Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	F	A	L	L	A	G	L	F	V	F	A	P	M	T	W	A	Q	D	Y	N	I	K	N	G	L	P	S	E	T	Y	I	T	C	A	E	A	N	E	M	A	K	T	D	S	A	Q	V	A	E	I	V	A	V	M	G	N	A
Secondary structure
SS confidence
Disorder		?	?	?																					?															?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.
Sequence		S	V	A	S	R	D	L	K	I	E	Q	S	P	E	L	S	A	K	V	V	E	K	L	N	Q	V	C	A	K	D	P	Q	M	L	L	I	T	A	I	D	D	T	M	R	A	I	G	K	K
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 1ej7 chain L domain 2 Region: 18 - 56 Aligned: 39 Modelled: 39 Confidence: 19.6% Identity: 15% Fold: Ferredoxin-like Superfamily: RuBisCO, large subunit, small (N-terminal) domain Family: Ribulose 1,5-bisphosphate carboxylase-oxygenase Phyre2 PDB 1onv chain B Region: 38 - 53 Aligned: 16 Modelled: 16 Confidence: 17.4% Identity: 44% PDB header:transcription Chain: B: PDB Molecule:serine phosphatase fcp1a; PDBTitle: nmr structure of a complex containing the tfiif subunit2 rap74 and the rnap ii ctd phosphatase fcp1 Phyre2 PDB 2kou chain A Region: 80 - 92 Aligned: 13 Modelled: 13 Confidence: 16.9% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:dicer-like protein 4; PDBTitle: dicer like protein Phyre2 PDB 2xpn chain A Region: 49 - 89 Aligned: 39 Modelled: 41 Confidence: 15.6% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:iws1; PDBTitle: crystal structure of a spt6-iws1(spn1) complex from2 encephalitozoon cuniculi, form i Phyre2 PDB 1in0 chain A domain 2 Region: 17 - 32 Aligned: 16 Modelled: 16 Confidence: 11.1% Identity: 19% Fold: Ferredoxin-like Superfamily: YajQ-like Family: YajQ-like Phyre2 PDB 3h05 chain A Region: 1 - 103 Aligned: 100 Modelled: 103 Confidence: 10.4% Identity: 16% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vpa0413; PDBTitle: the crystal structure of a putative nicotinate-nucleotide2 adenylyltransferase from vibrio parahaemolyticus Phyre2 PDB 1wdd chain A domain 2 Region: 16 - 56 Aligned: 41 Modelled: 41 Confidence: 8.4% Identity: 15% Fold: Ferredoxin-like Superfamily: RuBisCO, large subunit, small (N-terminal) domain Family: Ribulose 1,5-bisphosphate carboxylase-oxygenase Phyre2 PDB 2a7o chain A Region: 61 - 101 Aligned: 41 Modelled: 41 Confidence: 8.1% Identity: 27% PDB header:transcription Chain: A: PDB Molecule:huntingtin interacting protein b; PDBTitle: solution structure of the hset2/hypb sri domain Phyre2 PDB 2r7g chain A domain 1 Region: 69 - 86 Aligned: 18 Modelled: 18 Confidence: 7.6% Identity: 17% Fold: Cyclin-like Superfamily: Cyclin-like Family: Retinoblastoma tumor suppressor domains Phyre2 PDB 5mdh chain A domain 1 Region: 63 - 109 Aligned: 47 Modelled: 47 Confidence: 6.3% Identity: 11% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: LDH N-terminal domain-like Phyre2 PDB 7mdh chain A domain 1 Region: 63 - 109 Aligned: 47 Modelled: 47 Confidence: 5.6% Identity: 21% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: LDH N-terminal domain-like Phyre2 PDB 1q90 chain G Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 50% PDB header:photosynthesis Chain: G: PDB Molecule:cytochrome b6f complex subunit petg; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii Phyre2 PDB 1q90 chain G Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 50% Fold: Single transmembrane helix Superfamily: PetG subunit of the cytochrome b6f complex Family: PetG subunit of the cytochrome b6f complex Phyre2 1 d1ej7l2 2 c1onvB_ 3 c2kouA_ 4 c2xpnA_ 5 d1in0a2 6 c3h05A_ 7 d1wdda2 8 c2a7oA_ 9 d2r7ga1 10 d5mdha1 11 d7mdha1 12 c1q90G_ 13 d1q90g_

Detailed template information

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

1 d1ej7l2 19.6 15 Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase 2 c1onvB_ 17.4 44 PDB header:transcription Chain: B: PDB Molecule:serine phosphatase fcp1a; PDBTitle: nmr structure of a complex containing the tfiif subunit2 rap74 and the rnap ii ctd phosphatase fcp1 3 c2kouA_ 16.9 15 PDB header:hydrolase Chain: A: PDB Molecule:dicer-like protein 4; PDBTitle: dicer like protein 4 c2xpnA_ 15.6 13 PDB header:transcription Chain: A: PDB Molecule:iws1; PDBTitle: crystal structure of a spt6-iws1(spn1) complex from2 encephalitozoon cuniculi, form i 5 d1in0a2 11.1 19 Fold:Ferredoxin-like Superfamily:YajQ-like Family:YajQ-like 6 c3h05A_ 10.4 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein vpa0413; PDBTitle: the crystal structure of a putative nicotinate-nucleotide2 adenylyltransferase from vibrio parahaemolyticus 7 d1wdda2 8.4 15 Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase 8 c2a7oA_ 8.1 27 PDB header:transcription Chain: A: PDB Molecule:huntingtin interacting protein b; PDBTitle: solution structure of the hset2/hypb sri domain 9 d2r7ga1 7.6 17 Fold:Cyclin-like Superfamily:Cyclin-like Family:Retinoblastoma tumor suppressor domains 10 d5mdha1 6.3 11 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like 11 d7mdha1 5.6 21 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:LDH N-terminal domain-like 12 c1q90G_ 5.6 50 PDB header:photosynthesis Chain: G: PDB Molecule:cytochrome b6f complex subunit petg; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 13 d1q90g_ 5.6 50 Fold:Single transmembrane helix Superfamily:PetG subunit of the cytochrome b6f complex Family:PetG subunit of the cytochrome b6f complex

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

---

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