Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	V	L	F	F	L	L	M	I	F	V	S	F	G	V	I	A	D	C	E	I	Q	A	K	D	H	D	C	F	T	I	F	A	K	G	T	I	F	S	A	F	P	V	L	N	N	K	A	M	W	R	W	Y	Q	N	E	D	I
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	E	Y	Y	W	Q	T	E	L	G	T	C	K	N	N	K	F	T	P	S	G	A	R	L	L	I	R	V	G	S	L	R	L	N	E	N	H	A	I	K	G	T	L	Q	E	L	I	N	T	A	E	K	T	A	F	L	G	D	R	F
Secondary structure
SS confidence
Disorder														?	?																	?	?	?		?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	S	Y	I	R	A	G	I	Y	Q	K	K	S	S	D	P	V	Q	L	L	A	V	L	D	N	S	I	M	V	K	Y	F	K	D	E	K	P	T	Y	A	R	M	T	A	H	L	P	N	K	N	E	S	Y	E	C	L	I	K	I	Q
Secondary structure
SS confidence
Disorder													?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		H	E	L	I	R	S	E	E	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 1gzs chain B Region: 70 - 82 Aligned: 13 Modelled: 13 Confidence: 50.3% Identity: 77% Fold: SopE-like GEF domain Superfamily: SopE-like GEF domain Family: SopE-like GEF domain Phyre2 PDB 2jok chain A domain 1 Region: 70 - 82 Aligned: 13 Modelled: 13 Confidence: 48.8% Identity: 62% Fold: SopE-like GEF domain Superfamily: SopE-like GEF domain Family: SopE-like GEF domain Phyre2 PDB 1r6e chain A Region: 70 - 82 Aligned: 13 Modelled: 13 Confidence: 46.9% Identity: 62% Fold: SopE-like GEF domain Superfamily: SopE-like GEF domain Family: SopE-like GEF domain Phyre2 PDB 1jqs chain B Region: 141 - 158 Aligned: 18 Modelled: 18 Confidence: 33.4% Identity: 50% PDB header:ribosome Chain: B: PDB Molecule:elongation factor g; PDBTitle: fitting of l11 protein and elongation factor g (domain g'2 and v) in the cryo-em map of e. coli 70s ribosome bound3 with ef-g and gmppcp, a nonhydrolysable gtp analog Phyre2 PDB 1bec chain A domain 1 Region: 56 - 87 Aligned: 32 Modelled: 32 Confidence: 27.9% Identity: 16% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2nts chain P domain 1 Region: 56 - 87 Aligned: 32 Modelled: 32 Confidence: 25.2% Identity: 22% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2cde chain B domain 1 Region: 56 - 87 Aligned: 32 Modelled: 32 Confidence: 24.2% Identity: 13% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2oez chain A domain 1 Region: 125 - 142 Aligned: 17 Modelled: 18 Confidence: 18.4% Identity: 35% Fold: YacF-like Superfamily: YacF-like Family: YacF-like Phyre2 PDB 3i5d chain C Region: 31 - 91 Aligned: 51 Modelled: 61 Confidence: 17.7% Identity: 24% PDB header:transport protein Chain: C: PDB Molecule:p2x purinoceptor; PDBTitle: crystal structure of the atp-gated p2x4 ion channel in the closed, apo2 state at 3.5 angstroms (r3) Phyre2 PDB 1gso chain A domain 1 Region: 70 - 89 Aligned: 19 Modelled: 20 Confidence: 15.8% Identity: 32% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: BC C-terminal domain-like Phyre2 PDB 2rhe chain A Region: 56 - 86 Aligned: 30 Modelled: 31 Confidence: 15.1% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1j8h chain D domain 1 Region: 56 - 87 Aligned: 32 Modelled: 32 Confidence: 14.9% Identity: 31% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2nxy chain C domain 1 Region: 56 - 87 Aligned: 31 Modelled: 32 Confidence: 13.9% Identity: 35% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2axh chain A domain 1 Region: 56 - 87 Aligned: 31 Modelled: 32 Confidence: 13.1% Identity: 26% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2rcj chain A domain 1 Region: 56 - 84 Aligned: 28 Modelled: 29 Confidence: 12.7% Identity: 21% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1nl0 chain L domain 1 Region: 56 - 87 Aligned: 31 Modelled: 32 Confidence: 12.4% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2rf4 chain A Region: 16 - 103 Aligned: 81 Modelled: 87 Confidence: 11.2% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 Phyre2 PDB 1hng chain A domain 1 Region: 56 - 95 Aligned: 40 Modelled: 40 Confidence: 11.1% Identity: 28% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 2rnn chain A Region: 107 - 142 Aligned: 35 Modelled: 36 Confidence: 10.2% Identity: 26% PDB header:ligase Chain: A: PDB Molecule:e3 sumo-protein ligase siz1; PDBTitle: solution structure of the n-terminal sap domain of sumo e3 ligases2 from saccharomyces cerevisiae Phyre2 PDB 1kgc chain E domain 1 Region: 56 - 87 Aligned: 31 Modelled: 32 Confidence: 9.4% Identity: 35% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 1 d1gzsb_ 2 d2joka1 3 d1r6ea_ 4 c1jqsB_ 5 d1beca1 6 d2ntsp1 7 d2cdeb1 8 d2oeza1 9 c3i5dC_ 10 d1gsoa1 11 d2rhea_ 12 d1j8hd1 13 d2nxyc1 14 d2axha1 15 d2rcja1 16 d1nl0l1 17 c2rf4A_ 18 d1hnga1 19 c2rnnA_ 20 d1kgce1 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

Detailed template information

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

1 d1gzsb_ 50.3 77 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 2 d2joka1 48.8 62 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 3 d1r6ea_ 46.9 62 Fold:SopE-like GEF domain Superfamily:SopE-like GEF domain Family:SopE-like GEF domain 4 c1jqsB_ 33.4 50 PDB header:ribosome Chain: B: PDB Molecule:elongation factor g; PDBTitle: fitting of l11 protein and elongation factor g (domain g'2 and v) in the cryo-em map of e. coli 70s ribosome bound3 with ef-g and gmppcp, a nonhydrolysable gtp analog 5 d1beca1 27.9 16 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 6 d2ntsp1 25.2 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 7 d2cdeb1 24.2 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 8 d2oeza1 18.4 35 Fold:YacF-like Superfamily:YacF-like Family:YacF-like 9 c3i5dC_ 17.7 24 PDB header:transport protein Chain: C: PDB Molecule:p2x purinoceptor; PDBTitle: crystal structure of the atp-gated p2x4 ion channel in the closed, apo2 state at 3.5 angstroms (r3) 10 d1gsoa1 15.8 32 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 11 d2rhea_ 15.1 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 12 d1j8hd1 14.9 31 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 13 d2nxyc1 13.9 35 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 14 d2axha1 13.1 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 15 d2rcja1 12.7 21 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 16 d1nl0l1 12.4 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 17 c2rf4A_ 11.2 16 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 18 d1hnga1 11.1 28 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 19 c2rnnA_ 10.2 26 PDB header:ligase Chain: A: PDB Molecule:e3 sumo-protein ligase siz1; PDBTitle: solution structure of the n-terminal sap domain of sumo e3 ligases2 from saccharomyces cerevisiae 20 d1kgce1 9.4 35 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 21 d1aqkl1 not modelled 8.8 29 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 22 d1nfdb1 not modelled 8.6 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 23 d1u3hb1 not modelled 8.5 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 24 c2ckzB_ not modelled 8.2 15 PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase iii 25 kd PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25. 25 c3l15A_ not modelled 7.6 30 PDB header:transcription Chain: A: PDB Molecule:transcriptional enhancer factor tef-4; PDBTitle: human tead2 transcriptional factor 26 c2kuyA_ not modelled 7.5 43 PDB header:antimicrobial protein Chain: A: PDB Molecule:prebacteriocin glycocin f; PDBTitle: structure of glycocin f 27 d1ktke1 not modelled 7.2 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 28 d1q1jl1 not modelled 7.2 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 29 d2aw2a1 not modelled 6.9 52 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 30 c3fd9C_ not modelled 6.9 25 PDB header:unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the transcriptional anti-activator exsd2 from pseudomonas aeruginosa 31 d1lc0a2 not modelled 6.9 18 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Biliverdin reductase 32 d1nfda1 not modelled 6.8 28 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 33 c1ye9E_ not modelled 6.7 35 PDB header:oxidoreductase Chain: E: PDB Molecule:catalase hpii; PDBTitle: crystal structure of proteolytically truncated catalase2 hpii from e. coli 34 d1xaua_ not modelled 6.6 29 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 35 d1nzpa_ not modelled 6.5 29 Fold:SAM domain-like Superfamily:DNA polymerase beta, N-terminal domain-like Family:DNA polymerase beta, N-terminal domain-like 36 c2hpvA_ not modelled 6.4 16 PDB header:oxidoreductase Chain: A: PDB Molecule:fmn-dependent nadh-azoreductase; PDBTitle: crystal structure of fmn-dependent azoreductase from enterococcus2 faecalis 37 d1vmaa1 not modelled 6.2 17 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 38 c3ayhB_ not modelled 6.2 8 PDB header:transcription Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc8; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii 39 d2pxyd2 not modelled 6.1 57 Fold:MHC antigen-recognition domain Superfamily:MHC antigen-recognition domain Family:MHC antigen-recognition domain 40 d2bnub1 not modelled 5.9 16 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 41 c3fe7A_ not modelled 5.8 15 PDB header:cell cycle Chain: A: PDB Molecule:mdm4 protein; PDBTitle: crystal structure of hdmx bound to the p53-peptidomimetic2 ac-phe-met-aib-pmp-trp-glu-ac3c-leu-nh2 at 1.35a 42 d2ak4d1 not modelled 5.6 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 43 d2ho2a1 not modelled 5.5 55 Fold:WW domain-like Superfamily:WW domain Family:WW domain 44 d2j6el1 not modelled 5.4 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 45 d1w72l1 not modelled 5.2 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 46 c2l0eA_ not modelled 5.2 67 PDB header:membrane protein Chain: A: PDB Molecule:sodium/hydrogen exchanger 1; PDBTitle: structural and functional analysis of tm vi of the nhe1 isoform of the2 na+/h+ exchanger 47 d2axia1 not modelled 5.1 15 Fold:SWIB/MDM2 domain Superfamily:SWIB/MDM2 domain Family:SWIB/MDM2 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