Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	K	S	V	I	A	I	I	I	I	V	L	V	V	L	Y	M	S	V	F	V	V	K	E	G	E	R	G	I	T	L	R	F	G	K	V	L	R	D	D	D	N	K	P	L	V	Y	E	P	G	L	H	F	K	I	P	F	I	E
Secondary structure
SS confidence
Disorder		?	?	?																																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	V	K	M	L	D	A	R	I	Q	T	M	D	N	Q	A	D	R	F	V	T	K	E	K	K	D	L	I	V	D	S	Y	I	K	W	R	I	S	D	F	S	R	Y	Y	L	A	T	G	G	G	D	I	S	Q	A	E	V	L	L	K
Secondary structure
SS confidence
Disorder															?	?	?	?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	K	F	S	D	R	L	R	S	E	I	G	R	L	D	V	K	D	I	V	T	D	S	R	G	R	L	T	L	E	V	R	D	A	L	N	S	G	S	A	G	T	E	D	E	V	T	T	P	A	A	D	N	A	I	A	E	A	A	E
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	V	T	A	E	T	K	G	K	V	P	V	I	N	P	N	S	M	A	A	L	G	I	E	V	V	D	V	R	I	K	Q	I	N	L	P	T	E	V	S	E	A	I	Y	N	R	M	R	A	E	R	E	A	V	A	R	R	H	R	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Q	G	Q	E	E	A	E	K	L	R	A	T	A	D	Y	E	V	T	R	T	L	A	E	A	E	R	Q	G	R	I	M	R	G	E	G	D	A	E	A	A	K	L	F	A	D	A	F	S	K	D	P	D	F	Y	A	F	I	R	S	L
Secondary structure
SS confidence
Disorder												?											?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.
Sequence		R	A	Y	E	N	S	F	S	G	N	Q	D	V	M	V	M	S	P	D	S	D	F	F	R	Y	M	K	T	P	T	S	A	T	R
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 3bk6 chain C Region: 58 - 259 Aligned: 157 Modelled: 163 Confidence: 99.9% Identity: 25% PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii Phyre2 PDB 1win chain A Region: 60 - 229 Aligned: 130 Modelled: 131 Confidence: 99.6% Identity: 21% Fold: EF-Ts domain-like Superfamily: Band 7/SPFH domain Family: Band 7/SPFH domain Phyre2 PDB 2rpb chain A Region: 64 - 218 Aligned: 110 Modelled: 111 Confidence: 99.5% Identity: 23% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein Phyre2 PDB 2zv4 chain O Region: 21 - 289 Aligned: 260 Modelled: 267 Confidence: 98.8% Identity: 15% PDB header:structural protein Chain: O: PDB Molecule:major vault protein; PDBTitle: the structure of rat liver vault at 3.5 angstrom resolution Phyre2 PDB 2kk7 chain A Region: 254 - 290 Aligned: 37 Modelled: 37 Confidence: 38.9% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:v-type atp synthase subunit e; PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii Phyre2 PDB 3k5b chain B Region: 226 - 292 Aligned: 66 Modelled: 67 Confidence: 33.7% Identity: 24% PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm); PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase Phyre2 PDB 3k5b chain E Region: 223 - 309 Aligned: 79 Modelled: 82 Confidence: 16.7% Identity: 13% PDB header:hydrolase Chain: E: PDB Molecule:v-type atp synthase subunit e; PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase Phyre2 PDB 3sbt chain B Region: 18 - 56 Aligned: 24 Modelled: 24 Confidence: 16.3% Identity: 42% PDB header:splicing Chain: B: PDB Molecule:a1 cistron-splicing factor aar2; PDBTitle: crystal structure of a aar2-prp8 complex Phyre2 PDB 1js8 chain A domain 2 Region: 56 - 92 Aligned: 34 Modelled: 37 Confidence: 15.0% Identity: 18% Fold: C-terminal domain of mollusc hemocyanin Superfamily: C-terminal domain of mollusc hemocyanin Family: C-terminal domain of mollusc hemocyanin Phyre2 PDB 2dii chain A Region: 280 - 300 Aligned: 21 Modelled: 21 Confidence: 13.6% Identity: 14% PDB header:transcription Chain: A: PDB Molecule:tfiih basal transcription factor complex p62 PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit Phyre2 PDB 2ke4 chain A Region: 254 - 293 Aligned: 40 Modelled: 40 Confidence: 12.2% Identity: 20% PDB header:membrane protein Chain: A: PDB Molecule:cdc42-interacting protein 4; PDBTitle: the nmr structure of the tc10 and cdc42 interacting domain2 of cip4 Phyre2 PDB 2dii chain A domain 1 Region: 280 - 300 Aligned: 21 Modelled: 21 Confidence: 10.9% Identity: 14% Fold: BSD domain-like Superfamily: BSD domain-like Family: BSD domain Phyre2 PDB 3l4h chain A Region: 34 - 84 Aligned: 51 Modelled: 51 Confidence: 9.8% Identity: 10% PDB header:protein binding Chain: A: PDB Molecule:e3 ubiquitin-protein ligase hecw1; PDBTitle: helical box domain and second ww domain of the human e3 ubiquitin-2 protein ligase hecw1 Phyre2 PDB 1lnl chain A domain 2 Region: 56 - 68 Aligned: 13 Modelled: 13 Confidence: 9.6% Identity: 8% Fold: C-terminal domain of mollusc hemocyanin Superfamily: C-terminal domain of mollusc hemocyanin Family: C-terminal domain of mollusc hemocyanin Phyre2 PDB 1wd6 chain B Region: 49 - 57 Aligned: 9 Modelled: 9 Confidence: 9.4% Identity: 44% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli Phyre2 PDB 1l2p chain A Region: 227 - 289 Aligned: 56 Modelled: 63 Confidence: 8.8% Identity: 20% Fold: Single transmembrane helix Superfamily: F1F0 ATP synthase subunit B, membrane domain Family: F1F0 ATP synthase subunit B, membrane domain Phyre2 PDB 1jey chain A domain 1 Region: 44 - 66 Aligned: 23 Modelled: 23 Confidence: 7.7% Identity: 26% Fold: SPOC domain-like Superfamily: SPOC domain-like Family: Ku70 subunit middle domain Phyre2 PDB 1y4c chain A Region: 145 - 289 Aligned: 142 Modelled: 142 Confidence: 7.2% Identity: 11% PDB header:de novo protein Chain: A: PDB Molecule:maltose binding protein fused with designed PDBTitle: designed helical protein fusion mbp Phyre2 PDB 1nyo chain A Region: 283 - 325 Aligned: 43 Modelled: 43 Confidence: 6.8% Identity: 16% Fold: FAS1 domain Superfamily: FAS1 domain Family: FAS1 domain Phyre2 PDB 2ix0 chain A domain 3 Region: 47 - 99 Aligned: 52 Modelled: 53 Confidence: 6.7% Identity: 6% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 1 c3bk6C_ 2 d1wina_ 3 c2rpbA_ 4 c2zv4O_ 5 c2kk7A_ 6 c3k5bB_ 7 c3k5bE_ 8 c3sbtB_ 9 d1js8a2 10 c2diiA_ 11 c2ke4A_ 12 d2diia1 13 c3l4hA_ 14 d1lnla2 15 c1wd6B_ 16 d1l2pa_ 17 d1jeya1 18 c1y4cA_ 19 d1nyoa_ 20 d2ix0a3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 c3bk6C_ 99.9 25 PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii 2 d1wina_ 99.6 21 Fold:EF-Ts domain-like Superfamily:Band 7/SPFH domain Family:Band 7/SPFH domain 3 c2rpbA_ 99.5 23 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein 4 c2zv4O_ 98.8 15 PDB header:structural protein Chain: O: PDB Molecule:major vault protein; PDBTitle: the structure of rat liver vault at 3.5 angstrom resolution 5 c2kk7A_ 38.9 24 PDB header:hydrolase Chain: A: PDB Molecule:v-type atp synthase subunit e; PDBTitle: nmr solution structure of the n terminal domain of subunit e2 (e1-52) of a1ao atp synthase from methanocaldococcus3 jannaschii 6 c3k5bB_ 33.7 24 PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase, subunit (vapc-therm); PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase 7 c3k5bE_ 16.7 13 PDB header:hydrolase Chain: E: PDB Molecule:v-type atp synthase subunit e; PDBTitle: crystal structure of the peripheral stalk of thermus thermophilus h+-2 atpase/synthase 8 c3sbtB_ 16.3 42 PDB header:splicing Chain: B: PDB Molecule:a1 cistron-splicing factor aar2; PDBTitle: crystal structure of a aar2-prp8 complex 9 d1js8a2 15.0 18 Fold:C-terminal domain of mollusc hemocyanin Superfamily:C-terminal domain of mollusc hemocyanin Family:C-terminal domain of mollusc hemocyanin 10 c2diiA_ 13.6 14 PDB header:transcription Chain: A: PDB Molecule:tfiih basal transcription factor complex p62 PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit 11 c2ke4A_ 12.2 20 PDB header:membrane protein Chain: A: PDB Molecule:cdc42-interacting protein 4; PDBTitle: the nmr structure of the tc10 and cdc42 interacting domain2 of cip4 12 d2diia1 10.9 14 Fold:BSD domain-like Superfamily:BSD domain-like Family:BSD domain 13 c3l4hA_ 9.8 10 PDB header:protein binding Chain: A: PDB Molecule:e3 ubiquitin-protein ligase hecw1; PDBTitle: helical box domain and second ww domain of the human e3 ubiquitin-2 protein ligase hecw1 14 d1lnla2 9.6 8 Fold:C-terminal domain of mollusc hemocyanin Superfamily:C-terminal domain of mollusc hemocyanin Family:C-terminal domain of mollusc hemocyanin 15 c1wd6B_ 9.4 44 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli 16 d1l2pa_ 8.8 20 Fold:Single transmembrane helix Superfamily:F1F0 ATP synthase subunit B, membrane domain Family:F1F0 ATP synthase subunit B, membrane domain 17 d1jeya1 7.7 26 Fold:SPOC domain-like Superfamily:SPOC domain-like Family:Ku70 subunit middle domain 18 c1y4cA_ 7.2 11 PDB header:de novo protein Chain: A: PDB Molecule:maltose binding protein fused with designed PDBTitle: designed helical protein fusion mbp 19 d1nyoa_ 6.8 16 Fold:FAS1 domain Superfamily:FAS1 domain Family:FAS1 domain 20 d2ix0a3 6.7 6 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 21 c1jeqA_ not modelled 6.6 26 PDB header:dna binding protein Chain: A: PDB Molecule:ku70; PDBTitle: crystal structure of the ku heterodimer 22 c2l9uA_ not modelled 6.6 25 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 23 d1o70a2 not modelled 6.3 7 Fold:FAS1 domain Superfamily:FAS1 domain Family:FAS1 domain 24 d1if1a_ not modelled 6.2 55 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Interferon regulatory factor 25 c2dllA_ not modelled 6.2 55 PDB header:cytokine Chain: A: PDB Molecule:interferon regulatory factor 4; PDBTitle: solution structure of the irf domain of human interferon2 regulator factors 4 26 c3lj5H_ not modelled 6.0 12 PDB header:viral protein Chain: H: PDB Molecule:portal protein; PDBTitle: full length bacteriophage p22 portal protein 27 c2ko6A_ not modelled 6.0 28 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 28 d1p5dx4 not modelled 5.9 15 Fold:TBP-like Superfamily:Phosphoglucomutase, C-terminal domain Family:Phosphoglucomutase, C-terminal domain 29 d2ix0a1 not modelled 5.7 39 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 30 d2irfg_ not modelled 5.7 55 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Interferon regulatory factor 31 c2k88A_ not modelled 5.6 7 PDB header:hydrolase Chain: A: PDB Molecule:vacuolar proton pump subunit g; PDBTitle: association of subunit d (vma6p) and e (vma4p) with g2 (vma10p) and the nmr solution structure of subunit g (g1-3 59) of the saccharomyces cerevisiae v1vo atpase 32 d1tf5a1 not modelled 5.5 39 Fold:Pre-protein crosslinking domain of SecA Superfamily:Pre-protein crosslinking domain of SecA Family:Pre-protein crosslinking domain of SecA 33 d2fhza1 not modelled 5.5 30 Fold:ImmE5-like Superfamily:ImmE5-like Family:ImmE5-like 34 d1ueba3 not modelled 5.5 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 35 d2f5tx2 not modelled 5.4 18 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:TrmB middle domain-like 36 d1gvia1 not modelled 5.4 21 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:E-set domains of sugar-utilizing enzymes 37 d1tfra2 not modelled 5.3 22 Fold:PIN domain-like Superfamily:PIN domain-like Family:5' to 3' exonuclease catalytic domain 38 c3bmaC_ not modelled 5.3 12 PDB header:ligase Chain: C: PDB Molecule:d-alanyl-lipoteichoic acid synthetase; PDBTitle: crystal structure of d-alanyl-lipoteichoic acid synthetase from2 streptococcus pneumoniae r6 39 c2kseA_ not modelled 5.3 24 PDB header:transferase Chain: A: PDB Molecule:sensor protein qsec; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor qsec, center for structures of3 membrane proteins (csmp) target 4311c 40 c2iruA_ not modelled 5.2 31 PDB header:transferase Chain: A: PDB Molecule:putative dna ligase-like protein rv0938/mt0965; PDBTitle: crystal structure of the polymerase domain from mycobacterium2 tuberculosis ligase d 41 d1h2ka_ not modelled 5.1 23 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:Hypoxia-inducible factor HIF ihhibitor (FIH1) 42 c1nohB_ not modelled 5.1 16 PDB header:viral protein Chain: B: PDB Molecule:head morphogenesis protein; PDBTitle: the structure of bacteriophage phi29 scaffolding protein2 gp7 after prohead assembly 43 d2o4ta1 not modelled 5.1 12 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like

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