Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	T	L	E	P	A	A	Q	S	K	P	P	G	G	F	K	L	W	L	S	Q	L	Q	M	K	H	G	R	K	L	V	I	A	L	P	Y	I	W	L	I	L	L	F	L	L	P	F	L	I	V	F	K	I	S	L	A	E	M	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?	?	?	?																														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	A	I	P	P	Y	T	E	L	M	E	W	A	D	G	Q	L	S	I	T	L	N	L	G	N	F	L	Q	L	T	D	D	P	L	Y	F	D	A	Y	L	Q	S	L	Q	V	A	A	I	S	T	F	C	C	L	L	I	G	Y	P	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	W	A	V	A	H	S	K	P	S	T	R	N	I	L	L	L	L	V	I	L	P	S	W	T	S	F	L	I	R	V	Y	A	W	M	G	I	L	K	N	N	G	V	L	N	N	F	L	L	W	L	G	V	I	D	Q	P	L	T	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	H	T	N	L	A	V	Y	I	G	I	V	Y	A	Y	V	P	F	M	V	L	P	I	Y	T	A	L	I	R	I	D	Y	S	L	V	E	A	A	L	D	L	G	A	R	P	L	K	T	F	F	T	V	I	V	P	L	T	K	G	G
Secondary structure
SS confidence
Disorder																													?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	I	A	G	S	M	L	V	F	I	P	A	V	G	E	F	V	I	P	E	L	L	G	G	P	D	S	I	M	I	G	R	V	L	W	Q	E	F	F	N	N	R	D	W	P	V	A	S	A	V	A	I	I	M	L	L	L	L	I	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.
Sequence		P	I	M	W	F	H	K	H	Q	Q	K	S	V	G	E	H	G
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 3fh6 chain F Region: 24 - 314 Aligned: 286 Modelled: 291 Confidence: 100.0% Identity: 17% 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 G domain 1 Region: 24 - 317 Aligned: 272 Modelled: 284 Confidence: 100.0% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 67 - 304 Aligned: 238 Modelled: 238 Confidence: 100.0% Identity: 21% 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 2onk chain C Region: 25 - 307 Aligned: 249 Modelled: 259 Confidence: 100.0% Identity: 24% 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 2onk chain C domain 1 Region: 25 - 307 Aligned: 249 Modelled: 259 Confidence: 100.0% Identity: 24% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 31 - 306 Aligned: 245 Modelled: 253 Confidence: 100.0% Identity: 17% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 31 - 306 Aligned: 245 Modelled: 253 Confidence: 100.0% Identity: 17% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 2r6g chain F domain 2 Region: 83 - 304 Aligned: 222 Modelled: 222 Confidence: 100.0% Identity: 21% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 95 - 304 Aligned: 198 Modelled: 207 Confidence: 99.9% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 1 Region: 25 - 63 Aligned: 39 Modelled: 39 Confidence: 70.6% Identity: 13% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1umq chain A Region: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 34.8% 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: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 34.8% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 201 - 232 Aligned: 32 Modelled: 32 Confidence: 34.3% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2hx6 chain A Region: 201 - 226 Aligned: 26 Modelled: 26 Confidence: 29.4% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb Phyre2 PDB 1fip chain A Region: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 25.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2jwa chain A Region: 100 - 133 Aligned: 34 Modelled: 34 Confidence: 24.3% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 1eto chain B Region: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 21.7% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1etx chain A Region: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 21.0% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 202 - 232 Aligned: 31 Modelled: 31 Confidence: 19.6% Identity: 23% 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 2rdd chain B Region: 292 - 316 Aligned: 25 Modelled: 25 Confidence: 19.2% Identity: 20% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 1 c3fh6F_ 2 d2r6gg1 3 c2r6gF_ 4 c2onkC_ 5 d2onkc1 6 d3d31c1 7 c3d31D_ 8 d2r6gf2 9 d3dhwa1 10 d2r6gf1 11 c1umqA_ 12 d1umqa_ 13 d1ntca_ 14 c2hx6A_ 15 d1fipa_ 16 c2jwaA_ 17 d1etob_ 18 d1etxa_ 19 c3e7lD_ 20 c2rddB_ 21 22 23 24 25 26

Detailed template information

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

1 c3fh6F_ 100.0 17 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 2 d2r6gg1 100.0 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 3 c2r6gF_ 100.0 21 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 4 c2onkC_ 100.0 24 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 5 d2onkc1 100.0 24 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 d3d31c1 100.0 17 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 c3d31D_ 100.0 17 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 8 d2r6gf2 100.0 21 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d3dhwa1 99.9 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d2r6gf1 70.6 13 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 11 c1umqA_ 34.8 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 12 d1umqa_ 34.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 d1ntca_ 34.3 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 c2hx6A_ 29.4 15 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 15 d1fipa_ 25.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 c2jwaA_ 24.3 15 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 17 d1etob_ 21.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 d1etxa_ 21.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 c3e7lD_ 19.6 23 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 20 c2rddB_ 19.2 20 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 21 d1g2ha_ not modelled 13.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 22 c1twcF_ not modelled 7.7 43 PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii 23 PDBTitle: rna polymerase ii complexed with gtp 23 d1twff_ not modelled 7.6 43 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6 24 c2pmzW_ not modelled 7.3 36 PDB header:translation, transferase Chain: W: PDB Molecule:dna-directed rna polymerase subunit k; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 25 c2cw1A_ not modelled 6.2 36 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 26 d1qkla_ not modelled 6.1 43 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6

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

---

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