Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	I	G	Q	A	L	D	L	V	S	R	Y	D	S	L	R	N	P	L	T	S	L	G	D	Y	L	D	P	E	L	I	S	R	C	L	A	E	S	G	T	V	T	L	R	K	R	R	L	P	L	E	M	M	V	W	C	I	V	G
Secondary structure
SS confidence
Disorder		?	?					?					?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	A	L	E	R	K	E	P	L	H	Q	I	V	N	R	L	D	I	M	L	P	G	N	R	P	F	V	A	P	S	A	V	I	Q	A	R	Q	R	L	G	S	E	A	V	R	R	V	F	T	K	T	A	Q	L	W	H	N	A	T	P
Secondary structure
SS confidence
Disorder					?	?																		?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		H	P	H	W	C	G	L	T	L	L	A	I	D	G	V	F	W	R	T	P	D	T	P	E	N	D	A	A	F	P	R	Q	T	H	A	G	N	P	A	L	Y	P	Q	V	K	M	V	C	Q	M	E	L	T	S	H	L	L	T	A	A
Secondary structure
SS confidence
Disorder																																		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	F	G	T	M	K	N	S	E	N	E	L	A	E	Q	L	I	E	Q	T	G	D	N	T	L	T	L	M	D	K	G	Y	Y	S	L	G	L	L	N	A	W	S	L	A	G	E	H	R	H	W	M	I	P	L	R	K	G	A	Q	Y
Secondary structure
SS confidence
Disorder																																																									?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	E	I	R	K	L	G	K	G	D	H	L	V	K	L	K	T	S	P	Q	A	R	K	K	W	P	G	L	G	N	E	V	T	A	R	L	L	T	V	T	R	K	G	K	V	C	H	L	L	T	S	M	T	D	A	M	R	F	P	G
Secondary structure
SS confidence
Disorder						?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	E	M	G	D	L	Y	S	H	R	W	E	I	E	L	G	Y	R	E	I	K	Q	T	M	Q	R	S	R	L	T	L	R	S	K	K	P	E	L	V	E	Q	E	L	W	G	V	L	L	A	Y	N	L	V	R	Y	Q	M	I	K	M
Secondary structure
SS confidence
Disorder																																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	E	H	L	K	G	Y	W	P	N	Q	L	S	F	S	E	S	C	G	M	V	M	R	M	L	M	T	L	Q	G	A	S	P	G	R	I	P	E	L	M	R	D	L	A	S	M	G	Q	L	V	K	L	P	T	R	R	E	R	A	F
Secondary structure
SS confidence
Disorder					?		?																						?			?	?																		?	?			?	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.
Sequence		P	R	V	V	K	E	R	P	W	K	Y	P	T	A	P	K	K	S	Q	S	V	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 1mus chain A Region: 29 - 408 Aligned: 354 Modelled: 378 Confidence: 99.9% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 111 - 358 Aligned: 222 Modelled: 227 Confidence: 99.9% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 2gm3 chain A domain 1 Region: 129 - 200 Aligned: 72 Modelled: 71 Confidence: 41.0% Identity: 14% Fold: Adenine nucleotide alpha hydrolase-like Superfamily: Adenine nucleotide alpha hydrolases-like Family: Universal stress protein-like Phyre2 PDB 2yy0 chain D Region: 315 - 343 Aligned: 27 Modelled: 29 Confidence: 22.3% Identity: 19% 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 PDB 1ud9 chain A domain 1 Region: 100 - 149 Aligned: 50 Modelled: 50 Confidence: 17.8% Identity: 16% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 1rwz chain A domain 1 Region: 101 - 149 Aligned: 49 Modelled: 49 Confidence: 17.3% Identity: 20% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 1plq chain A domain 1 Region: 101 - 149 Aligned: 49 Modelled: 49 Confidence: 12.3% Identity: 12% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 1bco chain A Region: 129 - 193 Aligned: 52 Modelled: 65 Confidence: 11.8% Identity: 10% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 2cg5 chain A Region: 10 - 64 Aligned: 54 Modelled: 55 Confidence: 11.6% Identity: 13% 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 Phyre2 PDB 1ro5 chain A Region: 289 - 313 Aligned: 25 Modelled: 25 Confidence: 11.0% Identity: 12% Fold: Acyl-CoA N-acyltransferases (Nat) Superfamily: Acyl-CoA N-acyltransferases (Nat) Family: Autoinducer synthetase Phyre2 PDB 2prd chain A Region: 272 - 321 Aligned: 50 Modelled: 50 Confidence: 10.4% Identity: 18% Fold: OB-fold Superfamily: Inorganic pyrophosphatase Family: Inorganic pyrophosphatase Phyre2 PDB 4a4k chain I Region: 301 - 324 Aligned: 24 Modelled: 24 Confidence: 8.7% Identity: 13% PDB header:hydrolase Chain: I: PDB Molecule:antiviral helicase ski2; PDBTitle: crystal structure of the s. cerevisiae ski2 insertion domain Phyre2 PDB 1iz5 chain A domain 1 Region: 100 - 149 Aligned: 50 Modelled: 50 Confidence: 8.5% Identity: 16% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 2cpw chain A Region: 13 - 40 Aligned: 28 Modelled: 28 Confidence: 8.3% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cbl-interacting protein sts-1 variant; PDBTitle: solution structure of rsgi ruh-031, a uba domain from human2 cdna Phyre2 PDB 1u7b chain A domain 1 Region: 100 - 149 Aligned: 50 Modelled: 50 Confidence: 8.3% Identity: 14% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 2dak chain A Region: 11 - 40 Aligned: 30 Modelled: 30 Confidence: 7.9% Identity: 7% PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the second uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) Phyre2 PDB 2ix2 chain A Region: 100 - 149 Aligned: 50 Modelled: 50 Confidence: 7.4% Identity: 2% PDB header:replication Chain: A: PDB Molecule:dna polymerase sliding clamp b; PDBTitle: crystal structure of the heterotrimeric pcna from2 sulfolobus solfataricus Phyre2 PDB 3rhf chain B Region: 192 - 222 Aligned: 31 Modelled: 31 Confidence: 6.8% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:putative polyphosphate kinase 2 family protein; PDBTitle: crystal structure of polyphosphate kinase 2 from arthrobacter2 aurescens tc1 Phyre2 PDB 1ud9 chain C Region: 100 - 149 Aligned: 50 Modelled: 50 Confidence: 6.0% Identity: 16% PDB header:dna binding protein Chain: C: PDB Molecule:dna polymerase sliding clamp a; PDBTitle: crystal structure of proliferating cell nuclear antigen (pcna) homolog2 from sulfolobus tokodaii Phyre2 PDB 1ngn chain A Region: 12 - 95 Aligned: 58 Modelled: 65 Confidence: 6.0% Identity: 14% Fold: DNA-glycosylase Superfamily: DNA-glycosylase Family: Mismatch glycosylase Phyre2 1 d1musa_ 2 d1b7ea_ 3 d2gm3a1 4 c2yy0D_ 5 d1ud9a1 6 d1rwza1 7 d1plqa1 8 c1bcoA_ 9 c2cg5A_ 10 d1ro5a_ 11 d2prda_ 12 c4a4kI_ 13 d1iz5a1 14 c2cpwA_ 15 d1u7ba1 16 c2dakA_ 17 c2ix2A_ 18 c3rhfB_ 19 c1ud9C_ 20 d1ngna_ 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 d1musa_ 99.9 14 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 d2gm3a1 41.0 14 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Adenine nucleotide alpha hydrolases-like Family:Universal stress protein-like 4 c2yy0D_ 22.3 19 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 5 d1ud9a1 17.8 16 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 6 d1rwza1 17.3 20 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 7 d1plqa1 12.3 12 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 8 c1bcoA_ 11.8 10 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 9 c2cg5A_ 11.6 13 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 10 d1ro5a_ 11.0 12 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:Autoinducer synthetase 11 d2prda_ 10.4 18 Fold:OB-fold Superfamily:Inorganic pyrophosphatase Family:Inorganic pyrophosphatase 12 c4a4kI_ 8.7 13 PDB header:hydrolase Chain: I: PDB Molecule:antiviral helicase ski2; PDBTitle: crystal structure of the s. cerevisiae ski2 insertion domain 13 d1iz5a1 8.5 16 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 14 c2cpwA_ 8.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cbl-interacting protein sts-1 variant; PDBTitle: solution structure of rsgi ruh-031, a uba domain from human2 cdna 15 d1u7ba1 8.3 14 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 16 c2dakA_ 7.9 7 PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the second uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) 17 c2ix2A_ 7.4 2 PDB header:replication Chain: A: PDB Molecule:dna polymerase sliding clamp b; PDBTitle: crystal structure of the heterotrimeric pcna from2 sulfolobus solfataricus 18 c3rhfB_ 6.8 13 PDB header:transferase Chain: B: PDB Molecule:putative polyphosphate kinase 2 family protein; PDBTitle: crystal structure of polyphosphate kinase 2 from arthrobacter2 aurescens tc1 19 c1ud9C_ 6.0 16 PDB header:dna binding protein Chain: C: PDB Molecule:dna polymerase sliding clamp a; PDBTitle: crystal structure of proliferating cell nuclear antigen (pcna) homolog2 from sulfolobus tokodaii 20 d1ngna_ 6.0 14 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:Mismatch glycosylase 21 c2kkuA_ not modelled 5.8 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein af2351 from archaeoglobus2 fulgidus. northeast structural genomics consortium target3 att9/ontario center for structural proteomics target af2351 22 c3czqA_ not modelled 5.7 10 PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from2 sinorhizobium meliloti 23 c1rwzA_ not modelled 5.7 20 PDB header:replication Chain: A: PDB Molecule:dna polymerase sliding clamp; PDBTitle: crystal structure of proliferating cell nuclear antigen (pcna) from a.2 fulgidus 24 c3qjaA_ not modelled 5.6 13 PDB header:lyase Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase; PDBTitle: crystal structure of the mycobacterium tuberculosis indole-3-glycerol2 phosphate synthase (trpc) in apo form 25 d1a53a_ not modelled 5.5 14 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Tryptophan biosynthesis enzymes 26 c2vs1A_ not modelled 5.5 11 PDB header:transferase Chain: A: PDB Molecule:uncharacterized rna methyltransferase pyrab10780; PDBTitle: the crystal structure of pyrococcus abyssi trna (uracil-54,2 c5)-methyltransferase in complex with s-adenosyl-l-3 homocysteine 27 d2itba1 not modelled 5.5 21 Fold:Ferritin-like Superfamily:Ferritin-like Family:MiaE-like 28 c2ix2B_ not modelled 5.3 12 PDB header:replication Chain: B: PDB Molecule:dna polymerase sliding clamp c; PDBTitle: crystal structure of the heterotrimeric pcna from2 sulfolobus solfataricus 29 c3emjL_ not modelled 5.2 22 PDB header:hydrolase Chain: L: PDB Molecule:inorganic pyrophosphatase; PDBTitle: 2.2 a crystal structure of inorganic pyrophosphatase from2 rickettsia prowazekii (p21 form) 30 c3czpA_ not modelled 5.2 13 PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from pseudomonas2 aeruginosa pa01 31 d2jfga2 not modelled 5.2 14 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 32 d2cpwa1 not modelled 5.1 18 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA 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