Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	R	R	R	V	I	G	Q	R	K	I	L	P	D	P	K	F	G	S	E	L	L	A	K	F	V	N	I	L	M	V	D	G	K	K	S	T	A	E	S	I	V	Y	S	A	L	E	T	L	A	Q	R	S	G	K	S	E	L	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?		?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	F	E	V	A	L	E	N	V	R	P	T	V	E	V	K	S	R	R	V	G	G	S	T	Y	Q	V	P	V	E	V	R	P	V	R	R	N	A	L	A	M	R	W	I	V	E	A	A	R	K	R	G	D	K	S	M	A	L	R	L
Secondary structure
SS confidence
Disorder													?	?					?	?	?	?	?	?	?																												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.
Sequence		A	N	E	L	S	D	A	A	E	N	K	G	T	A	V	K	K	R	E	D	V	H	R	M	A	E	A	N	K	A	F	A	H	Y	R	W	L	S	L	R	S	F	S	H	Q	A	G	A	S	S	K	Q	P	A	L	G	Y	L	N
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 3gty chain S Region: 10 - 156 Aligned: 147 Modelled: 147 Confidence: 100.0% Identity: 56% PDB header:chaperone/ribosomal protein Chain: S: PDB Molecule:30s ribosomal protein s7; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone Phyre2 PDB 3bbn chain G Region: 2 - 155 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 44% PDB header:ribosome Chain: G: PDB Molecule:ribosomal protein s7; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 2qal chain G domain 1 Region: 3 - 152 Aligned: 150 Modelled: 150 Confidence: 100.0% Identity: 100% Fold: Ribosomal protein S7 Superfamily: Ribosomal protein S7 Family: Ribosomal protein S7 Phyre2 PDB 1vs5 chain G Region: 3 - 152 Aligned: 150 Modelled: 150 Confidence: 100.0% Identity: 100% PDB header:ribosome Chain: G: PDB Molecule:30s ribosomal protein s7; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with the antibiotic kasugamyin3 at 3.5a resolution. this file contains the 30s subunit of4 one 70s ribosome. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. Phyre2 PDB 1rss chain A Region: 12 - 156 Aligned: 140 Modelled: 145 Confidence: 100.0% Identity: 53% Fold: Ribosomal protein S7 Superfamily: Ribosomal protein S7 Family: Ribosomal protein S7 Phyre2 PDB 1hus chain A Region: 10 - 148 Aligned: 139 Modelled: 139 Confidence: 100.0% Identity: 55% Fold: Ribosomal protein S7 Superfamily: Ribosomal protein S7 Family: Ribosomal protein S7 Phyre2 PDB 2xzm chain G Region: 16 - 149 Aligned: 134 Modelled: 134 Confidence: 100.0% Identity: 28% PDB header:ribosome Chain: G: PDB Molecule:ribosomal protein s7 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 1iqv chain A Region: 19 - 149 Aligned: 131 Modelled: 131 Confidence: 100.0% Identity: 31% Fold: Ribosomal protein S7 Superfamily: Ribosomal protein S7 Family: Ribosomal protein S7 Phyre2 PDB 1s1h chain G Region: 13 - 149 Aligned: 137 Modelled: 137 Confidence: 100.0% Identity: 29% PDB header:ribosome Chain: G: PDB Molecule:40s ribosomal protein s5; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. Phyre2 PDB 3izb chain F Region: 17 - 149 Aligned: 133 Modelled: 133 Confidence: 100.0% Identity: 29% PDB header:ribosome Chain: F: PDB Molecule:40s ribosomal protein rps5 (s7p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 2zkq chain G Region: 19 - 149 Aligned: 130 Modelled: 131 Confidence: 100.0% Identity: 28% PDB header:ribosomal protein/rna Chain: G: PDB Molecule:rna helix; PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1u5t chain A domain 1 Region: 62 - 90 Aligned: 29 Modelled: 29 Confidence: 26.5% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 PDB 1ahs chain A Region: 156 - 174 Aligned: 19 Modelled: 19 Confidence: 24.1% Identity: 37% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 2kn8 chain A Region: 29 - 73 Aligned: 45 Modelled: 45 Confidence: 20.0% Identity: 11% PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:dna cleavage and packaging protein large subunit, ul89; PDBTitle: nmr structure of the c-terminal domain of pul89 Phyre2 PDB 2hv8 chain D Region: 115 - 154 Aligned: 35 Modelled: 40 Confidence: 17.9% Identity: 23% 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 2cg4 chain A domain 1 Region: 122 - 177 Aligned: 54 Modelled: 56 Confidence: 17.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 1o7f chain A domain 1 Region: 60 - 127 Aligned: 61 Modelled: 68 Confidence: 13.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DEP domain Phyre2 PDB 1bvp chain 1 domain 2 Region: 156 - 174 Aligned: 19 Modelled: 19 Confidence: 13.4% Identity: 26% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 2e5z chain A Region: 151 - 174 Aligned: 23 Modelled: 24 Confidence: 11.7% Identity: 26% PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor, arginine/serine-rich 8; PDBTitle: solution structure of the surp2 domain in splicing factor,2 arginine/serine-rich 8 Phyre2 PDB 1u5t chain A Region: 62 - 101 Aligned: 40 Modelled: 40 Confidence: 11.4% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:appears to be functionally related to snf7; PDBTitle: structure of the escrt-ii endosomal trafficking complex Phyre2 1 c3gtyS_ 2 c3bbnG_ 3 d2qalg1 4 c1vs5G_ 5 d1rssa_ 6 d1husa_ 7 c2xzmG_ 8 d1iqva_ 9 c1s1hG_ 10 c3izbF_ 11 c2zkqg_ 12 d1u5ta1 13 d1ahsa_ 14 c2kn8A_ 15 c2hv8D_ 16 d2cg4a1 17 d1o7fa1 18 d1bvp12 19 c2e5zA_ 20 c1u5tA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 c3gtyS_ 100.0 56 PDB header:chaperone/ribosomal protein Chain: S: PDB Molecule:30s ribosomal protein s7; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone 2 c3bbnG_ 100.0 44 PDB header:ribosome Chain: G: PDB Molecule:ribosomal protein s7; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 3 d2qalg1 100.0 100 Fold:Ribosomal protein S7 Superfamily:Ribosomal protein S7 Family:Ribosomal protein S7 4 c1vs5G_ 100.0 100 PDB header:ribosome Chain: G: PDB Molecule:30s ribosomal protein s7; PDBTitle: crystal structure of the bacterial ribosome from2 escherichia coli in complex with the antibiotic kasugamyin3 at 3.5a resolution. this file contains the 30s subunit of4 one 70s ribosome. the entire crystal structure contains5 two 70s ribosomes and is described in remark 400. 5 d1rssa_ 100.0 53 Fold:Ribosomal protein S7 Superfamily:Ribosomal protein S7 Family:Ribosomal protein S7 6 d1husa_ 100.0 55 Fold:Ribosomal protein S7 Superfamily:Ribosomal protein S7 Family:Ribosomal protein S7 7 c2xzmG_ 100.0 28 PDB header:ribosome Chain: G: PDB Molecule:ribosomal protein s7 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 8 d1iqva_ 100.0 31 Fold:Ribosomal protein S7 Superfamily:Ribosomal protein S7 Family:Ribosomal protein S7 9 c1s1hG_ 100.0 29 PDB header:ribosome Chain: G: PDB Molecule:40s ribosomal protein s5; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 10 c3izbF_ 100.0 29 PDB header:ribosome Chain: F: PDB Molecule:40s ribosomal protein rps5 (s7p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 11 c2zkqg_ 100.0 28 PDB header:ribosomal protein/rna Chain: G: PDB Molecule:rna helix; PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 12 d1u5ta1 26.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 13 d1ahsa_ 24.1 37 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 14 c2kn8A_ 20.0 11 PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:dna cleavage and packaging protein large subunit, ul89; PDBTitle: nmr structure of the c-terminal domain of pul89 15 c2hv8D_ 17.9 23 PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3 16 d2cg4a1 17.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 17 d1o7fa1 13.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 18 d1bvp12 13.4 26 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 19 c2e5zA_ 11.7 26 PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor, arginine/serine-rich 8; PDBTitle: solution structure of the surp2 domain in splicing factor,2 arginine/serine-rich 8 20 c1u5tA_ 11.4 15 PDB header:transport protein Chain: A: PDB Molecule:appears to be functionally related to snf7; PDBTitle: structure of the escrt-ii endosomal trafficking complex 21 d1ojha_ not modelled 10.1 36 Fold:NblA-like Superfamily:NblA-like Family:NblA-like 22 c1ojhK_ not modelled 9.9 36 PDB header:protein binding Chain: K: PDB Molecule:nbla; PDBTitle: crystal structure of nbla from pcc 7120 23 c1w7pD_ not modelled 6.3 8 PDB header:protein transport Chain: D: PDB Molecule:vps36p, ylr417w; PDBTitle: the crystal structure of endosomal complex escrt-ii2 (vps22/vps25/vps36) 24 d1n8va_ not modelled 6.2 31 Fold:alpha-alpha superhelix Superfamily:Chemosensory protein Csp2 Family:Chemosensory protein Csp2 25 c3csxA_ not modelled 6.1 40 PDB header:metal binding protein,unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: structural characterization of a protein in the duf6832 family- crystal structure of cce_0567 from the3 cyanobacterium cyanothece 51142. 26 d1qe6a_ not modelled 6.1 17 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 27 d1kx9b_ not modelled 6.0 31 Fold:alpha-alpha superhelix Superfamily:Chemosensory protein Csp2 Family:Chemosensory protein Csp2 28 c3g36D_ not modelled 6.0 18 PDB header:nuclear protein Chain: D: PDB Molecule:protein dpy-30 homolog; PDBTitle: crystal structure of the human dpy-30-like c-terminal domain 29 c2js5B_ not modelled 5.9 37 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 30 d1y6xa1 not modelled 5.7 12 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 31 d2j5ya1 not modelled 5.7 27 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Bacterial immunoglobulin/albumin-binding domains Family:GA module, an albumin-binding domain 32 d1yxba1 not modelled 5.3 17 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 33 d1ia9a_ not modelled 5.2 19 Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:MHCK/EF2 kinase 34 d1s16a1 not modelled 5.2 13 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:DNA gyrase/MutL, second domain 35 d1pd3a_ not modelled 5.1 25 Fold:ROP-like Superfamily:Nonstructural protein ns2, Nep, M1-binding domain Family:Nonstructural protein ns2, Nep, M1-binding 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