Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	D	R	H	L	H	P	R	I	K	P	L	L	H	Q	C	V	R	V	L	D	K	P	G	I	T	P	D	G	L	T	L	V	G	F	A	I	G	V	L	A	L	P	F	L	A	L	G	W	Y	L	A	A	L	V	V	I	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	R	L	L	D	G	L	D	G	A	L	A	R	R	R	E	L	T	D	A	G	G	F	L	D	I	S	L	D	F	L	F	Y	A	L	V	P	F	G	F	I	L	A	A	P	E	Q	N	A	L	A	G	G	W	L	L	F	A	F	I
Secondary structure
SS confidence
Disorder															?	?				?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	T	G	S	S	F	L	A	F	A	A	L	A	A	K	H	Q	I	D	N	P	G	Y	A	H	K	S	F	Y	Y	L	G	G	L	T	E	G	T	E	T	I	L	L	F	V	L	G	C	L	F	P	A	W	F	A	W	F	A	W	I
Secondary structure
SS confidence
Disorder																			?	?	?	?		?				?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.
Sequence		F	G	A	L	C	W	M	T	T	F	T	R	V	W	S	G	Y	L	T	L	K	S	L	Q	R	Q
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 2rkh chain A Region: 59 - 91 Aligned: 33 Modelled: 33 Confidence: 14.0% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:putative apha-like transcription factor; PDBTitle: crystal structure of a putative apha-like transcription factor2 (zp_00208345.1) from magnetospirillum magnetotacticum ms-1 at 2.00 a3 resolution Phyre2 PDB 3bj6 chain B Region: 4 - 37 Aligned: 34 Modelled: 34 Confidence: 13.3% Identity: 12% PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcription regulator sp03579 Phyre2 PDB 2voy chain G Region: 77 - 102 Aligned: 26 Modelled: 26 Confidence: 11.1% Identity: 15% PDB header:hydrolase Chain: G: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus Phyre2 PDB 1gdh chain A domain 2 Region: 64 - 98 Aligned: 34 Modelled: 35 Confidence: 10.5% Identity: 15% Fold: Flavodoxin-like Superfamily: Formate/glycerate dehydrogenase catalytic domain-like Family: Formate/glycerate dehydrogenases, substrate-binding domain Phyre2 PDB 2a61 chain A domain 1 Region: 2 - 37 Aligned: 36 Modelled: 36 Confidence: 8.7% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MarR-like transcriptional regulators Phyre2 PDB 1yhu chain A Region: 7 - 72 Aligned: 65 Modelled: 66 Confidence: 8.0% Identity: 14% PDB header:oxygen storage/transport Chain: A: PDB Molecule:hemoglobin a1 chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits. Phyre2 PDB 2d2m chain B Region: 7 - 69 Aligned: 63 Modelled: 63 Confidence: 7.5% Identity: 16% PDB header:oxygen storage/transport Chain: B: PDB Molecule:giant hemoglobin, a2(a5) globin chain; PDBTitle: structure of an extracellular giant hemoglobin of the2 gutless beard worm oligobrachia mashikoi Phyre2 PDB 1t6f chain A Region: 68 - 75 Aligned: 8 Modelled: 8 Confidence: 6.7% Identity: 38% PDB header:cell cycle Chain: A: PDB Molecule:geminin; PDBTitle: crystal structure of the coiled-coil dimerization motif of2 geminin Phyre2 PDB 1q1f chain A Region: 10 - 69 Aligned: 60 Modelled: 60 Confidence: 6.4% Identity: 17% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 1 c2rkhA_ 2 c3bj6B_ 3 c2voyG_ 4 d1gdha2 5 d2a61a1 6 c1yhuA_ 7 c2d2mB_ 8 c1t6fA_ 9 d1q1fa_

Detailed template information

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

1 c2rkhA_ 14.0 30 PDB header:transcription Chain: A: PDB Molecule:putative apha-like transcription factor; PDBTitle: crystal structure of a putative apha-like transcription factor2 (zp_00208345.1) from magnetospirillum magnetotacticum ms-1 at 2.00 a3 resolution 2 c3bj6B_ 13.3 12 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcription regulator sp03579 3 c2voyG_ 11.1 15 PDB header:hydrolase Chain: G: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 4 d1gdha2 10.5 15 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:Formate/glycerate dehydrogenases, substrate-binding domain 5 d2a61a1 8.7 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 6 c1yhuA_ 8.0 14 PDB header:oxygen storage/transport Chain: A: PDB Molecule:hemoglobin a1 chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits. 7 c2d2mB_ 7.5 16 PDB header:oxygen storage/transport Chain: B: PDB Molecule:giant hemoglobin, a2(a5) globin chain; PDBTitle: structure of an extracellular giant hemoglobin of the2 gutless beard worm oligobrachia mashikoi 8 c1t6fA_ 6.7 38 PDB header:cell cycle Chain: A: PDB Molecule:geminin; PDBTitle: crystal structure of the coiled-coil dimerization motif of2 geminin 9 d1q1fa_ 6.4 17 Fold:Globin-like Superfamily:Globin-like Family:Globins

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