Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	T	A	L	T	D	N	T	Q	G	A	A	G	L	E	L	Y	E	V	Y	N	N	G	Y	P	T	A	Y	G	N	I	I	H	L	K	G	M	T	A	V	G	E	G	E	L	L	I	G	W	S	G	T	S	G	A	H	A	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																												?	?	?	?														?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	F	I	R	S	R	R	D	T	T	D	A	N	W	S	P	W	A	Q	L	Y	T	S	A	H	P	P	A	E	F	Y	P	V	G	A	P	I	P	W	P	S	D	T	V	P	S	G	Y	A	L	M	Q	G	Q	T	F	D	K	S	A
Secondary structure
SS confidence
Disorder									?	?	?	?	?	?											?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	P	K	L	A	V	A	Y	P	S	G	V	I	P	D	M	R	G	W	T	I	K	G	K	P	A	S	G	R	A	V	L	S	Q	E	Q	D	G	I	K	S	H	T	H	S	A	S	A	S	S	T	D	L	G	T	E	T	T	S	S
Secondary structure
SS confidence
Disorder																																		?	?	?	?					?	?			?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	D	Y	G	T	K	S	T	N	N	T	G	A	H	T	H	S	I	S	G	T	A	N	S	A	G	A	H	Q	H	K	S	S	G	A	F	G	G	T	N	T	S	I	F	P	N	G	Y	T	A	I	S	N	L	S	A	G	I	M	S
Secondary structure
SS confidence
Disorder						?	?	?		?	?		?	?	?	?		?					?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?								?		?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		T	T	S	G	S	G	Q	T	R	N	A	G	K	T	S	S	D	G	A	H	T	H	S	L	S	G	T	A	A	S	A	G	A	H	A	H	T	V	G	I	G	A	H	T	H	S	V	A	I	G	S	H	G	H	T	I	T	V	N	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?															?	?		?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320
Sequence		A	G	N	A	E	N	T	V	K	N	I	A	F	N	Y	I	V	R	L	A
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 2xgf chain A Region: 90 - 320 Aligned: 215 Modelled: 216 Confidence: 100.0% Identity: 70% PDB header:viral protein Chain: A: PDB Molecule:long tail fiber protein p37; PDBTitle: structure of the bacteriophage t4 long tail fibre needle-2 shaped receptor-binding tip Phyre2 PDB 1pdi chain Q Region: 81 - 319 Aligned: 186 Modelled: 186 Confidence: 100.0% Identity: 19% PDB header:structural protein Chain: Q: PDB Molecule:short tail fiber protein; PDBTitle: fitting of the c-terminal part of the short tail fibers2 into the cryo-em reconstruction of t4 baseplate Phyre2 PDB 1ocy chain A Region: 83 - 319 Aligned: 177 Modelled: 179 Confidence: 100.0% Identity: 21% Fold: Receptor-binding domain of short tail fibre protein gp12 Superfamily: Receptor-binding domain of short tail fibre protein gp12 Family: Receptor-binding domain of short tail fibre protein gp12 Phyre2 PDB 1h6w chain A Region: 4 - 137 Aligned: 131 Modelled: 134 Confidence: 99.5% Identity: 17% PDB header:structural protein Chain: A: PDB Molecule:bacteriophage t4 short tail fibre; PDBTitle: crystal structure of a heat- and protease-stable fragment2 of the bacteriophage t4 short fibre Phyre2 PDB 2fkk chain A Region: 79 - 200 Aligned: 104 Modelled: 105 Confidence: 88.3% Identity: 15% PDB header:viral protein Chain: A: PDB Molecule:baseplate structural protein gp10; PDBTitle: crystal structure of the c-terminal domain of the bacteriophage t42 gene product 10 Phyre2 PDB 2fl8 chain N Region: 79 - 213 Aligned: 122 Modelled: 134 Confidence: 68.1% Identity: 16% PDB header:virus/viral protein Chain: N: PDB Molecule:baseplate structural protein gp10; PDBTitle: fitting of the gp10 trimer structure into the cryoem map of the2 bacteriophage t4 baseplate in the hexagonal conformation. Phyre2 PDB 1m5h chain A domain 2 Region: 94 - 138 Aligned: 39 Modelled: 45 Confidence: 38.2% Identity: 26% Fold: Ferredoxin-like Superfamily: Formylmethanofuran:tetrahydromethanopterin formyltransferase Family: Formylmethanofuran:tetrahydromethanopterin formyltransferase Phyre2 PDB 1m5s chain A domain 2 Region: 93 - 138 Aligned: 40 Modelled: 46 Confidence: 33.9% Identity: 23% Fold: Ferredoxin-like Superfamily: Formylmethanofuran:tetrahydromethanopterin formyltransferase Family: Formylmethanofuran:tetrahydromethanopterin formyltransferase Phyre2 PDB 1m5h chain F Region: 94 - 139 Aligned: 40 Modelled: 46 Confidence: 21.3% Identity: 25% PDB header:transferase Chain: F: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: formylmethanofuran:tetrahydromethanopterin2 formyltransferase from archaeoglobus fulgidus Phyre2 PDB 1m5s chain C Region: 94 - 138 Aligned: 39 Modelled: 45 Confidence: 17.6% Identity: 23% PDB header:transferase Chain: C: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: formylmethanofuran:tetrahydromethanopterin2 fromyltransferase from methanosarcina barkeri Phyre2 PDB 2pfc chain A Region: 116 - 141 Aligned: 26 Modelled: 26 Confidence: 9.9% Identity: 38% PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein rv0098/mt0107; PDBTitle: structure of mycobacterium tuberculosis rv0098 Phyre2 PDB 2x3l chain A Region: 91 - 104 Aligned: 14 Modelled: 14 Confidence: 7.8% Identity: 43% PDB header:lyase Chain: A: PDB Molecule:orn/lys/arg decarboxylase family protein; PDBTitle: crystal structure of the orn_lys_arg decarboxylase family2 protein sar0482 from methicillin-resistant staphylococcus3 aureus Phyre2 PDB 1fmd chain 1 Region: 91 - 189 Aligned: 58 Modelled: 72 Confidence: 7.4% Identity: 28% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Picornaviridae-like VP (VP1, VP2, VP3 and VP4) Phyre2 PDB 1ftr chain A domain 2 Region: 94 - 137 Aligned: 38 Modelled: 44 Confidence: 7.2% Identity: 24% Fold: Ferredoxin-like Superfamily: Formylmethanofuran:tetrahydromethanopterin formyltransferase Family: Formylmethanofuran:tetrahydromethanopterin formyltransferase Phyre2 PDB 1k25 chain A domain 2 Region: 133 - 142 Aligned: 10 Modelled: 10 Confidence: 7.0% Identity: 60% Fold: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Phyre2 PDB 1pyy chain A domain 2 Region: 132 - 142 Aligned: 11 Modelled: 11 Confidence: 6.8% Identity: 55% Fold: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family: Penicillin-binding protein 2x (pbp-2x), c-terminal domain Phyre2 PDB 1c4k chain A domain 3 Region: 91 - 101 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 36% Fold: Ornithine decarboxylase C-terminal domain Superfamily: Ornithine decarboxylase C-terminal domain Family: Ornithine decarboxylase C-terminal domain Phyre2 PDB 2wzr chain 1 Region: 91 - 130 Aligned: 39 Modelled: 40 Confidence: 5.8% Identity: 18% PDB header:virus Chain: 1: PDB Molecule:polyprotein; PDBTitle: the structure of foot and mouth disease virus serotype sat1 Phyre2 PDB 3kio chain B Region: 95 - 142 Aligned: 37 Modelled: 48 Confidence: 5.7% Identity: 19% PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease h2 subunit b; PDBTitle: mouse rnase h2 complex Phyre2 PDB 3n75 chain E Region: 91 - 101 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 45% PDB header:lyase Chain: E: PDB Molecule:lysine decarboxylase, inducible; PDBTitle: x-ray crystal structure of the escherichia coli inducible lysine2 decarboxylase ldci Phyre2 1 c2xgfA_ 2 c1pdiQ_ 3 d1ocya_ 4 c1h6wA_ 5 c2fkkA_ 6 c2fl8N_ 7 d1m5ha2 8 d1m5sa2 9 c1m5hF_ 10 c1m5sC_ 11 c2pfcA_ 12 c2x3lA_ 13 d1fmd1_ 14 d1ftra2 15 d1k25a2 16 d1pyya2 17 d1c4ka3 18 c2wzr1_ 19 c3kioB_ 20 c3n75E_ 21 22

Detailed template information

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

1 c2xgfA_ 100.0 70 PDB header:viral protein Chain: A: PDB Molecule:long tail fiber protein p37; PDBTitle: structure of the bacteriophage t4 long tail fibre needle-2 shaped receptor-binding tip 2 c1pdiQ_ 100.0 19 PDB header:structural protein Chain: Q: PDB Molecule:short tail fiber protein; PDBTitle: fitting of the c-terminal part of the short tail fibers2 into the cryo-em reconstruction of t4 baseplate 3 d1ocya_ 100.0 21 Fold:Receptor-binding domain of short tail fibre protein gp12 Superfamily:Receptor-binding domain of short tail fibre protein gp12 Family:Receptor-binding domain of short tail fibre protein gp12 4 c1h6wA_ 99.5 17 PDB header:structural protein Chain: A: PDB Molecule:bacteriophage t4 short tail fibre; PDBTitle: crystal structure of a heat- and protease-stable fragment2 of the bacteriophage t4 short fibre 5 c2fkkA_ 88.3 15 PDB header:viral protein Chain: A: PDB Molecule:baseplate structural protein gp10; PDBTitle: crystal structure of the c-terminal domain of the bacteriophage t42 gene product 10 6 c2fl8N_ 68.1 16 PDB header:virus/viral protein Chain: N: PDB Molecule:baseplate structural protein gp10; PDBTitle: fitting of the gp10 trimer structure into the cryoem map of the2 bacteriophage t4 baseplate in the hexagonal conformation. 7 d1m5ha2 38.2 26 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 8 d1m5sa2 33.9 23 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 9 c1m5hF_ 21.3 25 PDB header:transferase Chain: F: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: formylmethanofuran:tetrahydromethanopterin2 formyltransferase from archaeoglobus fulgidus 10 c1m5sC_ 17.6 23 PDB header:transferase Chain: C: PDB Molecule:formylmethanofuran--tetrahydromethanopterin PDBTitle: formylmethanofuran:tetrahydromethanopterin2 fromyltransferase from methanosarcina barkeri 11 c2pfcA_ 9.9 38 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein rv0098/mt0107; PDBTitle: structure of mycobacterium tuberculosis rv0098 12 c2x3lA_ 7.8 43 PDB header:lyase Chain: A: PDB Molecule:orn/lys/arg decarboxylase family protein; PDBTitle: crystal structure of the orn_lys_arg decarboxylase family2 protein sar0482 from methicillin-resistant staphylococcus3 aureus 13 d1fmd1_ 7.4 28 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Picornaviridae-like VP (VP1, VP2, VP3 and VP4) 14 d1ftra2 7.2 24 Fold:Ferredoxin-like Superfamily:Formylmethanofuran:tetrahydromethanopterin formyltransferase Family:Formylmethanofuran:tetrahydromethanopterin formyltransferase 15 d1k25a2 7.0 60 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 16 d1pyya2 6.8 55 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 17 d1c4ka3 6.3 36 Fold:Ornithine decarboxylase C-terminal domain Superfamily:Ornithine decarboxylase C-terminal domain Family:Ornithine decarboxylase C-terminal domain 18 c2wzr1_ 5.8 18 PDB header:virus Chain: 1: PDB Molecule:polyprotein; PDBTitle: the structure of foot and mouth disease virus serotype sat1 19 c3kioB_ 5.7 19 PDB header:hydrolase Chain: B: PDB Molecule:ribonuclease h2 subunit b; PDBTitle: mouse rnase h2 complex 20 c3n75E_ 5.5 45 PDB header:lyase Chain: E: PDB Molecule:lysine decarboxylase, inducible; PDBTitle: x-ray crystal structure of the escherichia coli inducible lysine2 decarboxylase ldci 21 c2vycA_ not modelled 5.4 25 PDB header:lyase Chain: A: PDB Molecule:biodegradative arginine decarboxylase; PDBTitle: crystal structure of acid induced arginine decarboxylase2 from e. coli 22 d1uptb_ not modelled 5.4 22 Fold:GRIP domain Superfamily:GRIP domain Family:GRIP 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