Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	V	I	W	S	H	R	T	G	F	I	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
Secondary structure
SS confidence
Disorder		?	?		?	?	?						?	?	?															?	?	?	?	?	?	?																								?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	N	G	R	R	P	Y	P	L	E	T	M	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
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	H	L	L	E	Q	H	Q	L	A	R	Q	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
Secondary structure
SS confidence
Disorder																																																							?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		K	G	N	Q	W	H	F	G	M	K	A	H	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
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	E	E	L	A	E	V	D	V	D	W	L	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
Secondary structure
SS confidence
Disorder																			?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.
Sequence		V	K	A	R	Y	K	G	L	L	K	N	D	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: 123 - 321 Aligned: 187 Modelled: 198 Confidence: 98.2% Identity: 12% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 187 - 332 Aligned: 145 Modelled: 146 Confidence: 97.5% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1cxq chain A Region: 144 - 323 Aligned: 130 Modelled: 131 Confidence: 84.2% Identity: 22% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3hef chain B Region: 87 - 212 Aligned: 115 Modelled: 126 Confidence: 79.7% Identity: 14% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 1asu chain A Region: 191 - 323 Aligned: 108 Modelled: 111 Confidence: 70.0% Identity: 20% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3nf9 chain A Region: 188 - 323 Aligned: 111 Modelled: 114 Confidence: 47.7% 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: 36 - 98 Aligned: 50 Modelled: 63 Confidence: 39.7% Identity: 16% 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: 191 - 323 Aligned: 111 Modelled: 111 Confidence: 35.3% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1c0m chain A Region: 191 - 296 Aligned: 84 Modelled: 84 Confidence: 30.6% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase Phyre2 PDB 1slm chain A domain 1 Region: 77 - 117 Aligned: 37 Modelled: 41 Confidence: 29.6% Identity: 27% Fold: PGBD-like Superfamily: PGBD-like Family: MMP N-terminal domain Phyre2 PDB 3ohw chain B Region: 63 - 112 Aligned: 45 Modelled: 50 Confidence: 22.4% Identity: 16% PDB header:protein binding Chain: B: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: x-ray structure of phycobilisome lcm core-membrane linker polypeptide2 (fragment 721-860) from synechocystis sp. pcc 6803, northeast3 structural genomics consortium target sgr209e Phyre2 PDB 2ky4 chain A Region: 63 - 112 Aligned: 45 Modelled: 50 Confidence: 22.4% Identity: 16% PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e Phyre2 PDB 2l3w chain A Region: 63 - 112 Aligned: 45 Modelled: 50 Confidence: 20.8% Identity: 20% PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome rod linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome rod2 linker polypeptide from synechococcus elongatus, northeast structural3 genomics consortium target snr168a Phyre2 PDB 1k78 chain A domain 1 Region: 62 - 128 Aligned: 48 Modelled: 50 Confidence: 19.8% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 3pru chain D Region: 63 - 112 Aligned: 45 Modelled: 50 Confidence: 19.4% Identity: 13% PDB header:photosynthesis Chain: D: PDB Molecule:phycobilisome 32.1 kda linker polypeptide, phycocyanin- PDBTitle: crystal structure of phycobilisome 32.1 kda linker polypeptide,2 phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis3 sp. pcc 6803, northeast structural genomics consortium target sgr182a Phyre2 PDB 2l06 chain A Region: 63 - 112 Aligned: 45 Modelled: 50 Confidence: 18.7% Identity: 22% PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c Phyre2 PDB 1hyv chain A Region: 191 - 326 Aligned: 103 Modelled: 107 Confidence: 18.2% Identity: 16% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 1q2i chain A Region: 16 - 40 Aligned: 25 Modelled: 25 Confidence: 17.8% Identity: 28% PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells Phyre2 PDB 1exq chain A Region: 193 - 323 Aligned: 99 Modelled: 102 Confidence: 16.0% Identity: 17% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 3pvp chain A Region: 44 - 143 Aligned: 83 Modelled: 83 Confidence: 15.9% Identity: 14% 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 Phyre2 1 d1musa_ 2 d1b7ea_ 3 d1cxqa_ 4 c3hefB_ 5 d1asua_ 6 c3nf9A_ 7 d1a9xa1 8 d1c0ma2 9 c1c0mA_ 10 d1slma1 11 c3ohwB_ 12 c2ky4A_ 13 c2l3wA_ 14 d1k78a1 15 c3pruD_ 16 c2l06A_ 17 d1hyva_ 18 c1q2iA_ 19 d1exqa_ 20 c3pvpA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46

Detailed template information

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

1 d1musa_ 98.2 12 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 97.5 13 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d1cxqa_ 84.2 22 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 4 c3hefB_ 79.7 14 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 5 d1asua_ 70.0 20 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 6 c3nf9A_ 47.7 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 7 d1a9xa1 39.7 16 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 8 d1c0ma2 35.3 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 9 c1c0mA_ 30.6 19 PDB header:transferase Chain: A: PDB Molecule:protein (integrase); PDBTitle: crystal structure of rsv two-domain integrase 10 d1slma1 29.6 27 Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain 11 c3ohwB_ 22.4 16 PDB header:protein binding Chain: B: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: x-ray structure of phycobilisome lcm core-membrane linker polypeptide2 (fragment 721-860) from synechocystis sp. pcc 6803, northeast3 structural genomics consortium target sgr209e 12 c2ky4A_ 22.4 16 PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e 13 c2l3wA_ 20.8 20 PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome rod linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome rod2 linker polypeptide from synechococcus elongatus, northeast structural3 genomics consortium target snr168a 14 d1k78a1 19.8 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 15 c3pruD_ 19.4 13 PDB header:photosynthesis Chain: D: PDB Molecule:phycobilisome 32.1 kda linker polypeptide, phycocyanin- PDBTitle: crystal structure of phycobilisome 32.1 kda linker polypeptide,2 phycocyanin-associated, rod 1 (fragment 14-158) from synechocystis3 sp. pcc 6803, northeast structural genomics consortium target sgr182a 16 c2l06A_ 18.7 22 PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c 17 d1hyva_ 18.2 16 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 18 c1q2iA_ 17.8 28 PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells 19 d1exqa_ 16.0 17 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 20 c3pvpA_ 15.9 14 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 21 c3f9kV_ not modelled 15.1 14 PDB header:viral protein, recombination Chain: V: PDB Molecule:integrase; PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd 22 d1su3a1 not modelled 14.8 28 Fold:PGBD-like Superfamily:PGBD-like Family:MMP N-terminal domain 23 c2o8kA_ not modelled 14.2 27 PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element 24 c3u1nC_ not modelled 14.2 12 PDB header:hydrolase Chain: C: PDB Molecule:sam domain and hd domain-containing protein 1; PDBTitle: structure of the catalytic core of human samhd1 25 c1k6yB_ not modelled 12.7 19 PDB header:transferase Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase 26 c1x6iB_ not modelled 12.2 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ygfy; PDBTitle: crystal structure of ygfy from escherichia coli 27 c1bg1A_ not modelled 10.9 11 PDB header:transcription/dna Chain: A: PDB Molecule:protein (transcription factor stat3b); PDBTitle: transcription factor stat3b/dna complex 28 d2fug11 not modelled 9.9 19 Fold:Bromodomain-like Superfamily:Nqo1C-terminal domain-like Family:Nqo1C-terminal domain-like 29 d1nkua_ not modelled 9.1 13 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag) 30 d2d1ha1 not modelled 8.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like 31 c3iwfA_ not modelled 8.3 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 32 c2kvcA_ not modelled 8.2 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 33 d1sfka_ not modelled 7.6 19 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 34 d1s1ma2 not modelled 7.4 24 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 35 d1c6va_ not modelled 7.3 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 36 d1vcoa2 not modelled 6.8 18 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 37 c1r6rA_ not modelled 5.9 10 PDB header:viral protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold 38 d1r6ra_ not modelled 5.9 10 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 39 c1yvlB_ not modelled 5.7 9 PDB header:signaling protein Chain: B: PDB Molecule:signal transducer and activator of transcription PDBTitle: structure of unphosphorylated stat1 40 c1ud0B_ not modelled 5.6 20 PDB header:chaperone Chain: B: PDB Molecule:70 kda heat-shock-like protein; PDBTitle: crystal structure of the c-terminal 10-kda subdomain of hsc70 41 d1h3fa1 not modelled 5.6 9 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 42 c2vkpA_ not modelled 5.6 12 PDB header:protein-binding Chain: A: PDB Molecule:btb/poz domain-containing protein 6; PDBTitle: crystal structure of btb domain from btbd6 43 c3d3kD_ not modelled 5.4 12 PDB header:protein binding Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p 44 c1m6vE_ not modelled 5.4 16 PDB header:ligase Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain; PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase 45 d1j1va_ not modelled 5.3 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Chromosomal replication initiation factor DnaA C-terminal domain IV 46 c2lkyA_ not modelled 5.2 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of msmeg_1053, the second duf3349 annotated protein2 in the genome of mycobacterium smegmatis, seattle structural genomics3 center for infectious disease target mysma.17112.b

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