Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	Q	L	T	F	A	D	S	E	F	S	S	K	R	R	Q	T	R	K	E	I	F	L	S	R	M	E	Q	I	L	P	W	Q	N	M	V	E	V	I	E	P	F	Y	P	K	A	G	N	G	R	R	P	Y	P	L	E	T	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?										?	?	?	?	?	?																									?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	R	I	H	C	M	Q	H	W	Y	N	L	S	D	G	A	M	E	D	A	L	Y	E	I	A	S	M	R	L	F	A	R	L	S	L	D	S	A	L	P	D	R	T	T	I	M	N	F	R	H	L	L	E	Q	H	Q	L	A	R	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	F	K	T	I	N	R	W	L	A	E	A	G	V	M	M	T	Q	G	T	L	V	D	A	T	I	I	E	A	P	S	S	T	K	N	K	E	Q	Q	R	D	P	E	M	H	Q	T	K	K	G	N	Q	W	H	F	G	M	K	A	H
Secondary structure
SS confidence
Disorder																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	G	V	D	A	K	S	G	L	T	H	S	L	V	T	T	A	A	N	E	H	D	L	N	Q	L	G	N	L	L	H	G	E	E	Q	F	V	S	A	D	A	G	Y	Q	G	A	P	Q	R	E	E	L	A	E	V	D	V	D	W	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	A	E	R	P	G	K	V	R	T	L	K	Q	H	P	R	K	N	K	T	A	I	N	I	E	Y	M	K	A	S	I	R	A	R	V	E	H	P	F	R	I	I	K	R	Q	F	G	F	V	K	A	R	Y	K	G	L	L	K	N	D
Secondary structure
SS confidence
Disorder							?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.
Sequence		N	Q	L	A	M	L	F	T	L	A	N	L	F	R	A	D	Q	M	I	R	Q	W	E	R	S	H
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: 106 - 309 Aligned: 194 Modelled: 204 Confidence: 98.5% Identity: 10% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 121 - 321 Aligned: 171 Modelled: 175 Confidence: 98.1% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1cxq chain A Region: 132 - 311 Aligned: 130 Modelled: 132 Confidence: 91.1% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1asu chain A Region: 179 - 311 Aligned: 111 Modelled: 111 Confidence: 85.6% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A domain 2 Region: 132 - 311 Aligned: 134 Modelled: 134 Confidence: 67.9% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1bg1 chain A Region: 32 - 137 Aligned: 88 Modelled: 101 Confidence: 66.6% Identity: 14% PDB header:transcription/dna Chain: A: PDB Molecule:protein (transcription factor stat3b); PDBTitle: transcription factor stat3b/dna complex Phyre2 PDB 3nf9 chain A Region: 179 - 311 Aligned: 108 Modelled: 111 Confidence: 64.5% Identity: 13% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design Phyre2 PDB 1yvl chain B Region: 32 - 137 Aligned: 87 Modelled: 101 Confidence: 62.4% Identity: 14% PDB header:signaling protein Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: structure of unphosphorylated stat1 Phyre2 PDB 3hef chain B Region: 75 - 111 Aligned: 34 Modelled: 37 Confidence: 51.6% 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 1c0m chain A Region: 179 - 284 Aligned: 84 Modelled: 84 Confidence: 47.2% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1bco chain A domain 2 Region: 132 - 283 Aligned: 116 Modelled: 117 Confidence: 46.2% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 PDB 1hyv chain A Region: 179 - 314 Aligned: 103 Modelled: 107 Confidence: 40.9% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1bf5 chain A Region: 32 - 137 Aligned: 78 Modelled: 83 Confidence: 36.9% Identity: 17% PDB header:gene regulation/dna Chain: A: PDB Molecule:signal transducer and activator of transcription PDBTitle: tyrosine phosphorylated stat-1/dna complex Phyre2 PDB 3f9k chain V Region: 179 - 311 Aligned: 108 Modelled: 111 Confidence: 36.4% Identity: 13% PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd Phyre2 PDB 1exq chain A Region: 181 - 311 Aligned: 99 Modelled: 102 Confidence: 31.9% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1bco chain A Region: 132 - 285 Aligned: 119 Modelled: 119 Confidence: 30.9% Identity: 16% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 1k78 chain A domain 1 Region: 50 - 116 Aligned: 48 Modelled: 50 Confidence: 30.8% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 3nzq chain B Region: 60 - 105 Aligned: 46 Modelled: 46 Confidence: 29.0% Identity: 17% PDB header:lyase Chain: B: PDB Molecule:biosynthetic arginine decarboxylase; PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600 Phyre2 PDB 6pax chain A domain 1 Region: 50 - 116 Aligned: 48 Modelled: 50 Confidence: 24.9% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1a9x chain A domain 1 Region: 24 - 86 Aligned: 50 Modelled: 60 Confidence: 21.6% Identity: 12% Fold: Carbamoyl phosphate synthetase, large subunit connection domain Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain Family: Carbamoyl phosphate synthetase, large subunit connection domain Phyre2 1 d1musa_ 2 d1b7ea_ 3 d1cxqa_ 4 d1asua_ 5 d1c0ma2 6 c1bg1A_ 7 c3nf9A_ 8 c1yvlB_ 9 c3hefB_ 10 c1c0mA_ 11 d1bcoa2 12 d1hyva_ 13 c1bf5A_ 14 c3f9kV_ 15 d1exqa_ 16 c1bcoA_ 17 d1k78a1 18 c3nzqB_ 19 d6paxa1 20 d1a9xa1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Detailed template information

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

1 d1musa_ 98.5 10 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 98.1 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d1cxqa_ 91.1 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 d1asua_ 85.6 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 5 d1c0ma2 67.9 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 6 c1bg1A_ 66.6 14 PDB header:transcription/dna Chain: A: PDB Molecule:protein (transcription factor stat3b); PDBTitle: transcription factor stat3b/dna complex 7 c3nf9A_ 64.5 13 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:integrase; PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design 8 c1yvlB_ 62.4 14 PDB header:signaling protein Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: structure of unphosphorylated stat1 9 c3hefB_ 51.6 15 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 10 c1c0mA_ 47.2 19 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 11 d1bcoa2 46.2 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 12 d1hyva_ 40.9 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 13 c1bf5A_ 36.9 17 PDB header:gene regulation/dna Chain: A: PDB Molecule:signal transducer and activator of transcription PDBTitle: tyrosine phosphorylated stat-1/dna complex 14 c3f9kV_ 36.4 13 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 15 d1exqa_ 31.9 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 16 c1bcoA_ 30.9 16 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 17 d1k78a1 30.8 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 18 c3nzqB_ 29.0 17 PDB header:lyase Chain: B: PDB Molecule:biosynthetic arginine decarboxylase; PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600 19 d6paxa1 24.9 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 20 d1a9xa1 21.6 12 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 21 c3n2oA_ not modelled 20.4 32 PDB header:lyase Chain: A: PDB Molecule:biosynthetic arginine decarboxylase; PDBTitle: x-ray crystal structure of arginine decarboxylase complexed with2 arginine from vibrio vulnificus 22 c1k6yB_ not modelled 19.7 15 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 23 d1c6va_ not modelled 18.7 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 24 c3iwfA_ not modelled 14.1 4 PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a 25 c2jg6A_ not modelled 11.6 9 PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus 26 d1slma1 not modelled 10.2 27 Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain 27 c3nzpA_ not modelled 10.2 25 PDB header:lyase Chain: A: PDB Molecule:arginine decarboxylase; PDBTitle: crystal structure of the biosynthetic arginine decarboxylase spea from2 campylobacter jejuni, northeast structural genomics consortium target3 br53 28 c2vkpA_ not modelled 9.7 12 PDB header:protein-binding Chain: A: PDB Molecule:btb/poz domain-containing protein 6; PDBTitle: crystal structure of btb domain from btbd6 29 c3cwgA_ not modelled 9.5 13 PDB header:transcription Chain: A: PDB Molecule:signal transducer and activator of transcription PDBTitle: unphosphorylated mouse stat3 core fragment 30 c1y1uA_ not modelled 9.1 16 PDB header:signaling protein Chain: A: PDB Molecule:signal transducer and activator of transcription 5a; PDBTitle: structure of unphosphorylated stat5a 31 c3eusB_ not modelled 8.9 16 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi 32 c2o3fC_ not modelled 8.0 12 PDB header:transcription Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh; PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168. 33 d2o3fa1 not modelled 8.0 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like 34 d1nkua_ not modelled 8.0 10 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag) 35 c1ex4A_ not modelled 7.7 17 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 36 d1a6qa1 not modelled 6.9 27 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 37 c2kvcA_ not modelled 5.8 20 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a 38 d1v77a_ not modelled 5.8 7 Fold:7-stranded beta/alpha barrel Superfamily:PHP domain-like Family:RNase P subunit p30 39 d1sbza_ not modelled 5.5 19 Fold:Homo-oligomeric flavin-containing Cys decarboxylases, HFCD Superfamily:Homo-oligomeric flavin-containing Cys decarboxylases, HFCD Family:Homo-oligomeric flavin-containing Cys decarboxylases, HFCD 40 c3hpgC_ not modelled 5.3 13 PDB header:transferase Chain: C: PDB Molecule:integrase; PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces 41 c3g7pA_ not modelled 5.2 15 PDB header:unknown function Chain: A: PDB Molecule:nitrogen fixation protein; PDBTitle: crystal structure of a nifx-associated protein of unknown function2 (afe_1514) from acidithiobacillus ferrooxidans atcc at 2.00 a3 resolution 42 c2lm4A_ not modelled 5.1 14 PDB header:protein binding Chain: A: PDB Molecule:succinate dehydrogenase assembly factor 2, mitochondrial; PDBTitle: solution nmr structure of mitochondrial succinate dehydrogenase2 assembly factor 2 from saccharomyces cerevisiae, northeast structural3 genomics consortium target yt682a

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