Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	Y	S	H	D	N	W	S	A	I	L	A	H	I	G	K	P	E	E	L	D	T	S	A	R	N	A	G	A	L	T	R	R	R	E	I	R	D	A	A	T	L	L	R	L	G	L	A	Y	G	P	G	G	M	S	L	R	E	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																									?																				?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	A	W	A	Q	L	H	D	V	A	T	L	S	D	V	A	L	L	K	R	L	R	N	A	A	D	W	F	G	I	L	A	A	Q	T	L	A	V	R	A	A	V	T	G	C	T	S	G	K	R	L	R	L	V	D	G	T	A	I	S
Secondary structure
SS confidence
Disorder								?	?																																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	P	G	G	G	S	A	E	W	R	L	H	M	G	Y	D	P	H	T	C	Q	F	T	D	F	E	L	T	D	S	R	D	A	E	R	L	D	R	F	A	Q	T	A	D	E	I	R	I	A	D	R	G	F	G	S	R	P	E	C	I
Secondary structure
SS confidence
Disorder				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	S	L	A	F	G	E	A	D	Y	I	V	R	V	H	W	R	G	L	R	W	L	T	A	E	G	M	R	F	D	M	M	G	F	L	R	G	L	D	C	G	K	N	G	E	T	T	V	M	I	G	N	S	G	N	K	K	A	G	A
Secondary structure
SS confidence
Disorder																											?	?													?	?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	F	P	A	R	L	I	A	V	S	L	P	P	E	K	A	L	I	S	K	T	R	L	L	S	E	N	R	R	K	G	R	V	V	Q	A	E	T	L	E	A	A	G	H	V	L	L	L	T	S	L	P	E	D	E	Y	S	A	E	Q
Secondary structure
SS confidence
Disorder														?								?	?	?		?	?																											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	A	D	C	Y	R	L	R	W	Q	I	E	L	A	F	K	R	L	K	S	L	L	H	L	D	A	L	R	A	K	E	P	E	L	A	K	A	W	I	F	A	N	L	L	A	A	F	L	I	D	D	I	I	Q	P	S	L	D	F	P
Secondary structure
SS confidence
Disorder																																																										?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370
Sequence		P	R	S	A	G	S	E	K	K	N
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 1mus chain A Region: 18 - 364 Aligned: 322 Modelled: 332 Confidence: 99.9% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 111 - 364 Aligned: 224 Modelled: 232 Confidence: 99.9% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 3pvi chain A Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 28.3% Identity: 23% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease PvuII Phyre2 PDB 2adc chain A Region: 271 - 307 Aligned: 37 Modelled: 37 Confidence: 26.8% Identity: 19% PDB header:rna binding protein/rna Chain: A: PDB Molecule:polypyrimidine tract-binding protein 1; PDBTitle: solution structure of polypyrimidine tract binding protein2 rbd34 complexed with cucucu rna Phyre2 PDB 3hyi chain A Region: 19 - 91 Aligned: 61 Modelled: 73 Confidence: 19.7% Identity: 21% PDB header:transcription regulator Chain: A: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima Phyre2 PDB 2adc chain A domain 1 Region: 282 - 307 Aligned: 26 Modelled: 26 Confidence: 18.8% Identity: 15% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 3hef chain B Region: 47 - 91 Aligned: 40 Modelled: 45 Confidence: 18.1% Identity: 15% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 1qm9 chain A Region: 281 - 307 Aligned: 27 Modelled: 27 Confidence: 17.3% Identity: 15% PDB header:ribonucleoprotein Chain: A: PDB Molecule:polypyrimidine tract-binding protein; PDBTitle: nmr, representative structure Phyre2 PDB 3ksk chain A Region: 4 - 29 Aligned: 26 Modelled: 26 Confidence: 15.6% Identity: 23% PDB header:hydrolase Chain: A: PDB Molecule:type-2 restriction enzyme pvuii; PDBTitle: crystal structure of single chain pvuii Phyre2 PDB 2kvi chain A Region: 283 - 307 Aligned: 25 Modelled: 25 Confidence: 12.9% Identity: 20% PDB header:rna binding protein Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein 3; PDBTitle: structure of nab3 rrm Phyre2 PDB 2cts chain A Region: 21 - 97 Aligned: 77 Modelled: 77 Confidence: 11.8% Identity: 10% Fold: Citrate synthase Superfamily: Citrate synthase Family: Citrate synthase Phyre2 PDB 2xig chain A Region: 21 - 86 Aligned: 65 Modelled: 66 Confidence: 10.9% Identity: 11% PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites Phyre2 PDB 1ug7 chain A Region: 5 - 27 Aligned: 20 Modelled: 23 Confidence: 10.5% Identity: 30% Fold: Four-helical up-and-down bundle Superfamily: Domain from hypothetical 2610208m17rik protein Family: Domain from hypothetical 2610208m17rik protein Phyre2 PDB 2q9r chain A Region: 27 - 49 Aligned: 23 Modelled: 23 Confidence: 10.1% Identity: 13% PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a duf416 family protein (sbal_3149) from2 shewanella baltica os155 at 1.91 a resolution Phyre2 PDB 1x4d chain A domain 1 Region: 277 - 304 Aligned: 28 Modelled: 28 Confidence: 9.6% Identity: 7% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 1csh chain A Region: 21 - 97 Aligned: 77 Modelled: 77 Confidence: 9.1% Identity: 12% Fold: Citrate synthase Superfamily: Citrate synthase Family: Citrate synthase Phyre2 PDB 2qkl chain B domain 1 Region: 287 - 315 Aligned: 23 Modelled: 29 Confidence: 9.1% Identity: 48% Fold: Dcp2 domain-like Superfamily: Dcp2 domain-like Family: Dcp2 box A domain Phyre2 PDB 2ezh chain A Region: 58 - 86 Aligned: 29 Modelled: 29 Confidence: 8.9% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 2ezi chain A Region: 58 - 83 Aligned: 26 Modelled: 26 Confidence: 7.8% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 2yy0 chain D Region: 313 - 339 Aligned: 27 Modelled: 27 Confidence: 7.6% Identity: 26% PDB header:transcription Chain: D: PDB Molecule:c-myc-binding protein; PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens Phyre2 1 d1musa_ 2 d1b7ea_ 3 d3pvia_ 4 c2adcA_ 5 c3hyiA_ 6 d2adca1 7 c3hefB_ 8 c1qm9A_ 9 c3kskA_ 10 c2kviA_ 11 d2ctsa_ 12 c2xigA_ 13 d1ug7a_ 14 c2q9rA_ 15 d1x4da1 16 d1csha_ 17 d2qklb1 18 d2ezha_ 19 d2ezia_ 20 c2yy0D_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d1musa_ 99.9 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 99.9 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d3pvia_ 28.3 23 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease PvuII 4 c2adcA_ 26.8 19 PDB header:rna binding protein/rna Chain: A: PDB Molecule:polypyrimidine tract-binding protein 1; PDBTitle: solution structure of polypyrimidine tract binding protein2 rbd34 complexed with cucucu rna 5 c3hyiA_ 19.7 21 PDB header:transcription regulator Chain: A: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima 6 d2adca1 18.8 15 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 7 c3hefB_ 18.1 15 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 8 c1qm9A_ 17.3 15 PDB header:ribonucleoprotein Chain: A: PDB Molecule:polypyrimidine tract-binding protein; PDBTitle: nmr, representative structure 9 c3kskA_ 15.6 23 PDB header:hydrolase Chain: A: PDB Molecule:type-2 restriction enzyme pvuii; PDBTitle: crystal structure of single chain pvuii 10 c2kviA_ 12.9 20 PDB header:rna binding protein Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein 3; PDBTitle: structure of nab3 rrm 11 d2ctsa_ 11.8 10 Fold:Citrate synthase Superfamily:Citrate synthase Family:Citrate synthase 12 c2xigA_ 10.9 11 PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites 13 d1ug7a_ 10.5 30 Fold:Four-helical up-and-down bundle Superfamily:Domain from hypothetical 2610208m17rik protein Family:Domain from hypothetical 2610208m17rik protein 14 c2q9rA_ 10.1 13 PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a duf416 family protein (sbal_3149) from2 shewanella baltica os155 at 1.91 a resolution 15 d1x4da1 9.6 7 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 16 d1csha_ 9.1 12 Fold:Citrate synthase Superfamily:Citrate synthase Family:Citrate synthase 17 d2qklb1 9.1 48 Fold:Dcp2 domain-like Superfamily:Dcp2 domain-like Family:Dcp2 box A domain 18 d2ezha_ 8.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 19 d2ezia_ 7.8 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 20 c2yy0D_ 7.6 26 PDB header:transcription Chain: D: PDB Molecule:c-myc-binding protein; PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens 21 d1ftha_ not modelled 7.6 4 Fold:4'-phosphopantetheinyl transferase Superfamily:4'-phosphopantetheinyl transferase Family:Holo-(acyl carrier protein) synthase ACPS 22 d1nkua_ not modelled 7.3 14 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag) 23 c2cg5A_ not modelled 7.1 15 PDB header:transferase/hydrolase Chain: A: PDB Molecule:l-aminoadipate-semialdehyde dehydrogenase- PDBTitle: structure of aminoadipate-semialdehyde dehydrogenase-2 phosphopantetheinyl transferase in complex with cytosolic3 acyl carrier protein and coenzyme a 24 d2fq4a1 not modelled 7.0 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 25 c1u78A_ not modelled 7.0 14 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 26 c2osqA_ not modelled 6.8 16 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: nmr structure of rrm-1 of yeast npl3 protein 27 c1bcoA_ not modelled 6.2 13 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 28 d1wf1a_ not modelled 6.2 7 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 29 d1x5ua1 not modelled 6.1 9 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 30 c2xnqA_ not modelled 6.0 20 PDB header:rna binding protein Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein 3; PDBTitle: structural insights into cis element recognition of non-2 polyadenylated rnas by the nab3-rrm 31 c3d1nK_ not modelled 5.9 18 PDB header:transcription regulator/dna Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1; PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter 32 d1ro5a_ not modelled 5.8 16 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:Autoinducer synthetase 33 c2jg6A_ not modelled 5.6 7 PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus 34 d1wg1a_ not modelled 5.6 25 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 35 c3nnhA_ not modelled 5.5 8 PDB header:rna binding protein/rna Chain: A: PDB Molecule:cugbp elav-like family member 1; PDBTitle: crystal structure of the cugbp1 rrm1 with guuguuuuguuu rna 36 c2jvoA_ not modelled 5.3 15 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: segmental isotope labeling of npl3

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