Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	K	M	N	H	Q	D	E	L	P	L	A	K	V	S	E	V	D	E	A	K	R	Q	W	L	Q	G	M	R	H	P	V	D	T	V	T	E	P	E	P	A	E	I	L	A	E	F	I	R	Q	H	S	A	A	G	Q	L	V	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?	?		?	?	?	?	?	?	?	?	?	?	?								?	?	?	?	?	?	?	?	?																	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	A	V	F	L	S	P	P	Y	L	V	A	E	E	E	L	S	V	L	L	E	S	I	K	Q	N	G	D	Y	A	D	I	A	C	L	T	G	S	K	D	D	Y	Y	Y	S	T	Q	A	M	S	E	N	Y	A	A	M	S	L	Q	V
Secondary structure
SS confidence
Disorder		?				?	?		?		?	?	?											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	E	Q	D	I	C	R	A	I	A	H	A	V	R	F	E	C	Q	T	Y	P	R	P	Y	K	V	A	M	L	M	Q	A	P	Y	Y	F	Q	E	A	Q	I	E	A	A	I	A	A	M	D	V	A	P	E	Y	A	D	I	R	Q	V
Secondary structure
SS confidence
Disorder																																?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.
Sequence		E	S	S	T	A	V	L	Y	L	F	S	E	R	F	M	T	Y	G	K	A	Y	G	L	C	E	W	F	E	V	E	Q	F	Q	N	P
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 1kbh chain B Region: 13 - 54 Aligned: 42 Modelled: 42 Confidence: 63.9% Identity: 24% Fold: Nuclear receptor coactivator interlocking domain Superfamily: Nuclear receptor coactivator interlocking domain Family: Nuclear receptor coactivator interlocking domain Phyre2 PDB 1a9x chain A domain 1 Region: 155 - 192 Aligned: 38 Modelled: 38 Confidence: 37.1% Identity: 24% 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 3c7c chain B Region: 99 - 214 Aligned: 116 Modelled: 116 Confidence: 25.5% Identity: 10% PDB header:oxidoreductase Chain: B: PDB Molecule:octopine dehydrogenase; PDBTitle: a structural basis for substrate and stereo selectivity in2 octopine dehydrogenase (odh-nadh-l-arginine) Phyre2 PDB 1m6v chain E Region: 154 - 192 Aligned: 39 Modelled: 39 Confidence: 24.3% Identity: 23% 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 Phyre2 PDB 2xu8 chain B Region: 98 - 134 Aligned: 36 Modelled: 37 Confidence: 19.3% Identity: 19% PDB header:structural genomics Chain: B: PDB Molecule:pa1645; PDBTitle: structure of pa1645 Phyre2 PDB 1ej5 chain A Region: 14 - 52 Aligned: 39 Modelled: 39 Confidence: 19.2% Identity: 18% Fold: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Phyre2 PDB 1ega chain A domain 2 Region: 34 - 74 Aligned: 35 Modelled: 41 Confidence: 12.2% Identity: 31% Fold: Alpha-lytic protease prodomain-like Superfamily: Prokaryotic type KH domain (KH-domain type II) Family: Prokaryotic type KH domain (KH-domain type II) Phyre2 PDB 1yvr chain A domain 1 Region: 97 - 146 Aligned: 50 Modelled: 50 Confidence: 10.0% Identity: 14% Fold: alpha-alpha superhelix Superfamily: TROVE domain-like Family: TROVE domain-like Phyre2 PDB 1ega chain B Region: 31 - 74 Aligned: 38 Modelled: 44 Confidence: 9.1% Identity: 29% PDB header:hydrolase Chain: B: PDB Molecule:protein (gtp-binding protein era); PDBTitle: crystal structure of a widely conserved gtpase era Phyre2 PDB 1rh6 chain A Region: 135 - 146 Aligned: 12 Modelled: 12 Confidence: 7.9% Identity: 33% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 1p9q chain C domain 1 Region: 129 - 171 Aligned: 42 Modelled: 42 Confidence: 7.8% Identity: 21% Fold: RuvA C-terminal domain-like Superfamily: Hypothetical protein AF0491, middle domain Family: Hypothetical protein AF0491, middle domain Phyre2 PDB 1pm6 chain A Region: 135 - 146 Aligned: 12 Modelled: 12 Confidence: 7.1% Identity: 33% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 1yvr chain A Region: 97 - 146 Aligned: 50 Modelled: 50 Confidence: 6.9% Identity: 18% PDB header:rna binding protein Chain: A: PDB Molecule:60-kda ss-a/ro ribonucleoprotein; PDBTitle: ro autoantigen Phyre2 PDB 1z0j chain B domain 1 Region: 37 - 91 Aligned: 47 Modelled: 55 Confidence: 6.8% Identity: 23% Fold: Long alpha-hairpin Superfamily: Rabenosyn-5 Rab-binding domain-like Family: Rabenosyn-5 Rab-binding domain-like Phyre2 PDB 1sse chain B Region: 161 - 177 Aligned: 17 Modelled: 17 Confidence: 6.7% Identity: 24% PDB header:transcription activator Chain: B: PDB Molecule:ap-1 like transcription factor yap1; PDBTitle: solution structure of the oxidized form of the yap1 redox2 domain Phyre2 PDB 1gw4 chain A Region: 67 - 87 Aligned: 21 Modelled: 21 Confidence: 6.7% Identity: 38% PDB header:high density lipoproteins Chain: A: PDB Molecule:apoa-i; PDBTitle: the helix-hinge-helix structural motif in human2 apolipoprotein a-i determined by nmr spectroscopy, 13 structure Phyre2 PDB 1zoq chain C domain 1 Region: 43 - 54 Aligned: 12 Modelled: 12 Confidence: 6.1% Identity: 42% Fold: Nuclear receptor coactivator interlocking domain Superfamily: Nuclear receptor coactivator interlocking domain Family: Nuclear receptor coactivator interlocking domain Phyre2 PDB 1oj4 chain A domain 2 Region: 65 - 103 Aligned: 35 Modelled: 39 Confidence: 6.0% Identity: 14% Fold: Ferredoxin-like Superfamily: GHMP Kinase, C-terminal domain Family: 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE Phyre2 PDB 1wf3 chain A domain 2 Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 6.0% Identity: 24% Fold: Alpha-lytic protease prodomain-like Superfamily: Prokaryotic type KH domain (KH-domain type II) Family: Prokaryotic type KH domain (KH-domain type II) Phyre2 PDB 1g47 chain A domain 1 Region: 171 - 188 Aligned: 18 Modelled: 18 Confidence: 5.9% Identity: 22% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 1 d1kbhb_ 2 d1a9xa1 3 c3c7cB_ 4 c1m6vE_ 5 c2xu8B_ 6 d1ej5a_ 7 d1egaa2 8 d1yvra1 9 c1egaB_ 10 d1rh6a_ 11 d1p9qc1 12 d1pm6a_ 13 c1yvrA_ 14 d1z0jb1 15 c1sseB_ 16 c1gw4A_ 17 d1zoqc1 18 d1oj4a2 19 d1wf3a2 20 d1g47a1 21

Detailed template information

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

1 d1kbhb_ 63.9 24 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking domain 2 d1a9xa1 37.1 24 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 3 c3c7cB_ 25.5 10 PDB header:oxidoreductase Chain: B: PDB Molecule:octopine dehydrogenase; PDBTitle: a structural basis for substrate and stereo selectivity in2 octopine dehydrogenase (odh-nadh-l-arginine) 4 c1m6vE_ 24.3 23 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 5 c2xu8B_ 19.3 19 PDB header:structural genomics Chain: B: PDB Molecule:pa1645; PDBTitle: structure of pa1645 6 d1ej5a_ 19.2 18 Fold:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain 7 d1egaa2 12.2 31 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 8 d1yvra1 10.0 14 Fold:alpha-alpha superhelix Superfamily:TROVE domain-like Family:TROVE domain-like 9 c1egaB_ 9.1 29 PDB header:hydrolase Chain: B: PDB Molecule:protein (gtp-binding protein era); PDBTitle: crystal structure of a widely conserved gtpase era 10 d1rh6a_ 7.9 33 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 11 d1p9qc1 7.8 21 Fold:RuvA C-terminal domain-like Superfamily:Hypothetical protein AF0491, middle domain Family:Hypothetical protein AF0491, middle domain 12 d1pm6a_ 7.1 33 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 13 c1yvrA_ 6.9 18 PDB header:rna binding protein Chain: A: PDB Molecule:60-kda ss-a/ro ribonucleoprotein; PDBTitle: ro autoantigen 14 d1z0jb1 6.8 23 Fold:Long alpha-hairpin Superfamily:Rabenosyn-5 Rab-binding domain-like Family:Rabenosyn-5 Rab-binding domain-like 15 c1sseB_ 6.7 24 PDB header:transcription activator Chain: B: PDB Molecule:ap-1 like transcription factor yap1; PDBTitle: solution structure of the oxidized form of the yap1 redox2 domain 16 c1gw4A_ 6.7 38 PDB header:high density lipoproteins Chain: A: PDB Molecule:apoa-i; PDBTitle: the helix-hinge-helix structural motif in human2 apolipoprotein a-i determined by nmr spectroscopy, 13 structure 17 d1zoqc1 6.1 42 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking domain 18 d1oj4a2 6.0 14 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE 19 d1wf3a2 6.0 24 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 20 d1g47a1 5.9 22 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 21 c2nrzB_ not modelled 5.7 20 PDB header:hydrolase Chain: B: PDB Molecule:uvrabc system protein c; PDBTitle: crystal structure of the c-terminal half of uvrc bound to2 its catalytic divalent cation

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