Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	F	D	W	S	A	I	W	P	A	I	P	L	L	I	E	G	A	K	M	T	L	W	I	S	V	L	G	L	A	G	G	L	V	I	G	L	L	A	G	F	A	R	T	F	G	G	W	I	A	N	H	V	A	L	V	F	I	E
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	I	R	G	T	P	I	V	V	Q	V	M	F	I	Y	F	A	L	P	M	A	F	N	D	L	R	I	D	P	F	T	A	A	V	V	T	I	M	I	N	S	G	A	Y	I	A	E	I	T	R	G	A	V	L	S	I	H	K	G	F
Secondary structure
SS confidence
Disorder																							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	E	A	G	L	A	L	G	L	S	R	W	E	T	I	R	Y	V	I	L	P	L	A	L	R	R	M	L	P	P	L	G	N	Q	W	I	I	S	I	K	D	T	S	L	F	I	V	I	G	V	A	E	L	T	R	Q	G	Q	E	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.
Sequence		I	A	G	N	F	R	A	L	E	I	W	S	A	V	A	V	F	Y	L	I	I	T	L	V	L	S	F	I	L	R	R	L	E	R	R	M	K	I	L
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 2onk chain C domain 1 Region: 2 - 212 Aligned: 211 Modelled: 211 Confidence: 100.0% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 2 - 212 Aligned: 211 Modelled: 211 Confidence: 100.0% Identity: 15% PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda Phyre2 PDB 3d31 chain D Region: 4 - 210 Aligned: 207 Modelled: 207 Confidence: 100.0% Identity: 19% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 3d31 chain C domain 1 Region: 4 - 210 Aligned: 207 Modelled: 207 Confidence: 100.0% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3fh6 chain F Region: 4 - 217 Aligned: 214 Modelled: 213 Confidence: 100.0% Identity: 13% PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli Phyre2 PDB 2r6g chain F Region: 15 - 208 Aligned: 194 Modelled: 194 Confidence: 100.0% Identity: 14% PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter Phyre2 PDB 2r6g chain F domain 2 Region: 15 - 208 Aligned: 194 Modelled: 193 Confidence: 100.0% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 14 - 208 Aligned: 194 Modelled: 195 Confidence: 100.0% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain G domain 1 Region: 15 - 215 Aligned: 201 Modelled: 201 Confidence: 99.9% Identity: 12% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2jwa chain A Region: 20 - 53 Aligned: 34 Modelled: 34 Confidence: 35.6% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1ntc chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 25.9% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 23.7% Identity: 16% PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity Phyre2 PDB 1umq chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 23.7% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1fip chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 16.7% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 15.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 13.0% Identity: 6% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 PDB 1etx chain A Region: 107 - 138 Aligned: 32 Modelled: 32 Confidence: 12.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1g2h chain A Region: 108 - 138 Aligned: 30 Modelled: 31 Confidence: 9.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2hx6 chain A Region: 107 - 132 Aligned: 26 Modelled: 26 Confidence: 8.6% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb Phyre2 PDB 2d7d chain B Region: 110 - 142 Aligned: 33 Modelled: 33 Confidence: 7.2% Identity: 27% PDB header:hydrolase/dna Chain: B: PDB Molecule:40-mer from uvrabc system protein b; PDBTitle: structural insights into the cryptic dna dependent atp-ase2 activity of uvrb Phyre2 1 d2onkc1 2 c2onkC_ 3 c3d31D_ 4 d3d31c1 5 c3fh6F_ 6 c2r6gF_ 7 d2r6gf2 8 d3dhwa1 9 d2r6gg1 10 c2jwaA_ 11 d1ntca_ 12 c1umqA_ 13 d1umqa_ 14 d1fipa_ 15 d1etob_ 16 c3e7lD_ 17 d1etxa_ 18 d1g2ha_ 19 c2hx6A_ 20 c2d7dB_ 21 22

Detailed template information

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

1 d2onkc1 100.0 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 2 c2onkC_ 100.0 15 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 3 c3d31D_ 100.0 19 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 4 d3d31c1 100.0 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 c3fh6F_ 100.0 13 PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli 6 c2r6gF_ 100.0 14 PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter 7 d2r6gf2 100.0 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 8 d3dhwa1 100.0 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d2r6gg1 99.9 12 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 c2jwaA_ 35.6 15 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 11 d1ntca_ 25.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 c1umqA_ 23.7 16 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 13 d1umqa_ 23.7 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d1fipa_ 16.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 15 d1etob_ 15.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 c3e7lD_ 13.0 6 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 17 d1etxa_ 12.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 d1g2ha_ 9.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 c2hx6A_ 8.6 27 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 20 c2d7dB_ 7.2 27 PDB header:hydrolase/dna Chain: B: PDB Molecule:40-mer from uvrabc system protein b; PDBTitle: structural insights into the cryptic dna dependent atp-ase2 activity of uvrb 21 d2ns0a1 not modelled 6.3 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RHA1 ro06458-like 22 c2lhuA_ not modelled 6.0 5 PDB header:structural protein Chain: A: PDB Molecule:mybpc3 protein; PDBTitle: structural insight into the unique cardiac myosin binding protein-c2 motif: a partially folded domain

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