Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	Q	V	V	C	A	T	T	N	P	A	K	I	Q	A	I	L	Q	A	F	H	E	I	F	G	E	G	S	C	H	I	A	S	V	A	V	E	S	G	V	P	E	Q	P	F	G	S	E	E	T	R	A	G	A	R	N	R	V	A
Secondary structure
SS confidence
Disorder		?																																				?	?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	A	R	R	L	L	P	E	A	D	F	W	V	A	I	E	A	G	I	D	G	D	S	T	F	S	W	V	V	I	E	N	A	S	Q	R	G	E	A	R	S	A	T	L	P	L	P	A	V	I	L	E	K	V	R	E	G	E	A	L
Secondary structure
SS confidence
Disorder																																									?																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170
Sequence		G	P	V	M	S	R	Y	T	G	I	D	E	I	G	R	K	E	G	A	I	G	V	F	T	A	G	K	L	T	R	A	S	V	Y	H	Q	A	V	I	L	A	L	S	P	F	H	N	A	V	Y
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 1u14 chain A Region: 2 - 168 Aligned: 167 Modelled: 167 Confidence: 100.0% Identity: 88% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: YjjX-like Phyre2 PDB 1u5w chain A domain 1 Region: 1 - 170 Aligned: 161 Modelled: 170 Confidence: 100.0% Identity: 99% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: YjjX-like Phyre2 PDB 1zwy chain A domain 1 Region: 1 - 170 Aligned: 162 Modelled: 169 Confidence: 100.0% Identity: 46% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: YjjX-like Phyre2 PDB 1k7k chain A Region: 1 - 65 Aligned: 60 Modelled: 64 Confidence: 83.4% Identity: 20% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: ITPase (Ham1) Phyre2 PDB 1v7r chain A Region: 2 - 61 Aligned: 55 Modelled: 60 Confidence: 62.3% Identity: 15% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: ITPase (Ham1) Phyre2 PDB 3brc chain A Region: 2 - 106 Aligned: 95 Modelled: 102 Confidence: 58.3% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein of unknown function; PDBTitle: crystal structure of a conserved protein of unknown function from2 methanobacterium thermoautotrophicum Phyre2 PDB 2car chain A domain 1 Region: 1 - 77 Aligned: 69 Modelled: 77 Confidence: 51.4% Identity: 20% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: ITPase (Ham1) Phyre2 PDB 2kgj chain A Region: 108 - 148 Aligned: 41 Modelled: 41 Confidence: 41.2% Identity: 12% PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis-trans isomerase d; PDBTitle: solution structure of parvulin domain of ppid from e.coli Phyre2 PDB 1bwv chain S Region: 1 - 41 Aligned: 41 Modelled: 41 Confidence: 37.1% Identity: 12% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 2rqs chain A Region: 108 - 148 Aligned: 41 Modelled: 41 Confidence: 35.2% Identity: 22% PDB header:isomerase Chain: A: PDB Molecule:parvulin-like peptidyl-prolyl isomerase; PDBTitle: 3d structure of pin from the psychrophilic archeon cenarcheaum2 symbiosum (cspin) Phyre2 PDB 1o66 chain A Region: 41 - 78 Aligned: 35 Modelled: 38 Confidence: 22.9% Identity: 29% Fold: TIM beta/alpha-barrel Superfamily: Phosphoenolpyruvate/pyruvate domain Family: Ketopantoate hydroxymethyltransferase PanB Phyre2 PDB 2jzv chain A Region: 108 - 151 Aligned: 44 Modelled: 44 Confidence: 22.3% Identity: 16% PDB header:isomerase Chain: A: PDB Molecule:foldase protein prsa; PDBTitle: solution structure of s. aureus prsa-ppiase Phyre2 PDB 1m5y chain A domain 3 Region: 108 - 149 Aligned: 42 Modelled: 42 Confidence: 18.9% Identity: 12% Fold: FKBP-like Superfamily: FKBP-like Family: FKBP immunophilin/proline isomerase Phyre2 PDB 1rdu chain A Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 17.5% Identity: 18% Fold: Ribonuclease H-like motif Superfamily: Nitrogenase accessory factor-like Family: MTH1175-like Phyre2 PDB 3cgi chain D Region: 124 - 144 Aligned: 21 Modelled: 21 Confidence: 17.5% Identity: 19% PDB header:unknown function Chain: D: PDB Molecule:propanediol utilization protein pduu; PDBTitle: crystal structure of the pduu shell protein from the pdu2 microcompartment Phyre2 PDB 1svd chain M domain 1 Region: 1 - 39 Aligned: 39 Modelled: 39 Confidence: 14.8% Identity: 10% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 2wfb chain A Region: 1 - 11 Aligned: 11 Modelled: 11 Confidence: 14.0% Identity: 18% PDB header:biosynthetic protein Chain: A: PDB Molecule:putative uncharacterized protein orp; PDBTitle: high resolution structure of the apo form of the orange2 protein (orp) from desulfovibrio gigas Phyre2 PDB 2h29 chain A Region: 1 - 53 Aligned: 53 Modelled: 53 Confidence: 12.9% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:probable nicotinate-nucleotide PDBTitle: crystal structure of nicotinic acid mononucleotide2 adenylyltransferase from staphylococcus aureus: product3 bound form 1 Phyre2 PDB 1s6l chain A domain 1 Region: 44 - 71 Aligned: 27 Modelled: 28 Confidence: 12.4% Identity: 30% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 1yw5 chain A Region: 108 - 158 Aligned: 48 Modelled: 51 Confidence: 12.2% Identity: 21% PDB header:isomerase Chain: A: PDB Molecule:peptidyl prolyl cis/trans isomerase; PDBTitle: peptidyl-prolyl isomerase ess1 from candida albicans Phyre2 1 d1u14a_ 2 d1u5wa1 3 d1zwya1 4 d1k7ka_ 5 d1v7ra_ 6 c3brcA_ 7 d2cara1 8 c2kgjA_ 9 d1bwvs_ 10 c2rqsA_ 11 d1o66a_ 12 c2jzvA_ 13 d1m5ya3 14 d1rdua_ 15 c3cgiD_ 16 d1svdm1 17 c2wfbA_ 18 c2h29A_ 19 d1s6la1 20 c1yw5A_ 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 47 48 49 50

Detailed template information

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

1 d1u14a_ 100.0 88 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:YjjX-like 2 d1u5wa1 100.0 99 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:YjjX-like 3 d1zwya1 100.0 46 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:YjjX-like 4 d1k7ka_ 83.4 20 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 5 d1v7ra_ 62.3 15 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 6 c3brcA_ 58.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein of unknown function; PDBTitle: crystal structure of a conserved protein of unknown function from2 methanobacterium thermoautotrophicum 7 d2cara1 51.4 20 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 8 c2kgjA_ 41.2 12 PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis-trans isomerase d; PDBTitle: solution structure of parvulin domain of ppid from e.coli 9 d1bwvs_ 37.1 12 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 10 c2rqsA_ 35.2 22 PDB header:isomerase Chain: A: PDB Molecule:parvulin-like peptidyl-prolyl isomerase; PDBTitle: 3d structure of pin from the psychrophilic archeon cenarcheaum2 symbiosum (cspin) 11 d1o66a_ 22.9 29 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Ketopantoate hydroxymethyltransferase PanB 12 c2jzvA_ 22.3 16 PDB header:isomerase Chain: A: PDB Molecule:foldase protein prsa; PDBTitle: solution structure of s. aureus prsa-ppiase 13 d1m5ya3 18.9 12 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 14 d1rdua_ 17.5 18 Fold:Ribonuclease H-like motif Superfamily:Nitrogenase accessory factor-like Family:MTH1175-like 15 c3cgiD_ 17.5 19 PDB header:unknown function Chain: D: PDB Molecule:propanediol utilization protein pduu; PDBTitle: crystal structure of the pduu shell protein from the pdu2 microcompartment 16 d1svdm1 14.8 10 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 17 c2wfbA_ 14.0 18 PDB header:biosynthetic protein Chain: A: PDB Molecule:putative uncharacterized protein orp; PDBTitle: high resolution structure of the apo form of the orange2 protein (orp) from desulfovibrio gigas 18 c2h29A_ 12.9 15 PDB header:transferase Chain: A: PDB Molecule:probable nicotinate-nucleotide PDBTitle: crystal structure of nicotinic acid mononucleotide2 adenylyltransferase from staphylococcus aureus: product3 bound form 1 19 d1s6la1 12.4 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 20 c1yw5A_ 12.2 21 PDB header:isomerase Chain: A: PDB Molecule:peptidyl prolyl cis/trans isomerase; PDBTitle: peptidyl-prolyl isomerase ess1 from candida albicans 21 c3tquD_ not modelled 12.0 18 PDB header:hydrolase Chain: D: PDB Molecule:non-canonical purine ntp pyrophosphatase; PDBTitle: structure of a ham1 protein from coxiella burnetii 22 c2l33A_ not modelled 11.8 30 PDB header:transcription regulator Chain: A: PDB Molecule:interleukin enhancer-binding factor 3; PDBTitle: solution nmr structure of drbm 2 domain of interleukin enhancer-2 binding factor 3 from homo sapiens, northeast structural genomics3 consortium target hr4527e 23 c3d3kD_ not modelled 11.5 9 PDB header:protein binding Chain: D: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p 24 d1oy0a_ not modelled 11.2 28 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Ketopantoate hydroxymethyltransferase PanB 25 c2gezF_ not modelled 10.7 18 PDB header:hydrolase Chain: F: PDB Molecule:l-asparaginase beta subunit; PDBTitle: crystal structure of potassium-independent plant asparaginase 26 d1eq3a_ not modelled 10.7 26 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 27 c3gpkA_ not modelled 10.5 17 PDB header:isomerase Chain: A: PDB Molecule:ppic-type peptidyl-prolyl cis-trans isomerase; PDBTitle: crystal structure of ppic-type peptidyl-prolyl cis-trans isomerase2 domain at 1.55a resolution. 28 d1jnsa_ not modelled 10.5 23 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 29 d1vp2a_ not modelled 9.3 25 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 30 d2pv2a1 not modelled 8.9 20 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 31 c2kwvA_ not modelled 8.6 43 PDB header:protein binding/signaling protein Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution structure of ubm1 of murine polymerase iota in complex with2 ubiquitin 32 c1apzB_ not modelled 7.9 23 PDB header:complex (hydrolase/peptide) Chain: B: PDB Molecule:aspartylglucosaminidase; PDBTitle: human aspartylglucosaminidase complex with reaction product 33 c3pe0B_ not modelled 7.8 14 PDB header:structural protein Chain: B: PDB Molecule:plectin; PDBTitle: structure of the central region of the plakin domain of plectin 34 d1bxni_ not modelled 7.6 11 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 35 d1c1da2 not modelled 7.3 9 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 36 c3e27B_ not modelled 7.3 11 PDB header:transferase Chain: B: PDB Molecule:nicotinate (nicotinamide) nucleotide PDBTitle: nicotinic acid mononucleotide (namn) adenylyltransferase2 from bacillus anthracis: product complex 37 c3bd1B_ not modelled 7.1 18 PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1 38 d1b78a_ not modelled 7.0 24 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 39 d1jzta_ not modelled 6.3 38 Fold:YjeF N-terminal domain-like Superfamily:YjeF N-terminal domain-like Family:YjeF N-terminal domain-like 40 d2ozza1 not modelled 6.2 32 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 41 c3idfA_ not modelled 6.1 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:usp-like protein; PDBTitle: the crystal structure of a usp-like protein from wolinella2 succinogenes to 2.0a 42 c1zk6A_ not modelled 5.9 12 PDB header:isomerase Chain: A: PDB Molecule:foldase protein prsa; PDBTitle: nmr solution structure of b. subtilis prsa ppiase 43 d1hcua_ not modelled 5.8 26 Fold:alpha/alpha toroid Superfamily:Seven-hairpin glycosidases Family:Class I alpha-1;2-mannosidase, catalytic domain 44 d1j6ya_ not modelled 5.8 22 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 45 d1e8ca2 not modelled 5.7 11 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 46 d2b7va1 not modelled 5.4 28 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 47 c3mvnA_ not modelled 5.4 21 PDB header:ligase Chain: A: PDB Molecule:udp-n-acetylmuramate:l-alanyl-gamma-d-glutamayl-medo- PDBTitle: crystal structure of a domain from a putative udp-n-acetylmuramate:l-2 alanyl-gamma-d-glutamayl-medo-diaminopimelate ligase from haemophilus3 ducreyi 35000hp 48 c3d3jA_ not modelled 5.2 8 PDB header:protein binding Chain: A: PDB Molecule:enhancer of mrna-decapping protein 3; PDBTitle: crystal structure of human edc3p 49 d2a9sa1 not modelled 5.1 29 Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like 50 d1zbsa2 not modelled 5.1 21 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:BadF/BadG/BcrA/BcrD-like

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