Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	T	L	L	A	A	G	A	V	L	A	L	S	S	S	F	T	V	N	A	A	E	N	D	K	P	Q	Y	L	S	D	W	W	H	Q	S	V	N	V	V	G	S	Y	H	T	R	F	G	P	Q	I	R	N	D	T	Y	L	E
Secondary structure
SS confidence
Disorder		?	?													?	?	?	?	?	?	?	?	?	?	?	?	?	?																			?	?	?	?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	E	A	F	A	K	K	D	W	F	D	F	Y	G	Y	A	D	A	P	V	F	F	G	G	N	S	D	A	K	G	I	W	N	H	G	S	P	L	F	M	E	I	E	P	R	F	S	I	D	K	L	T	N	T	D	L	S	F	G	P
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?	?	?	?	?	?																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		F	K	E	W	Y	F	A	N	N	Y	I	Y	D	M	G	R	N	K	D	G	R	Q	S	T	W	Y	M	G	L	G	T	D	I	D	T	G	L	P	M	S	L	S	M	N	V	Y	A	K	Y	Q	W	Q	N	Y	G	A	A	N	E	N
Secondary structure
SS confidence
Disorder													?	?			?	?	?	?		?																														?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	W	D	G	Y	R	F	K	I	K	Y	F	V	P	I	T	D	L	W	G	G	Q	L	S	Y	I	G	F	T	N	F	D	W	G	S	D	L	G	D	D	S	G	N	A	I	N	G	I	K	T	R	T	N	N	S	I	A	S	S	H
Secondary structure
SS confidence
Disorder		?	?	?																																	?	?	?	?	?	?	?	?	?	?	?		?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.
Sequence		I	L	A	L	N	Y	D	H	W	H	Y	S	V	V	A	R	Y	W	H	D	G	G	Q	W	N	D	D	A	E	L	N	F	G	N	G	N	F	N	V	R	S	T	G	W	G	G	Y	L	V	V	G	Y	N	F
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 1tly chain A Region: 31 - 294 Aligned: 248 Modelled: 248 Confidence: 100.0% Identity: 100% Fold: Transmembrane beta-barrels Superfamily: Tsx-like channel Family: Tsx-like channel Phyre2 PDB 2e9x chain B domain 2 Region: 101 - 122 Aligned: 22 Modelled: 22 Confidence: 20.4% Identity: 41% Fold: GINS/PriA/YqbF domain Superfamily: PriA/YqbF domain Family: PSF2 N-terminal domain-like Phyre2 PDB 2jna chain A domain 1 Region: 1 - 42 Aligned: 41 Modelled: 42 Confidence: 20.3% Identity: 39% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 3epz chain A Region: 116 - 127 Aligned: 12 Modelled: 12 Confidence: 20.2% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:dna (cytosine-5)-methyltransferase 1; PDBTitle: structure of the replication foci-targeting sequence of human dna2 cytosine methyltransferase dnmt1 Phyre2 PDB 3f09 chain B Region: 143 - 153 Aligned: 11 Modelled: 11 Confidence: 18.9% Identity: 27% PDB header:transferase Chain: B: PDB Molecule:holo-[acyl-carrier-protein] synthase; PDBTitle: 1.82 angstrom resolution crystal structure of holo-(acyl-carrier-2 protein) synthase (acps) from staphylococcus aureus Phyre2 PDB 1u8c chain B Region: 36 - 88 Aligned: 45 Modelled: 53 Confidence: 17.7% Identity: 16% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: a novel adaptation of the integrin psi domain revealed from its2 crystal structure Phyre2 PDB 3n6r chain K Region: 93 - 116 Aligned: 24 Modelled: 24 Confidence: 16.7% Identity: 25% PDB header:ligase Chain: K: PDB Molecule:propionyl-coa carboxylase, alpha subunit; PDBTitle: crystal structure of the holoenzyme of propionyl-coa carboxylase (pcc) Phyre2 PDB 2e9x chain F Region: 101 - 122 Aligned: 22 Modelled: 22 Confidence: 15.5% Identity: 41% PDB header:replication Chain: F: PDB Molecule:dna replication complex gins protein psf2; PDBTitle: the crystal structure of human gins core complex Phyre2 PDB 2j9g chain A domain 3 Region: 93 - 116 Aligned: 24 Modelled: 24 Confidence: 14.0% Identity: 29% Fold: ATP-grasp Superfamily: Glutathione synthetase ATP-binding domain-like Family: BC ATP-binding domain-like Phyre2 PDB 3u9s chain E Region: 93 - 116 Aligned: 24 Modelled: 24 Confidence: 13.7% Identity: 33% PDB header:ligase Chain: E: PDB Molecule:methylcrotonyl-coa carboxylase, alpha-subunit; PDBTitle: crystal structure of p. aeruginosa 3-methylcrotonyl-coa carboxylase2 (mcc) 750 kd holoenzyme, coa complex Phyre2 PDB 2x27 chain X Region: 241 - 294 Aligned: 54 Modelled: 54 Confidence: 13.1% Identity: 17% PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein oprg; PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa Phyre2 PDB 3g8c chain B Region: 91 - 116 Aligned: 26 Modelled: 26 Confidence: 12.5% Identity: 27% PDB header:ligase Chain: B: PDB Molecule:biotin carboxylase; PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion Phyre2 PDB 2k3a chain A Region: 1 - 34 Aligned: 34 Modelled: 34 Confidence: 12.5% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:chap domain protein; PDBTitle: nmr solution structure of staphylococcus saprophyticus chap2 (cysteine, histidine-dependent amidohydrolases/peptidases)3 domain protein. northeast structural genomics consortium4 target syr11 Phyre2 PDB 1w96 chain A domain 3 Region: 92 - 116 Aligned: 25 Modelled: 25 Confidence: 12.0% Identity: 24% Fold: ATP-grasp Superfamily: Glutathione synthetase ATP-binding domain-like Family: BC ATP-binding domain-like Phyre2 PDB 1gso chain A domain 3 Region: 94 - 116 Aligned: 23 Modelled: 23 Confidence: 10.0% Identity: 35% Fold: ATP-grasp Superfamily: Glutathione synthetase ATP-binding domain-like Family: BC ATP-binding domain-like Phyre2 PDB 2qdz chain A Region: 182 - 294 Aligned: 93 Modelled: 101 Confidence: 9.3% Identity: 17% PDB header:protein transport Chain: A: PDB Molecule:tpsb transporter fhac; PDBTitle: structure of the membrane protein fhac: a member of the2 omp85/tpsb transporter family Phyre2 PDB 2vpq chain A Region: 92 - 116 Aligned: 25 Modelled: 25 Confidence: 7.6% Identity: 32% PDB header:ligase Chain: A: PDB Molecule:acetyl-coa carboxylase; PDBTitle: crystal structure of biotin carboxylase from s. aureus2 complexed with amppnp Phyre2 PDB 3bg5 chain C Region: 93 - 116 Aligned: 24 Modelled: 24 Confidence: 7.6% Identity: 25% PDB header:ligase Chain: C: PDB Molecule:pyruvate carboxylase; PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase Phyre2 PDB 2pvp chain B Region: 203 - 236 Aligned: 34 Modelled: 34 Confidence: 7.5% Identity: 21% PDB header:ligase Chain: B: PDB Molecule:d-alanine-d-alanine ligase; PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori Phyre2 PDB 2gpw chain C Region: 91 - 116 Aligned: 26 Modelled: 26 Confidence: 7.3% Identity: 27% PDB header:ligase Chain: C: PDB Molecule:biotin carboxylase; PDBTitle: crystal structure of the biotin carboxylase subunit, f363a2 mutant, of acetyl-coa carboxylase from escherichia coli. Phyre2 1 d1tlya_ 2 d2e9xb2 3 d2jnaa1 4 c3epzA_ 5 c3f09B_ 6 c1u8cB_ 7 c3n6rK_ 8 c2e9xF_ 9 d2j9ga3 10 c3u9sE_ 11 c2x27X_ 12 c3g8cB_ 13 c2k3aA_ 14 d1w96a3 15 d1gsoa3 16 c2qdzA_ 17 c2vpqA_ 18 c3bg5C_ 19 c2pvpB_ 20 c2gpwC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1tlya_ 100.0 100 Fold:Transmembrane beta-barrels Superfamily:Tsx-like channel Family:Tsx-like channel 2 d2e9xb2 20.4 41 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:PSF2 N-terminal domain-like 3 d2jnaa1 20.3 39 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 4 c3epzA_ 20.2 33 PDB header:transferase Chain: A: PDB Molecule:dna (cytosine-5)-methyltransferase 1; PDBTitle: structure of the replication foci-targeting sequence of human dna2 cytosine methyltransferase dnmt1 5 c3f09B_ 18.9 27 PDB header:transferase Chain: B: PDB Molecule:holo-[acyl-carrier-protein] synthase; PDBTitle: 1.82 angstrom resolution crystal structure of holo-(acyl-carrier-2 protein) synthase (acps) from staphylococcus aureus 6 c1u8cB_ 17.7 16 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: a novel adaptation of the integrin psi domain revealed from its2 crystal structure 7 c3n6rK_ 16.7 25 PDB header:ligase Chain: K: PDB Molecule:propionyl-coa carboxylase, alpha subunit; PDBTitle: crystal structure of the holoenzyme of propionyl-coa carboxylase (pcc) 8 c2e9xF_ 15.5 41 PDB header:replication Chain: F: PDB Molecule:dna replication complex gins protein psf2; PDBTitle: the crystal structure of human gins core complex 9 d2j9ga3 14.0 29 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 10 c3u9sE_ 13.7 33 PDB header:ligase Chain: E: PDB Molecule:methylcrotonyl-coa carboxylase, alpha-subunit; PDBTitle: crystal structure of p. aeruginosa 3-methylcrotonyl-coa carboxylase2 (mcc) 750 kd holoenzyme, coa complex 11 c2x27X_ 13.1 17 PDB header:membrane protein Chain: X: PDB Molecule:outer membrane protein oprg; PDBTitle: crystal structure of the outer membrane protein oprg from2 pseudomonas aeruginosa 12 c3g8cB_ 12.5 27 PDB header:ligase Chain: B: PDB Molecule:biotin carboxylase; PDBTitle: crystal stucture of biotin carboxylase in complex with2 biotin, bicarbonate, adp and mg ion 13 c2k3aA_ 12.5 15 PDB header:hydrolase Chain: A: PDB Molecule:chap domain protein; PDBTitle: nmr solution structure of staphylococcus saprophyticus chap2 (cysteine, histidine-dependent amidohydrolases/peptidases)3 domain protein. northeast structural genomics consortium4 target syr11 14 d1w96a3 12.0 24 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 15 d1gsoa3 10.0 35 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 16 c2qdzA_ 9.3 17 PDB header:protein transport Chain: A: PDB Molecule:tpsb transporter fhac; PDBTitle: structure of the membrane protein fhac: a member of the2 omp85/tpsb transporter family 17 c2vpqA_ 7.6 32 PDB header:ligase Chain: A: PDB Molecule:acetyl-coa carboxylase; PDBTitle: crystal structure of biotin carboxylase from s. aureus2 complexed with amppnp 18 c3bg5C_ 7.6 25 PDB header:ligase Chain: C: PDB Molecule:pyruvate carboxylase; PDBTitle: crystal structure of staphylococcus aureus pyruvate2 carboxylase 19 c2pvpB_ 7.5 21 PDB header:ligase Chain: B: PDB Molecule:d-alanine-d-alanine ligase; PDBTitle: crystal structure of d-alanine-d-alanine ligase from helicobacter2 pylori 20 c2gpwC_ 7.3 27 PDB header:ligase Chain: C: PDB Molecule:biotin carboxylase; PDBTitle: crystal structure of the biotin carboxylase subunit, f363a2 mutant, of acetyl-coa carboxylase from escherichia coli. 21 c2hjwA_ not modelled 7.2 29 PDB header:ligase Chain: A: PDB Molecule:acetyl-coa carboxylase 2; PDBTitle: crystal structure of the bc domain of acc2 22 c1w96B_ not modelled 7.0 24 PDB header:ligase Chain: B: PDB Molecule:acetyl-coenzyme a carboxylase; PDBTitle: crystal structure of biotin carboxylase domain of acetyl-2 coenzyme a carboxylase from saccharomyces cerevisiae in3 complex with soraphen a 23 d1iu4a_ not modelled 6.5 21 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Microbial transglutaminase 24 d1ev11_ not modelled 6.4 19 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 25 c3iu0A_ not modelled 6.1 21 PDB header:transferase Chain: A: PDB Molecule:protein-glutamine gamma-glutamyltransferase; PDBTitle: structural basis for zymogen activation and substrate binding of2 transglutaminase from streptomyces mobaraense 26 c3lyvF_ not modelled 5.8 24 PDB header:chaperone Chain: F: PDB Molecule:ribosome-associated factor y; PDBTitle: crystal structure of a domain of ribosome-associated factor y from2 streptococcus pyogenes serotype m6. northeast structural genomics3 consortium target id dr64a 27 c3k6sB_ not modelled 5.8 15 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-2; PDBTitle: structure of integrin alphaxbeta2 ectodomain 28 c2ktlA_ not modelled 5.7 30 PDB header:ligase Chain: A: PDB Molecule:tyrosyl-trna synthetase; PDBTitle: structure of c-terminal domain from mttyrrs of a. nidulans 29 d1vkza3 not modelled 5.6 25 Fold:ATP-grasp Superfamily:Glutathione synthetase ATP-binding domain-like Family:BC ATP-binding domain-like 30 c2k0lA_ not modelled 5.6 12 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein a; PDBTitle: nmr structure of the transmembrane domain of the outer2 membrane protein a from klebsiella pneumoniae in dhpc3 micelles. 31 c3ouzA_ not modelled 5.5 15 PDB header:ligase Chain: A: PDB Molecule:biotin carboxylase; PDBTitle: crystal structure of biotin carboxylase-adp complex from campylobacter2 jejuni 32 c2q5xA_ not modelled 5.5 29 PDB header:protein transport Chain: A: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: crystal structure of the c-terminal domain of hnup98 33 c2jmmA_ not modelled 5.3 20 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein a; PDBTitle: nmr solution structure of a minimal transmembrane beta-2 barrel platform protein 34 d1jyaa_ not modelled 5.2 19 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone

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