Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	T	F	F	H	L	L	G	P	G	T	Q	P	N	D	D	S	F	S	M	N	P	L	P	I	T	C	Q	V	N	D	E	P	S	M	A	A	L	E	Q	C	A	H	S	P	Q	V	I	A	L	L	N	E	L	Q	H	Q	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?							?					?								?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	E	R	Q	P	P	L	G	E	V	L	A	V	D	L	L	N	L	N	A	D	D	R	H	F	I	N	T	L	L	G	E	G	E	V	S	V	R	I	Q	Q	A	D	D	S	E	S	E	I	Q	E	A	I	F	C	G	L	W	R	V
Secondary structure
SS confidence
Disorder					?	?	?	?	?																																		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	R	R	R	G	E	K	L	L	E	D	K	L	E	A	G	C	A	P	L	A	L	W	Q	A	A	T	Q	N	L	L	P	T	D	S	L	L	P	P	P	I	D	G	L	M	N	G	L	P	L	A	H	E	L	L	A	H	V	R	N
Secondary structure
SS confidence
Disorder									?																		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	D	A	Q	P	H	S	I	N	L	T	Q	L	P	I	S	E	A	D	R	L	F	L	S	R	L	C	G	P	G	N	I	Q	I	R	T	I	G	Y	G	E	S	Y	I	N	A	T	G	L	R	H	V	W	H	L	R	C	T	D	T
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.
Sequence		L	K	G	P	L	L	E	S	Y	E	I	C	P	I	P	E	V	V	L	A	A	P	E	D	L	V	D	S	A	Q	R	L	S	E	V	C	Q	W	L	A	E	A	A	P	T
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 3sb1 chain B Region: 166 - 279 Aligned: 113 Modelled: 114 Confidence: 100.0% Identity: 24% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hydrogenase expression protein; PDBTitle: hydrogenase expression protein huph from thiobacillus denitrificans2 atcc 25259 Phyre2 PDB 1vp7 chain D Region: 258 - 280 Aligned: 23 Modelled: 21 Confidence: 36.1% Identity: 13% PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution Phyre2 PDB 1vp7 chain A Region: 258 - 280 Aligned: 23 Modelled: 21 Confidence: 29.7% Identity: 13% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain B Region: 258 - 281 Aligned: 24 Modelled: 21 Confidence: 25.9% Identity: 13% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 2ka6 chain B Region: 191 - 212 Aligned: 22 Modelled: 22 Confidence: 24.7% Identity: 27% PDB header:transcription regulator Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: nmr structure of the cbp-taz2/stat1-tad complex Phyre2 PDB 2w56 chain B Region: 187 - 238 Aligned: 52 Modelled: 52 Confidence: 24.1% Identity: 13% PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island Phyre2 PDB 1vhi chain B Region: 4 - 17 Aligned: 14 Modelled: 14 Confidence: 20.0% Identity: 43% Fold: Ferredoxin-like Superfamily: Viral DNA-binding domain Family: Viral DNA-binding domain Phyre2 PDB 3gku chain B Region: 189 - 223 Aligned: 35 Modelled: 35 Confidence: 19.7% Identity: 11% PDB header:rna binding protein Chain: B: PDB Molecule:probable rna-binding protein; PDBTitle: crystal structure of a probable rna-binding protein from clostridium2 symbiosum atcc 14940 Phyre2 PDB 1p3w chain A Region: 262 - 284 Aligned: 23 Modelled: 23 Confidence: 18.5% Identity: 13% Fold: PLP-dependent transferase-like Superfamily: PLP-dependent transferases Family: Cystathionine synthase-like Phyre2 PDB 1b3t chain A Region: 4 - 15 Aligned: 12 Modelled: 12 Confidence: 16.4% Identity: 50% Fold: Ferredoxin-like Superfamily: Viral DNA-binding domain Family: Viral DNA-binding domain Phyre2 PDB 3h8d chain C Region: 233 - 265 Aligned: 33 Modelled: 33 Confidence: 14.6% Identity: 15% PDB header:motor protein/signaling protein Chain: C: PDB Molecule:myosin-vi; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide Phyre2 PDB 3lvm chain B Region: 262 - 284 Aligned: 23 Modelled: 23 Confidence: 14.0% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:cysteine desulfurase; PDBTitle: crystal structure of e.coli iscs Phyre2 PDB 3cvo chain A Region: 192 - 237 Aligned: 46 Modelled: 46 Confidence: 13.3% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution Phyre2 PDB 3d5j chain B Region: 195 - 221 Aligned: 27 Modelled: 27 Confidence: 12.5% Identity: 15% PDB header:oxidoreductase Chain: B: PDB Molecule:glutaredoxin-2, mitochondrial; PDBTitle: structure of yeast grx2-c30s mutant with glutathionyl mixed2 disulfide Phyre2 PDB 2f2a chain B domain 1 Region: 170 - 213 Aligned: 39 Modelled: 44 Confidence: 12.3% Identity: 13% Fold: GatB/YqeY motif Superfamily: GatB/YqeY motif Family: GatB/GatE C-terminal domain-like Phyre2 PDB 3if8 chain B Region: 166 - 257 Aligned: 67 Modelled: 74 Confidence: 12.3% Identity: 15% PDB header:cell cycle Chain: B: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex Phyre2 PDB 1gyv chain A Region: 118 - 144 Aligned: 27 Modelled: 27 Confidence: 12.1% Identity: 19% Fold: Immunoglobulin-like beta-sandwich Superfamily: Clathrin adaptor appendage domain Family: gamma-adaptin C-terminal appendage domain-like Phyre2 PDB 3n6q chain F Region: 190 - 212 Aligned: 23 Modelled: 23 Confidence: 12.0% Identity: 17% PDB header:oxidoreductase Chain: F: PDB Molecule:yghz aldo-keto reductase; PDBTitle: crystal structure of yghz from e. coli Phyre2 PDB 1gyw chain B Region: 118 - 144 Aligned: 27 Modelled: 27 Confidence: 11.9% Identity: 19% Fold: Immunoglobulin-like beta-sandwich Superfamily: Clathrin adaptor appendage domain Family: gamma-adaptin C-terminal appendage domain-like Phyre2 PDB 2ns0 chain A domain 1 Region: 83 - 126 Aligned: 39 Modelled: 41 Confidence: 11.5% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: RHA1 ro06458-like Phyre2 1 c3sb1B_ 2 c1vp7D_ 3 d1vp7a_ 4 d1vp7b_ 5 c2ka6B_ 6 c2w56B_ 7 d1vhib_ 8 c3gkuB_ 9 d1p3wa_ 10 d1b3ta_ 11 c3h8dC_ 12 c3lvmB_ 13 c3cvoA_ 14 c3d5jB_ 15 d2f2ab1 16 c3if8B_ 17 d1gyva_ 18 c3n6qF_ 19 d1gywb_ 20 d2ns0a1 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

Detailed template information

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

1 c3sb1B_ 100.0 24 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hydrogenase expression protein; PDBTitle: hydrogenase expression protein huph from thiobacillus denitrificans2 atcc 25259 2 c1vp7D_ 36.1 13 PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution 3 d1vp7a_ 29.7 13 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 4 d1vp7b_ 25.9 13 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 5 c2ka6B_ 24.7 27 PDB header:transcription regulator Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: nmr structure of the cbp-taz2/stat1-tad complex 6 c2w56B_ 24.1 13 PDB header:unknown function Chain: B: PDB Molecule:vc0508; PDBTitle: structure of the hypothetical protein vc0508 from vibrio cholerae2 vsp-ii pathogenicity island 7 d1vhib_ 20.0 43 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 8 c3gkuB_ 19.7 11 PDB header:rna binding protein Chain: B: PDB Molecule:probable rna-binding protein; PDBTitle: crystal structure of a probable rna-binding protein from clostridium2 symbiosum atcc 14940 9 d1p3wa_ 18.5 13 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like 10 d1b3ta_ 16.4 50 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 11 c3h8dC_ 14.6 15 PDB header:motor protein/signaling protein Chain: C: PDB Molecule:myosin-vi; PDBTitle: crystal structure of myosin vi in complex with dab2 peptide 12 c3lvmB_ 14.0 13 PDB header:transferase Chain: B: PDB Molecule:cysteine desulfurase; PDBTitle: crystal structure of e.coli iscs 13 c3cvoA_ 13.3 15 PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution 14 c3d5jB_ 12.5 15 PDB header:oxidoreductase Chain: B: PDB Molecule:glutaredoxin-2, mitochondrial; PDBTitle: structure of yeast grx2-c30s mutant with glutathionyl mixed2 disulfide 15 d2f2ab1 12.3 13 Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like 16 c3if8B_ 12.3 15 PDB header:cell cycle Chain: B: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex 17 d1gyva_ 12.1 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:gamma-adaptin C-terminal appendage domain-like 18 c3n6qF_ 12.0 17 PDB header:oxidoreductase Chain: F: PDB Molecule:yghz aldo-keto reductase; PDBTitle: crystal structure of yghz from e. coli 19 d1gywb_ 11.9 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:gamma-adaptin C-terminal appendage domain-like 20 d2ns0a1 11.5 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RHA1 ro06458-like 21 d1th0a_ not modelled 10.6 18 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Adenain-like 22 c2qf7A_ not modelled 10.5 17 PDB header:ligase Chain: A: PDB Molecule:pyruvate carboxylase protein; PDBTitle: crystal structure of a complete multifunctional pyruvate carboxylase2 from rhizobium etli 23 c3ipzA_ not modelled 10.2 11 PDB header:electron transport, oxidoreductase Chain: A: PDB Molecule:monothiol glutaredoxin-s14, chloroplastic; PDBTitle: crystal structure of arabidopsis monothiol glutaredoxin atgrxcp 24 c2wj8N_ not modelled 9.9 13 PDB header:rna binding protein/rna Chain: N: PDB Molecule:nucleoprotein; PDBTitle: respiratory syncitial virus ribonucleoprotein 25 d2bz2a1 not modelled 9.7 2 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 26 c1mszA_ not modelled 9.0 19 PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein smubp-2; PDBTitle: solution structure of the r3h domain from human smubp-2 27 d1msza_ not modelled 9.0 19 Fold:IF3-like Superfamily:R3H domain Family:R3H domain 28 c2kwtA_ not modelled 8.8 29 PDB header:viral protein Chain: A: PDB Molecule:protease ns2-3; PDBTitle: solution structure of ns2 [27-59] 29 c2f3jA_ not modelled 8.6 11 PDB header:transport protein Chain: A: PDB Molecule:rna and export factor binding protein 2; PDBTitle: the solution structure of the ref2-i mrna export factor2 (residues 1-155). 30 d2ppqa1 not modelled 8.2 10 Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:APH phosphotransferases 31 c3exnA_ not modelled 8.2 27 PDB header:transferase Chain: A: PDB Molecule:probable acetyltransferase; PDBTitle: crystal structure of acetyltransferase from thermus thermophilus hb8 32 c3c1sA_ not modelled 8.1 15 PDB header:oxidoreductase Chain: A: PDB Molecule:glutaredoxin-1; PDBTitle: crystal structure of grx1 in glutathionylated form 33 d1qk1a2 not modelled 8.0 9 Fold:Glutamine synthetase/guanido kinase Superfamily:Glutamine synthetase/guanido kinase Family:Guanido kinase catalytic domain 34 d2dwya1 not modelled 7.8 9 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:gamma-adaptin C-terminal appendage domain-like 35 d1na8a_ not modelled 6.9 9 Fold:Immunoglobulin-like beta-sandwich Superfamily:Clathrin adaptor appendage domain Family:gamma-adaptin C-terminal appendage domain-like 36 c2huuA_ not modelled 6.8 22 PDB header:transferase Chain: A: PDB Molecule:alanine glyoxylate aminotransferase; PDBTitle: crystal structure of aedes aegypti alanine glyoxylate2 aminotransferase in complex with alanine 37 d1j9ba_ not modelled 6.8 25 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:ArsC-like 38 c2e9gA_ not modelled 6.7 14 PDB header:protein binding Chain: A: PDB Molecule:ap-1 complex subunit gamma-2; PDBTitle: solution structure of the alpha adaptinc2 domain from human2 adapter-related protein complex 1 gamma 2 subunit 39 c2ee6A_ not modelled 6.4 17 PDB header:structural protein Chain: A: PDB Molecule:filamin-b; PDBTitle: solution structure of the 21th filamin domain from human2 filamin-b 40 d1qmra_ not modelled 6.3 14 Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like 41 d2bk0a1 not modelled 6.2 12 Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like 42 d1t07a_ not modelled 6.1 19 Fold:YggX-like Superfamily:YggX-like Family:YggX-like 43 c3e4fB_ not modelled 5.9 17 PDB header:transferase Chain: B: PDB Molecule:aminoglycoside n3-acetyltransferase; PDBTitle: crystal structure of ba2930- a putative aminoglycoside n3-2 acetyltransferase from bacillus anthracis 44 d1bwwa_ not modelled 5.8 12 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 45 c2hbpA_ not modelled 5.8 17 PDB header:endocytosis, protein binding Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1; PDBTitle: solution structure of sla1 homology domain 1 46 d2b79a1 not modelled 5.7 11 Fold:TBP-like Superfamily:Bet v1-like Family:Smu440-like 47 d1y7ta2 not modelled 5.7 11 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 48 d1c7na_ not modelled 5.7 22 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like 49 c2hqyB_ not modelled 5.6 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of conserved protein of unknown function from2 bacteroides thetaiotaomicron vpi-5482 50 c3rv2B_ not modelled 5.6 41 PDB header:transferase Chain: B: PDB Molecule:s-adenosylmethionine synthase; PDBTitle: crystal structure of s-adenosylmethionine synthetase from2 mycobacterium marinum 51 d1hy7a_ not modelled 5.5 24 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Matrix metalloproteases, catalytic domain 52 d2bp3a1 not modelled 5.5 20 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Filamin repeat (rod domain) 53 d3cmol1 not modelled 5.4 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 54 c1y03A_ not modelled 5.2 43 PDB header:antifreeze protein Chain: A: PDB Molecule:antifreeze peptide ss-3; PDBTitle: solution structure of a recombinant type i sculpin2 antifreeze protein 55 c1y04A_ not modelled 5.2 43 PDB header:antifreeze protein Chain: A: PDB Molecule:antifreeze peptide ss-3; PDBTitle: solution structure of a recombinant type i sculpin2 antifreeze protein 56 d2ad9a1 not modelled 5.1 21 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD

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