Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	K	V	Q	A	Y	V	K	L	Q	V	A	A	G	M	A	N	P	S	P	P	V	G	P	A	L	G	Q	Q	G	V	N	I	M	E	F	C	K	A	F	N	A	K	T	D	S	I	E	K	G	L	P	I	P	V	V	I	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?								?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	Y	A	D	R	S	F	T	F	V	T	K	T	P	P	A	A	V	L	L	K	K	A	A	G	I	K	S	G	S	G	K	P	N	K	D	K	V	G	K	I	S	R	A	Q	L	Q	E	I	A	Q	T	K	A	A	D	M	T	G	A
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?	?	?	?	?																					?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.
Sequence		D	I	E	A	M	T	R	S	I	E	G	T	A	R	S	M	G	L	V	V	E	D
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 3bbo chain K Region: 2 - 141 Aligned: 139 Modelled: 140 Confidence: 100.0% Identity: 54% PDB header:ribosome Chain: K: PDB Molecule:ribosomal protein l11; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2vhm chain I Region: 2 - 142 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 100% PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11; PDBTitle: structure of pdf binding helix in complex with the ribosome2 (part 1 of 4) Phyre2 PDB 1jqm chain A Region: 8 - 140 Aligned: 132 Modelled: 133 Confidence: 100.0% Identity: 61% PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l11; PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid Phyre2 PDB 2ftc chain G Region: 2 - 142 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 40% PDB header:ribosome Chain: G: PDB Molecule:39s ribosomal protein l11, mitochondrial; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome Phyre2 PDB 1s1i chain K Region: 9 - 140 Aligned: 131 Modelled: 132 Confidence: 100.0% Identity: 21% PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l12; 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, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. Phyre2 PDB 3iz5 chain J Region: 9 - 135 Aligned: 125 Modelled: 127 Confidence: 100.0% Identity: 26% PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 3cjt chain P Region: 3 - 74 Aligned: 71 Modelled: 72 Confidence: 100.0% Identity: 70% PDB header:transferase/ribosomal protein Chain: P: PDB Molecule:50s ribosomal protein l11; PDBTitle: ribosomal protein l11 methyltransferase (prma) in complex with2 dimethylated ribosomal protein l11 Phyre2 PDB 3cjs chain B domain 1 Region: 3 - 72 Aligned: 69 Modelled: 70 Confidence: 100.0% Identity: 70% Fold: Ribosomal L11/L12e N-terminal domain Superfamily: Ribosomal L11/L12e N-terminal domain Family: Ribosomal L11/L12e N-terminal domain Phyre2 PDB 1wib chain A Region: 6 - 85 Aligned: 77 Modelled: 80 Confidence: 100.0% Identity: 23% Fold: Ribosomal L11/L12e N-terminal domain Superfamily: Ribosomal L11/L12e N-terminal domain Family: Ribosomal L11/L12e N-terminal domain Phyre2 PDB 1hc8 chain A Region: 68 - 141 Aligned: 74 Modelled: 74 Confidence: 100.0% Identity: 68% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 2gyc chain G domain 2 Region: 3 - 73 Aligned: 71 Modelled: 71 Confidence: 100.0% Identity: 100% Fold: Ribosomal L11/L12e N-terminal domain Superfamily: Ribosomal L11/L12e N-terminal domain Family: Ribosomal L11/L12e N-terminal domain Phyre2 PDB 1xbp chain G domain 2 Region: 3 - 73 Aligned: 70 Modelled: 71 Confidence: 100.0% Identity: 69% Fold: Ribosomal L11/L12e N-terminal domain Superfamily: Ribosomal L11/L12e N-terminal domain Family: Ribosomal L11/L12e N-terminal domain Phyre2 PDB 1mms chain A domain 2 Region: 8 - 71 Aligned: 63 Modelled: 64 Confidence: 100.0% Identity: 67% Fold: Ribosomal L11/L12e N-terminal domain Superfamily: Ribosomal L11/L12e N-terminal domain Family: Ribosomal L11/L12e N-terminal domain Phyre2 PDB 1vq8 chain I Region: 72 - 141 Aligned: 70 Modelled: 70 Confidence: 99.9% Identity: 36% PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11p; PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui Phyre2 PDB 1mms chain A domain 1 Region: 72 - 141 Aligned: 70 Modelled: 70 Confidence: 99.9% Identity: 54% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 1vqo chain I domain 1 Region: 72 - 141 Aligned: 70 Modelled: 70 Confidence: 99.9% Identity: 36% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 1xbp chain G domain 1 Region: 74 - 141 Aligned: 68 Modelled: 68 Confidence: 99.9% Identity: 51% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 2zkr chain I Region: 72 - 141 Aligned: 70 Modelled: 70 Confidence: 99.9% Identity: 26% PDB header:ribosomal protein/rna Chain: I: PDB Molecule:rna expansion segment es15 part i; PDBTitle: structure of a mammalian ribosomal 60s 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 2gyc chain G domain 1 Region: 74 - 141 Aligned: 68 Modelled: 68 Confidence: 99.9% Identity: 100% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 PDB 3cjr chain B domain 1 Region: 92 - 139 Aligned: 48 Modelled: 48 Confidence: 99.5% Identity: 40% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein L11, C-terminal domain Family: Ribosomal protein L11, C-terminal domain Phyre2 1 c3bboK_ 2 c2vhmI_ 3 c1jqmA_ 4 c2ftcG_ 5 c1s1iK_ 6 c3iz5J_ 7 c3cjtP_ 8 d3cjsb1 9 d1wiba_ 10 d1hc8a_ 11 d2gycg2 12 d1xbpg2 13 d1mmsa2 14 c1vq8I_ 15 d1mmsa1 16 d1vqoi1 17 d1xbpg1 18 c2zkri_ 19 d2gycg1 20 d3cjrb1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58

Detailed template information

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

1 c3bboK_ 100.0 54 PDB header:ribosome Chain: K: PDB Molecule:ribosomal protein l11; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 2 c2vhmI_ 100.0 100 PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11; PDBTitle: structure of pdf binding helix in complex with the ribosome2 (part 1 of 4) 3 c1jqmA_ 100.0 61 PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l11; PDBTitle: fitting of l11 protein and elongation factor g (ef-g) in2 the cryo-em map of e. coli 70s ribosome bound with ef-g,3 gdp and fusidic acid 4 c2ftcG_ 100.0 40 PDB header:ribosome Chain: G: PDB Molecule:39s ribosomal protein l11, mitochondrial; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome 5 c1s1iK_ 100.0 21 PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l12; 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, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 6 c3iz5J_ 100.0 26 PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 7 c3cjtP_ 100.0 70 PDB header:transferase/ribosomal protein Chain: P: PDB Molecule:50s ribosomal protein l11; PDBTitle: ribosomal protein l11 methyltransferase (prma) in complex with2 dimethylated ribosomal protein l11 8 d3cjsb1 100.0 70 Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain 9 d1wiba_ 100.0 23 Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain 10 d1hc8a_ 100.0 68 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 11 d2gycg2 100.0 100 Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain 12 d1xbpg2 100.0 69 Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain 13 d1mmsa2 100.0 67 Fold:Ribosomal L11/L12e N-terminal domain Superfamily:Ribosomal L11/L12e N-terminal domain Family:Ribosomal L11/L12e N-terminal domain 14 c1vq8I_ 99.9 36 PDB header:ribosome Chain: I: PDB Molecule:50s ribosomal protein l11p; PDBTitle: the structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound2 to the large ribosomal subunit of haloarcula marismortui 15 d1mmsa1 99.9 54 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 16 d1vqoi1 99.9 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 17 d1xbpg1 99.9 51 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 18 c2zkri_ 99.9 26 PDB header:ribosomal protein/rna Chain: I: PDB Molecule:rna expansion segment es15 part i; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 19 d2gycg1 99.9 100 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 20 d3cjrb1 99.5 40 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein L11, C-terminal domain Family:Ribosomal protein L11, C-terminal domain 21 d1iwga2 not modelled 28.9 22 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 22 c3bboD_ not modelled 18.7 16 PDB header:ribosome Chain: D: PDB Molecule:ribosomal protein l1; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 23 c2jwlB_ not modelled 18.4 10 PDB header:membrane protein Chain: B: PDB Molecule:protein tolr; PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data 24 c3r2cJ_ not modelled 18.2 20 PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna 25 c3qoyA_ not modelled 15.2 14 PDB header:ribosomal protein Chain: A: PDB Molecule:50s ribosomal protein l1; PDBTitle: crystal structure of ribosomal protein l1 from aquifex aeolicus 26 c1nohB_ not modelled 13.9 38 PDB header:viral protein Chain: B: PDB Molecule:head morphogenesis protein; PDBTitle: the structure of bacteriophage phi29 scaffolding protein2 gp7 after prohead assembly 27 c2asbA_ not modelled 13.1 14 PDB header:transcription/rna Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex 28 d1hh2p2 not modelled 12.1 29 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 29 c1lshB_ not modelled 12.0 20 PDB header:lipid binding protein Chain: B: PDB Molecule:lipovitellin (lv-2); PDBTitle: lipid-protein interactions in lipovitellin 30 d1lshb_ not modelled 12.0 20 Fold:Lipovitellin-phosvitin complex; beta-sheet shell regions Superfamily:Lipovitellin-phosvitin complex; beta-sheet shell regions Family:Lipovitellin-phosvitin complex; beta-sheet shell regions 31 d2qalj1 not modelled 11.2 33 Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10 32 c1s1hJ_ not modelled 11.2 24 PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20; 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. 33 c2zkqj_ not modelled 11.1 19 PDB header:ribosomal protein/rna Chain: J: PDB Molecule: 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 34 c3bbnJ_ not modelled 9.8 26 PDB header:ribosome Chain: J: PDB Molecule:ribosomal protein s10; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 35 d2uubj1 not modelled 9.6 29 Fold:Ferredoxin-like Superfamily:Ribosomal protein S10 Family:Ribosomal protein S10 36 d1i94m_ not modelled 9.3 12 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 37 c3iz6J_ not modelled 9.2 19 PDB header:ribosome Chain: J: PDB Molecule:40s ribosomal protein s20 (s10p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 38 d1ny711 not modelled 8.9 30 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 39 d2hfha_ not modelled 8.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 40 c2k53A_ not modelled 8.7 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 41 d2ftxb1 not modelled 8.0 38 Fold:Kinetochore globular domain-like Superfamily:Kinetochore globular domain Family:Spc24-like 42 d2asba2 not modelled 7.5 14 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 43 c1hh2P_ not modelled 7.4 24 PDB header:transcription regulation Chain: P: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima 44 c1l2fA_ not modelled 7.3 23 PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain 45 c3mtuE_ not modelled 7.1 32 PDB header:contractile protein Chain: E: PDB Molecule:head morphogenesis protein, tropomyosin alpha-1 chain; PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle 46 d2d9ra1 not modelled 7.1 20 Fold:Double-split beta-barrel Superfamily:AF2212/PG0164-like Family:PG0164-like 47 d1k1sa1 not modelled 7.0 24 Fold:Lesion bypass DNA polymerase (Y-family), little finger domain Superfamily:Lesion bypass DNA polymerase (Y-family), little finger domain Family:Lesion bypass DNA polymerase (Y-family), little finger domain 48 c2cazB_ not modelled 6.8 25 PDB header:protein transport Chain: B: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: escrt-i core 49 d2cazb1 not modelled 6.8 25 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS28 N-terminal domain 50 c2khvA_ not modelled 6.5 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of protein nmul_a0922 from2 nitrosospira multiformis. northeast structural genomics3 consortium target nmr38b. 51 d1pgl11 not modelled 6.3 23 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 52 d2j01c1 not modelled 6.2 36 Fold:Ribosomal protein L1 Superfamily:Ribosomal protein L1 Family:Ribosomal protein L1 53 c4a18U_ not modelled 5.7 44 PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 54 c2vohB_ not modelled 5.7 25 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2 homologous antagonist/killer; PDBTitle: structure of mouse a1 bound to the bak bh3-domain 55 d1iwga6 not modelled 5.7 16 Fold:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains 56 c2a03A_ not modelled 5.5 11 PDB header:oxidoreductase Chain: A: PDB Molecule:fe-superoxide dismutase homolog; PDBTitle: superoxide dismutase protein from plasmodium berghei 57 d1vqod1 not modelled 5.4 30 Fold:RL5-like Superfamily:RL5-like Family:Ribosomal protein L5 58 d1k1ga_ not modelled 5.3 19 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I)

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