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	T	K	R	R	Q	T	R	K	E	I	F	L	S	R	M	E	Q	I	L	P	W	Q	N	M	T	A	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	K	T	L	K	Q	N	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	V	D	Q	M	I	R	Q	W	E	R	S	Q
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: 98.3% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 216 - 320 Aligned: 104 Modelled: 105 Confidence: 96.9% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1asu chain A Region: 179 - 311 Aligned: 111 Modelled: 111 Confidence: 87.3% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1cxq chain A Region: 132 - 311 Aligned: 130 Modelled: 132 Confidence: 84.1% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 179 - 311 Aligned: 108 Modelled: 111 Confidence: 69.3% Identity: 14% 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 1a9x chain A domain 1 Region: 24 - 86 Aligned: 50 Modelled: 63 Confidence: 47.7% Identity: 14% 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 PDB 1c0m chain A domain 2 Region: 179 - 311 Aligned: 111 Modelled: 111 Confidence: 43.7% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3f9k chain V Region: 179 - 311 Aligned: 108 Modelled: 111 Confidence: 43.6% 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 1bco chain A Region: 132 - 285 Aligned: 114 Modelled: 116 Confidence: 35.9% Identity: 15% PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain Phyre2 PDB 1k6y chain B Region: 179 - 311 Aligned: 99 Modelled: 102 Confidence: 24.1% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase Phyre2 PDB 3hef chain B Region: 75 - 111 Aligned: 34 Modelled: 37 Confidence: 23.1% 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 1hyv chain A Region: 179 - 314 Aligned: 103 Modelled: 107 Confidence: 21.4% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A Region: 179 - 311 Aligned: 110 Modelled: 111 Confidence: 16.1% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1exq chain A Region: 181 - 311 Aligned: 99 Modelled: 102 Confidence: 15.6% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1slm chain A domain 1 Region: 65 - 117 Aligned: 49 Modelled: 53 Confidence: 15.6% Identity: 22% Fold: PGBD-like Superfamily: PGBD-like Family: MMP N-terminal domain Phyre2 PDB 3nzq chain B Region: 60 - 105 Aligned: 46 Modelled: 46 Confidence: 13.4% 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 3n2o chain A Region: 75 - 105 Aligned: 31 Modelled: 31 Confidence: 10.7% Identity: 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 Phyre2 PDB 1c6v chain A Region: 176 - 311 Aligned: 100 Modelled: 103 Confidence: 10.0% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1k78 chain A domain 1 Region: 50 - 116 Aligned: 48 Modelled: 50 Confidence: 8.7% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1bco chain A domain 2 Region: 132 - 250 Aligned: 102 Modelled: 103 Confidence: 8.1% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: mu transposase, core domain Phyre2 1 d1musa_ 2 d1b7ea_ 3 d1asua_ 4 d1cxqa_ 5 c3nf9A_ 6 d1a9xa1 7 d1c0ma2 8 c3f9kV_ 9 c1bcoA_ 10 c1k6yB_ 11 c3hefB_ 12 d1hyva_ 13 c1c0mA_ 14 d1exqa_ 15 d1slma1 16 c3nzqB_ 17 c3n2oA_ 18 d1c6va_ 19 d1k78a1 20 d1bcoa2 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d1musa_ 98.3 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 96.9 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d1asua_ 87.3 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 d1cxqa_ 84.1 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 5 c3nf9A_ 69.3 14 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 6 d1a9xa1 47.7 14 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 7 d1c0ma2 43.7 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 8 c3f9kV_ 43.6 13 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 9 c1bcoA_ 35.9 15 PDB header:transposase Chain: A: PDB Molecule:bacteriophage mu transposase; PDBTitle: bacteriophage mu transposase core domain 10 c1k6yB_ 24.1 15 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 11 c3hefB_ 23.1 15 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 12 d1hyva_ 21.4 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 13 c1c0mA_ 16.1 20 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 14 d1exqa_ 15.6 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 15 d1slma1 15.6 22 Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain 16 c3nzqB_ 13.4 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 17 c3n2oA_ 10.7 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 18 d1c6va_ 10.0 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 19 d1k78a1 8.7 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 20 d1bcoa2 8.1 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:mu transposase, core domain 21 d1sfka_ not modelled 7.7 13 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 22 c1bg1A_ not modelled 7.5 15 PDB header:transcription/dna Chain: A: PDB Molecule:protein (transcription factor stat3b); PDBTitle: transcription factor stat3b/dna complex 23 c3pvpA_ not modelled 7.0 16 PDB header:dna binding protein/dna Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna 24 d2vo1a1 not modelled 6.6 18 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 25 d1s1ma2 not modelled 6.4 24 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 26 d2fm9a1 not modelled 6.4 6 Fold:SipA N-terminal domain-like Superfamily:SipA N-terminal domain-like Family:SipA N-terminal domain-like 27 d6paxa1 not modelled 6.3 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 28 c3ostA_ not modelled 6.1 18 PDB header:lipid binding protein Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4; PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p 29 d2ve8a1 not modelled 5.9 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like 30 c1ex4A_ not modelled 5.9 17 PDB header:viral protein Chain: A: PDB Molecule:integrase; PDBTitle: hiv-1 integrase catalytic core and c-terminal domain 31 c3nzpA_ not modelled 5.8 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

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