Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Y	L	R	P	D	E	V	A	R	V	L	E	K	V	G	F	T	V	D	V	V	T	Q	K	A	Y	G	Y	R	R	G	E	N	Y	V	Y	V	N	R	E	A	R	M	G	R	T	A	L	V	I	H	P	T	L	K	E	R	S	S
Secondary structure
SS confidence
Disorder		?	?	?	?																					?				?															?		?												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.
Sequence		T	L	A	E	P	A	S	D	I	K	T	C	D	H	Y	Q	Q	F	P	L	Y	L	A	G	E	R	H	E	H	Y	G	I	P	H	G	F	S	S	R	V	A	L	E	R	Y	L	N	G	L	F	G	E	A	S
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 2g7j chain A domain 1 Region: 1 - 112 Aligned: 112 Modelled: 112 Confidence: 100.0% Identity: 88% Fold: Secretion chaperone-like Superfamily: YgaC/TfoX-N like Family: YgaC-like Phyre2 PDB 1whz chain A Region: 3 - 33 Aligned: 31 Modelled: 31 Confidence: 38.4% Identity: 32% Fold: dsRBD-like Superfamily: YcfA/nrd intein domain Family: YcfA-like Phyre2 PDB 2odg chain C domain 1 Region: 90 - 95 Aligned: 6 Modelled: 6 Confidence: 18.6% Identity: 83% Fold: LEM/SAP HeH motif Superfamily: LEM domain Family: LEM domain Phyre2 PDB 2h7a chain A domain 1 Region: 30 - 79 Aligned: 50 Modelled: 50 Confidence: 14.0% Identity: 26% Fold: YcgL-like Superfamily: YcgL-like Family: YcgL-like Phyre2 PDB 3c2v chain A Region: 6 - 92 Aligned: 87 Modelled: 87 Confidence: 13.5% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase; PDBTitle: crystal structure of the quinolinate phosphoribosyl2 transferase (bna6) from saccharomyces cerevisiae complexed3 with prpp and the inhibitor phthalate Phyre2 PDB 2hqy chain A domain 1 Region: 33 - 45 Aligned: 13 Modelled: 13 Confidence: 12.3% Identity: 54% Fold: Acyl-CoA N-acyltransferases (Nat) Superfamily: Acyl-CoA N-acyltransferases (Nat) Family: FemXAB nonribosomal peptidyltransferases Phyre2 PDB 3h0g chain N Region: 93 - 114 Aligned: 22 Modelled: 22 Confidence: 11.7% Identity: 23% PDB header:transcription Chain: N: PDB Molecule:dna-directed rna polymerase ii subunit rpb2; PDBTitle: rna polymerase ii from schizosaccharomyces pombe Phyre2 PDB 1twf chain B Region: 93 - 113 Aligned: 21 Modelled: 21 Confidence: 10.5% Identity: 24% Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase Family: RNA-polymerase beta Phyre2 PDB 1q8l chain A Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 10.3% Identity: 28% Fold: Ferredoxin-like Superfamily: HMA, heavy metal-associated domain Family: HMA, heavy metal-associated domain Phyre2 PDB 1smy chain C Region: 93 - 114 Aligned: 22 Modelled: 22 Confidence: 9.8% Identity: 36% Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase Family: RNA-polymerase beta Phyre2 PDB 3deo chain A Region: 62 - 112 Aligned: 51 Modelled: 51 Confidence: 9.3% Identity: 35% PDB header:protein transport, membrane protein Chain: A: PDB Molecule:signal recognition particle 43 kda protein; PDBTitle: structural basis for specific substrate recognition by the2 chloroplast signal recognition particle protein cpsrp43 Phyre2 PDB 1zyl chain A domain 1 Region: 3 - 64 Aligned: 59 Modelled: 62 Confidence: 9.0% Identity: 29% Fold: Protein kinase-like (PK-like) Superfamily: Protein kinase-like (PK-like) Family: APH phosphotransferases Phyre2 PDB 2pmz chain B Region: 93 - 113 Aligned: 21 Modelled: 21 Confidence: 8.8% Identity: 33% PDB header:translation, transferase Chain: B: PDB Molecule:dna-directed rna polymerase subunit b; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 3dxs chain X Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 14% PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase Phyre2 PDB 2gzs chain A domain 1 Region: 91 - 112 Aligned: 22 Modelled: 22 Confidence: 7.9% Identity: 23% Fold: alpha/beta-Hydrolases Superfamily: alpha/beta-Hydrolases Family: IroE-like Phyre2 PDB 1ynj chain C domain 1 Region: 93 - 113 Aligned: 21 Modelled: 21 Confidence: 6.7% Identity: 38% Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase Family: RNA-polymerase beta Phyre2 PDB 2yh5 chain A Region: 6 - 20 Aligned: 15 Modelled: 15 Confidence: 6.6% Identity: 40% PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc Phyre2 PDB 3ktw chain A Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 6.4% Identity: 25% PDB header:rna/rna binding protein Chain: A: PDB Molecule:signal recognition particle 19 kda protein; PDBTitle: crystal structure of the srp19/s-domain srp rna complex of sulfolobus2 solfataricus Phyre2 PDB 1j5j chain A Region: 68 - 79 Aligned: 12 Modelled: 12 Confidence: 6.2% Identity: 58% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 3pfh chain D Region: 2 - 23 Aligned: 22 Modelled: 22 Confidence: 6.2% Identity: 14% PDB header:transferase Chain: D: PDB Molecule:n-methyltransferase; PDBTitle: x-ray crystal structure the n,n-dimethyltransferase tylm1 from2 streptomyces fradiae in complex with sah and dtdp-quip3n Phyre2 1 d2g7ja1 2 d1whza_ 3 d2odgc1 4 d2h7aa1 5 c3c2vA_ 6 d2hqya1 7 c3h0gN_ 8 d1twfb_ 9 d1q8la_ 10 d1smyc_ 11 c3deoA_ 12 d1zyla1 13 c2pmzB_ 14 c3dxsX_ 15 d2gzsa1 16 d1ynjc1 17 c2yh5A_ 18 c3ktwA_ 19 d1j5ja_ 20 c3pfhD_ 21 22 23 24 25 26 27

Detailed template information

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

1 d2g7ja1 100.0 88 Fold:Secretion chaperone-like Superfamily:YgaC/TfoX-N like Family:YgaC-like 2 d1whza_ 38.4 32 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YcfA-like 3 d2odgc1 18.6 83 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 4 d2h7aa1 14.0 26 Fold:YcgL-like Superfamily:YcgL-like Family:YcgL-like 5 c3c2vA_ 13.5 16 PDB header:transferase Chain: A: PDB Molecule:nicotinate-nucleotide pyrophosphorylase; PDBTitle: crystal structure of the quinolinate phosphoribosyl2 transferase (bna6) from saccharomyces cerevisiae complexed3 with prpp and the inhibitor phthalate 6 d2hqya1 12.3 54 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:FemXAB nonribosomal peptidyltransferases 7 c3h0gN_ 11.7 23 PDB header:transcription Chain: N: PDB Molecule:dna-directed rna polymerase ii subunit rpb2; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 8 d1twfb_ 10.5 24 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta 9 d1q8la_ 10.3 28 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 10 d1smyc_ 9.8 36 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta 11 c3deoA_ 9.3 35 PDB header:protein transport, membrane protein Chain: A: PDB Molecule:signal recognition particle 43 kda protein; PDBTitle: structural basis for specific substrate recognition by the2 chloroplast signal recognition particle protein cpsrp43 12 d1zyla1 9.0 29 Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:APH phosphotransferases 13 c2pmzB_ 8.8 33 PDB header:translation, transferase Chain: B: PDB Molecule:dna-directed rna polymerase subunit b; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 14 c3dxsX_ 8.3 14 PDB header:hydrolase Chain: X: PDB Molecule:copper-transporting atpase ran1; PDBTitle: crystal structure of a copper binding domain from hma7, a p-2 type atpase 15 d2gzsa1 7.9 23 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:IroE-like 16 d1ynjc1 6.7 38 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta 17 c2yh5A_ 6.6 40 PDB header:lipid binding protein Chain: A: PDB Molecule:dapx protein; PDBTitle: structure of the c-terminal domain of bamc 18 c3ktwA_ 6.4 25 PDB header:rna/rna binding protein Chain: A: PDB Molecule:signal recognition particle 19 kda protein; PDBTitle: crystal structure of the srp19/s-domain srp rna complex of sulfolobus2 solfataricus 19 d1j5ja_ 6.2 58 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 20 c3pfhD_ 6.2 14 PDB header:transferase Chain: D: PDB Molecule:n-methyltransferase; PDBTitle: x-ray crystal structure the n,n-dimethyltransferase tylm1 from2 streptomyces fradiae in complex with sah and dtdp-quip3n 21 c2rogA_ not modelled 6.1 22 PDB header:metal binding protein Chain: A: PDB Molecule:heavy metal binding protein; PDBTitle: solution structure of thermus thermophilus hb8 ttha17182 protein in living e. coli cells 22 d1yrea1 not modelled 6.0 17 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-acetyl transferase, NAT 23 c1gxsC_ not modelled 6.0 35 PDB header:lyase Chain: C: PDB Molecule:p-(s)-hydroxymandelonitrile lyase chain a; PDBTitle: crystal structure of hydroxynitrile lyase from sorghum2 bicolor in complex with inhibitor benzoic acid: a novel3 cyanogenic enzyme 24 c3eywA_ not modelled 5.9 25 PDB header:transport protein Chain: A: PDB Molecule:c-terminal domain of glutathione-regulated potassium-efflux PDBTitle: crystal structure of the c-terminal domain of e. coli kefc in complex2 with keff 25 c3iydC_ not modelled 5.7 33 PDB header:transcription/dna Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 26 c2gcfA_ not modelled 5.7 24 PDB header:hydrolase Chain: A: PDB Molecule:cation-transporting atpase pacs; PDBTitle: solution structure of the n-terminal domain of the coppper(i) atpase2 pacs in its apo form 27 d1civa2 not modelled 5.7 26 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal 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