Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	K	L	K	I	V	Y	R	P	L	Q	E	L	S	P	Y	A	H	N	A	R	T	H	S	T	E	Q	V	A	Q	L	V	E	S	I	K	Q	F	G	W	T	N	P	V	L	I	D	E	K	G	E	I	I	A	G	H	G	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.
Sequence		V	M	A	A	E	M	L	K	M	D	S	V	P	V	I	V	L	S	G	L	T	D	E	Q	K	Q	R
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 1vz0 chain A domain 2 Region: 7 - 86 Aligned: 79 Modelled: 80 Confidence: 99.8% Identity: 32% Fold: ParB/Sulfiredoxin Superfamily: ParB/Sulfiredoxin Family: ParB-like nuclease domain Phyre2 PDB 1vk1 chain A Region: 10 - 83 Aligned: 74 Modelled: 74 Confidence: 99.8% Identity: 19% Fold: ParB/Sulfiredoxin Superfamily: ParB/Sulfiredoxin Family: Hypothetical protein PF0380 Phyre2 PDB 1vz0 chain B Region: 7 - 86 Aligned: 80 Modelled: 80 Confidence: 99.8% Identity: 29% PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus Phyre2 PDB 2b6f chain A domain 1 Region: 1 - 86 Aligned: 84 Modelled: 86 Confidence: 99.8% Identity: 17% Fold: ParB/Sulfiredoxin Superfamily: ParB/Sulfiredoxin Family: Sulfiredoxin-like Phyre2 PDB 1xw3 chain A domain 1 Region: 2 - 86 Aligned: 83 Modelled: 85 Confidence: 99.7% Identity: 17% Fold: ParB/Sulfiredoxin Superfamily: ParB/Sulfiredoxin Family: Sulfiredoxin-like Phyre2 PDB 2hwj chain A domain 1 Region: 6 - 82 Aligned: 74 Modelled: 77 Confidence: 98.1% Identity: 14% Fold: ParB/Sulfiredoxin Superfamily: ParB/Sulfiredoxin Family: Atu1540-like Phyre2 PDB 1f75 chain A Region: 53 - 80 Aligned: 28 Modelled: 28 Confidence: 53.7% Identity: 32% Fold: Undecaprenyl diphosphate synthase Superfamily: Undecaprenyl diphosphate synthase Family: Undecaprenyl diphosphate synthase Phyre2 PDB 1jp3 chain A Region: 53 - 67 Aligned: 15 Modelled: 13 Confidence: 36.6% Identity: 27% PDB header:transferase Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: structure of e.coli undecaprenyl pyrophosphate synthase Phyre2 PDB 1ueh chain A Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 27.8% Identity: 27% Fold: Undecaprenyl diphosphate synthase Superfamily: Undecaprenyl diphosphate synthase Family: Undecaprenyl diphosphate synthase Phyre2 PDB 2d2r chain A Region: 53 - 62 Aligned: 10 Modelled: 10 Confidence: 26.5% Identity: 40% PDB header:transferase Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase Phyre2 PDB 2vfw chain B Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 23.8% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:short-chain z-isoprenyl diphosphate synthetase; PDBTitle: rv1086 native Phyre2 PDB 2vg2 chain C Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 23.5% Identity: 27% PDB header:transferase Chain: C: PDB Molecule:undecaprenyl pyrophosphate synthetase; PDBTitle: rv2361 with ipp Phyre2 PDB 2k8s chain A Region: 60 - 79 Aligned: 20 Modelled: 20 Confidence: 21.7% Identity: 40% PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution nmr structure of dimeric thioredoxin-like protein2 ne0084 from nitrosomonas europea: northeast structural3 genomics target net6 Phyre2 PDB 3ugs chain B Region: 53 - 75 Aligned: 23 Modelled: 23 Confidence: 18.0% Identity: 13% PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni Phyre2 PDB 1xho chain A Region: 27 - 75 Aligned: 48 Modelled: 48 Confidence: 12.4% Identity: 17% Fold: Bacillus chorismate mutase-like Superfamily: YjgF-like Family: Chorismate mutase Phyre2 PDB 1xho chain B Region: 27 - 75 Aligned: 48 Modelled: 48 Confidence: 12.4% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:chorismate mutase; PDBTitle: chorismate mutase from clostridium thermocellum cth-682 Phyre2 PDB 1ufy chain A Region: 62 - 75 Aligned: 14 Modelled: 14 Confidence: 10.8% Identity: 36% Fold: Bacillus chorismate mutase-like Superfamily: YjgF-like Family: Chorismate mutase Phyre2 PDB 3cvo chain A Region: 4 - 67 Aligned: 60 Modelled: 64 Confidence: 9.7% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution Phyre2 PDB 2vdc chain F Region: 12 - 58 Aligned: 46 Modelled: 47 Confidence: 8.7% Identity: 33% PDB header:oxidoreductase Chain: F: PDB Molecule:glutamate synthase [nadph] large chain; PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications. Phyre2 PDB 1r7h chain A Region: 60 - 79 Aligned: 20 Modelled: 20 Confidence: 7.2% Identity: 20% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Thioltransferase Phyre2 1 d1vz0a2 2 d1vk1a_ 3 c1vz0B_ 4 d2b6fa1 5 d1xw3a1 6 d2hwja1 7 d1f75a_ 8 c1jp3A_ 9 d1ueha_ 10 c2d2rA_ 11 c2vfwB_ 12 c2vg2C_ 13 c2k8sA_ 14 c3ugsB_ 15 d1xhoa_ 16 c1xhoB_ 17 d1ufya_ 18 c3cvoA_ 19 c2vdcF_ 20 d1r7ha_ 21 22 23

Detailed template information

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

1 d1vz0a2 99.8 32 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:ParB-like nuclease domain 2 d1vk1a_ 99.8 19 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:Hypothetical protein PF0380 3 c1vz0B_ 99.8 29 PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus 4 d2b6fa1 99.8 17 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:Sulfiredoxin-like 5 d1xw3a1 99.7 17 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:Sulfiredoxin-like 6 d2hwja1 98.1 14 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:Atu1540-like 7 d1f75a_ 53.7 32 Fold:Undecaprenyl diphosphate synthase Superfamily:Undecaprenyl diphosphate synthase Family:Undecaprenyl diphosphate synthase 8 c1jp3A_ 36.6 27 PDB header:transferase Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: structure of e.coli undecaprenyl pyrophosphate synthase 9 d1ueha_ 27.8 27 Fold:Undecaprenyl diphosphate synthase Superfamily:Undecaprenyl diphosphate synthase Family:Undecaprenyl diphosphate synthase 10 c2d2rA_ 26.5 40 PDB header:transferase Chain: A: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of helicobacter pylori undecaprenyl pyrophosphate2 synthase 11 c2vfwB_ 23.8 13 PDB header:transferase Chain: B: PDB Molecule:short-chain z-isoprenyl diphosphate synthetase; PDBTitle: rv1086 native 12 c2vg2C_ 23.5 27 PDB header:transferase Chain: C: PDB Molecule:undecaprenyl pyrophosphate synthetase; PDBTitle: rv2361 with ipp 13 c2k8sA_ 21.7 40 PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution nmr structure of dimeric thioredoxin-like protein2 ne0084 from nitrosomonas europea: northeast structural3 genomics target net6 14 c3ugsB_ 18.0 13 PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni 15 d1xhoa_ 12.4 17 Fold:Bacillus chorismate mutase-like Superfamily:YjgF-like Family:Chorismate mutase 16 c1xhoB_ 12.4 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:chorismate mutase; PDBTitle: chorismate mutase from clostridium thermocellum cth-682 17 d1ufya_ 10.8 36 Fold:Bacillus chorismate mutase-like Superfamily:YjgF-like Family:Chorismate mutase 18 c3cvoA_ 9.7 13 PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution 19 c2vdcF_ 8.7 33 PDB header:oxidoreductase Chain: F: PDB Molecule:glutamate synthase [nadph] large chain; PDBTitle: the 9.5 a resolution structure of glutamate synthase from2 cryo-electron microscopy and its oligomerization behavior3 in solution: functional implications. 20 d1r7ha_ 7.2 20 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase 21 d1kkga_ not modelled 5.3 16 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 22 c3u7vA_ not modelled 5.2 19 PDB header:hydrolase Chain: A: PDB Molecule:beta-galactosidase; PDBTitle: the structure of a putative beta-galactosidase from caulobacter2 crescentus cb15. 23 d1d1da2 not modelled 5.1 14 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain

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