cation efflux protein cytoplasmic domain-like Phyre2 PDB 3h4p chain J Region: 20 - 79 Aligned: 60 Modelled: 60 Confidence: 12.2% Identity: 12% PDB header:hydrolase Chain: J: PDB Molecule:proteasome subunit alpha; PDBTitle: proteasome 20s core particle from methanocaldococcus2 jannaschii Phyre2 PDB 1j98 chain A Region: 56 - 76 Aligned: 21 Modelled: 21 Confidence: 11.3% Identity: 14% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 1yar chain H domain 1 Region: 23 - 79 Aligned: 56 Modelled: 57 Confidence: 10.9% Identity: 11% Fold: Ntn hydrolase-like Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family: Proteasome subunits Phyre2 PDB 1ryp chain L Region: 21 - 77 Aligned: 56 Modelled: 57 Confidence: 10.3% Identity: 14% Fold: Ntn hydrolase-like Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family: Proteasome subunits Phyre2 1 c3ju0A_ 2 c3jtzA_ 3 c1z1bA_ 4 c3igmA_ 5 c1kjkA_ 6 d1z1ba1 7 d1j6xa_ 8 c2zcyM_ 9 c3pcqM_ 10 c1jb0M_ 11 d1jb0m_ 12 d1ryp2_ 13 d1gcca_ 14 d1vjea_ 15 d1j6wa_ 16 d3bypa1 17 c3h4pj_ 18 d1j98a_ 19 d1yarh1 20 d1rypl_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 c3ju0A_ 99.9 29 PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: structure of the arm-type binding domain of hai7 integrase 2 c3jtzA_ 99.9 39 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: structure of the arm-type binding domain of hpi integrase 3 c1z1bA_ 97.9 21 PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site 4 c3igmA_ 66.6 8 PDB header:transcription/dna Chain: A: PDB Molecule:pf14_0633 protein; PDBTitle: a 2.2a crystal structure of the ap2 domain of pf14_0633 from p.2 falciparum, bound as a domain-swapped dimer to its cognate dna 5 c1kjkA_ 49.4 30 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: solution structure of the lambda integrase amino-terminal2 domain 6 d1z1ba1 49.4 30 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:lambda integrase N-terminal domain 7 d1j6xa_ 20.6 13 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 8 c2zcyM_ 19.9 14 PDB header:hydrolase Chain: M: PDB Molecule:proteasome component pre4; PDBTitle: yeast 20s proteasome:syringolin a-complex 9 c3pcqM_ 17.2 50 PDB header:photosynthesis Chain: M: PDB Molecule:photosystem i reaction center subunit xii; PDBTitle: femtosecond x-ray protein nanocrystallography 10 c1jb0M_ 17.0 50 PDB header:photosynthesis Chain: M: PDB Molecule:photosystem 1 reaction centre subunit xii; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 11 d1jb0m_ 17.0 50 Fold:Single transmembrane helix Superfamily:Subunit XII of photosystem I reaction centre, PsaM Family:Subunit XII of photosystem I reaction centre, PsaM 12 d1ryp2_ 17.0 14 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 13 d1gcca_ 15.6 24 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:GCC-box binding domain 14 d1vjea_ 15.4 33 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 15 d1j6wa_ 14.9 33 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 16 d3bypa1 13.9 10 Fold:Alpha-lytic protease prodomain-like Superfamily:Cation efflux protein cytoplasmic domain-like Family:Cation efflux protein cytoplasmic domain-like 17 c3h4pj_ 12.2 12 PDB header:hydrolase Chain: J: PDB Molecule:proteasome subunit alpha; PDBTitle: proteasome 20s core particle from methanocaldococcus2 jannaschii 18 d1j98a_ 11.3 14 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 19 d1yarh1 10.9 11 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 20 d1rypl_ 10.3 14 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 21 d1irui_ not modelled 9.7 15 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 22 c3n3fB_ not modelled 9.4 14 PDB header:protein binding Chain: B: PDB Molecule:collagen alpha-1(xv) chain; PDBTitle: crystal structure of the human collagen xv trimerization domain: a2 potent trimerizing unit common to multiplexin collagens 23 c2zztA_ not modelled 8.4 33 PDB header:transport protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of the cytosolic domain of the cation2 diffusion facilitator family protein 24 d2outa2 not modelled 8.1 25 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:YqbF N-terminal domain-like 25 c3hshA_ not modelled 8.0 24 PDB header:protein binding Chain: A: PDB Molecule:collagen alpha-1(xviii) chain; PDBTitle: crystal structure of human collagen xviii trimerization domain2 (tetragonal crystal form) 26 c3imoC_ not modelled 7.5 15 PDB header:unknown function Chain: C: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of vibrio cholerae.2 integron cassette protein vch_cass14 27 c3ol0C_ not modelled 7.3 36 PDB header:de novo protein Chain: C: PDB Molecule:de novo designed monomer trefoil-fold sub-domain which PDBTitle: crystal structure of monofoil-4p homo-trimer: de novo designed monomer2 trefoil-fold sub-domain which forms homo-trimer assembly 28 d1vkza1 not modelled 7.3 19 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 29 d1iruh_ not modelled 7.0 16 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 30 d1x48a1 not modelled 6.0 15 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 31 d2fmla1 not modelled 5.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Nudix-associated domain 32 c2outA_ not modelled 5.5 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mu-like prophage flumu protein gp35, protein PDBTitle: solution structure of hi1506, a novel two domain protein2 from haemophilus influenzae 33 d1ryp1_ not modelled 5.4 21 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Proteasome subunits 34 c3g5oA_ not modelled 5.1 13 PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis

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