Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	P	A	A	R	R	R	A	R	E	C	A	V	Q	A	L	Y	S	W	Q	L	S	Q	N	D	I	A	D	V	E	Y	Q	F	L	A	E	Q	D	V	K	D	V	D	V	L	Y	F	R	E	L	L	A	G	V	A	T	N	T	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	L	D	G	L	M	K	P	Y	L	S	R	L	L	E	E	L	G	Q	V	E	K	A	V	L	R	I	A	L	Y	E	L	S	K	R	S	D	V	P	Y	K	V	A	I	N	E	A	I	E	L	A	K	S	F	G	A	E	D	S	H
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.
Sequence		K	F	V	N	G	V	L	D	K	A	A	P	V	I	R	P	N	K	K
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 1ey1 chain A Region: 1 - 139 Aligned: 139 Modelled: 139 Confidence: 100.0% Identity: 100% Fold: NusB-like Superfamily: NusB-like Family: Antitermination factor NusB Phyre2 PDB 1tzv chain A Region: 1 - 139 Aligned: 138 Modelled: 139 Confidence: 100.0% Identity: 35% Fold: NusB-like Superfamily: NusB-like Family: Antitermination factor NusB Phyre2 PDB 2jr0 chain A Region: 1 - 139 Aligned: 137 Modelled: 139 Confidence: 100.0% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein b homolog; PDBTitle: solution structure of nusb from aquifex aeolicus Phyre2 PDB 1eyv chain A Region: 6 - 130 Aligned: 125 Modelled: 125 Confidence: 100.0% Identity: 34% Fold: NusB-like Superfamily: NusB-like Family: Antitermination factor NusB Phyre2 PDB 1eyv chain A Region: 6 - 130 Aligned: 125 Modelled: 125 Confidence: 100.0% Identity: 34% PDB header:transcription Chain: A: PDB Molecule:n-utilizing substance protein b homolog; PDBTitle: the crystal structure of nusb from mycobacterium2 tuberculosis Phyre2 PDB 1sqg chain A domain 1 Region: 7 - 136 Aligned: 127 Modelled: 130 Confidence: 100.0% Identity: 23% Fold: NusB-like Superfamily: NusB-like Family: RmsB N-terminal domain-like Phyre2 PDB 1sqg chain A Region: 7 - 133 Aligned: 124 Modelled: 127 Confidence: 100.0% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:sun protein; PDBTitle: the crystal structure of the e. coli fmu apoenzyme at 1.652 a resolution Phyre2 PDB 2yxl chain A Region: 2 - 136 Aligned: 133 Modelled: 135 Confidence: 99.9% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:450aa long hypothetical fmu protein; PDBTitle: crystal structure of ph0851 Phyre2 PDB 1q8c chain A Region: 5 - 130 Aligned: 125 Modelled: 126 Confidence: 81.4% Identity: 18% Fold: NusB-like Superfamily: NusB-like Family: Hypothetical protein MG027 Phyre2 PDB 2zc2 chain A Region: 103 - 129 Aligned: 26 Modelled: 27 Confidence: 42.8% Identity: 15% PDB header:replication Chain: A: PDB Molecule:dnad-like replication protein; PDBTitle: crystal structure of dnad-like replication protein from2 streptococcus mutans ua159, gi 24377835, residues 127-199 Phyre2 PDB 2i5u chain A domain 1 Region: 100 - 129 Aligned: 29 Modelled: 30 Confidence: 35.7% Identity: 24% Fold: DnaD domain-like Superfamily: DnaD domain-like Family: DnaD domain Phyre2 PDB 3ls1 chain A Region: 38 - 114 Aligned: 77 Modelled: 77 Confidence: 32.8% Identity: 8% PDB header:photosynthesis Chain: A: PDB Molecule:sll1638 protein; PDBTitle: crystal structure of cyanobacterial psbq from synechocystis2 sp. pcc 6803 complexed with zn2+ Phyre2 PDB 3pub chain A Region: 104 - 137 Aligned: 34 Modelled: 34 Confidence: 30.8% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:30kda protein; PDBTitle: crystal structure of the bombyx mori low molecular weight lipoprotein2 7 (bmlp7) Phyre2 PDB 1v54 chain E Region: 60 - 129 Aligned: 65 Modelled: 70 Confidence: 24.5% Identity: 18% Fold: alpha-alpha superhelix Superfamily: Cytochrome c oxidase subunit E Family: Cytochrome c oxidase subunit E Phyre2 PDB 2keb chain A Region: 90 - 124 Aligned: 32 Modelled: 35 Confidence: 21.6% Identity: 19% PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit Phyre2 PDB 2y69 chain R Region: 59 - 130 Aligned: 67 Modelled: 72 Confidence: 20.9% Identity: 19% PDB header:electron transport Chain: R: PDB Molecule:cytochrome c oxidase subunit 5a; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 3c8g chain A domain 1 Region: 41 - 93 Aligned: 51 Modelled: 53 Confidence: 12.1% Identity: 14% Fold: MtlR-like Superfamily: MtlR-like Family: MtlR-like Phyre2 PDB 2kz5 chain A Region: 2 - 51 Aligned: 50 Modelled: 50 Confidence: 11.8% Identity: 16% PDB header:transcription Chain: A: PDB Molecule:transcription factor nf-e2 45 kda subunit; PDBTitle: solution nmr structure of transcription factor nf-e2 subunit's dna2 binding domain from homo sapiens, northeast structural genomics3 consortium target hr4653b Phyre2 PDB 2hv8 chain D Region: 18 - 62 Aligned: 45 Modelled: 45 Confidence: 11.0% Identity: 4% PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3 Phyre2 PDB 2ga1 chain A domain 1 Region: 14 - 66 Aligned: 47 Modelled: 53 Confidence: 10.9% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Alr1493-like Phyre2 1 d1ey1a_ 2 d1tzva_ 3 c2jr0A_ 4 d1eyva_ 5 c1eyvA_ 6 d1sqga1 7 c1sqgA_ 8 c2yxlA_ 9 d1q8ca_ 10 c2zc2A_ 11 d2i5ua1 12 c3ls1A_ 13 c3pubA_ 14 d1v54e_ 15 c2kebA_ 16 c2y69R_ 17 d3c8ga1 18 c2kz5A_ 19 c2hv8D_ 20 d2ga1a1 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 d1ey1a_ 100.0 100 Fold:NusB-like Superfamily:NusB-like Family:Antitermination factor NusB 2 d1tzva_ 100.0 35 Fold:NusB-like Superfamily:NusB-like Family:Antitermination factor NusB 3 c2jr0A_ 100.0 24 PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein b homolog; PDBTitle: solution structure of nusb from aquifex aeolicus 4 d1eyva_ 100.0 34 Fold:NusB-like Superfamily:NusB-like Family:Antitermination factor NusB 5 c1eyvA_ 100.0 34 PDB header:transcription Chain: A: PDB Molecule:n-utilizing substance protein b homolog; PDBTitle: the crystal structure of nusb from mycobacterium2 tuberculosis 6 d1sqga1 100.0 23 Fold:NusB-like Superfamily:NusB-like Family:RmsB N-terminal domain-like 7 c1sqgA_ 100.0 23 PDB header:transferase Chain: A: PDB Molecule:sun protein; PDBTitle: the crystal structure of the e. coli fmu apoenzyme at 1.652 a resolution 8 c2yxlA_ 99.9 14 PDB header:transferase Chain: A: PDB Molecule:450aa long hypothetical fmu protein; PDBTitle: crystal structure of ph0851 9 d1q8ca_ 81.4 18 Fold:NusB-like Superfamily:NusB-like Family:Hypothetical protein MG027 10 c2zc2A_ 42.8 15 PDB header:replication Chain: A: PDB Molecule:dnad-like replication protein; PDBTitle: crystal structure of dnad-like replication protein from2 streptococcus mutans ua159, gi 24377835, residues 127-199 11 d2i5ua1 35.7 24 Fold:DnaD domain-like Superfamily:DnaD domain-like Family:DnaD domain 12 c3ls1A_ 32.8 8 PDB header:photosynthesis Chain: A: PDB Molecule:sll1638 protein; PDBTitle: crystal structure of cyanobacterial psbq from synechocystis2 sp. pcc 6803 complexed with zn2+ 13 c3pubA_ 30.8 21 PDB header:unknown function Chain: A: PDB Molecule:30kda protein; PDBTitle: crystal structure of the bombyx mori low molecular weight lipoprotein2 7 (bmlp7) 14 d1v54e_ 24.5 18 Fold:alpha-alpha superhelix Superfamily:Cytochrome c oxidase subunit E Family:Cytochrome c oxidase subunit E 15 c2kebA_ 21.6 19 PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit 16 c2y69R_ 20.9 19 PDB header:electron transport Chain: R: PDB Molecule:cytochrome c oxidase subunit 5a; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 17 d3c8ga1 12.1 14 Fold:MtlR-like Superfamily:MtlR-like Family:MtlR-like 18 c2kz5A_ 11.8 16 PDB header:transcription Chain: A: PDB Molecule:transcription factor nf-e2 45 kda subunit; PDBTitle: solution nmr structure of transcription factor nf-e2 subunit's dna2 binding domain from homo sapiens, northeast structural genomics3 consortium target hr4653b 19 c2hv8D_ 11.0 4 PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3 20 d2ga1a1 10.9 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like 21 c2z1dA_ not modelled 9.3 15 PDB header:metal binding protein Chain: A: PDB Molecule:hydrogenase expression/formation protein hypd; PDBTitle: crystal structure of [nife] hydrogenase maturation protein, hypd from2 thermococcus kodakaraensis 22 c3kaeC_ not modelled 7.6 21 PDB header:protein binding Chain: C: PDB Molecule:possible protein of nuclear scaffold; PDBTitle: cdc27 n-terminus 23 d1xmka1 not modelled 6.9 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 24 c2vckC_ not modelled 6.7 39 PDB header:oxidoreductase Chain: C: PDB Molecule:cyanobacterial phycoerythrobilin; PDBTitle: structure of phycoerythrobilin synthase pebs from the2 cyanophage p-ssm2 in complex with the bound substrate3 biliverdin ixa 25 c3c9pA_ not modelled 6.1 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 26 c1dxzA_ not modelled 5.7 15 PDB header:transmembrane protein Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: m2 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 203 structures 27 d1rkta2 not modelled 5.6 9 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 28 d1cmia_ not modelled 5.6 5 Fold:DLC Superfamily:DLC Family:DLC 29 d1x4pa1 not modelled 5.3 25 Fold:Surp module (SWAP domain) Superfamily:Surp module (SWAP domain) Family:Surp module (SWAP 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