Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	F	I	K	P	A	D	L	R	E	I	V	T	F	P	L	F	S	D	L	V	Q	C	G	F	P	S	P	A	A	D	Y	V	E	Q	R	I	D	L	N	Q	L	L	I	Q	H	P	S	A	T	Y	F	V	K	A	S	G	D	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	I	D	G	G	I	S	D	G	D	L	L	I	V	D	S	A	I	T	A	S	H	G	D	I	V	I	A	A	V	D	G	E	F	T	V	K	K	L	Q	L	R	P	T	V	Q	L	I	P	M	N	S	A	Y	S	P	I	T	I	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.
Sequence		S	E	D	T	L	D	V	F	G	V	V	I	H	V	V	K	A	M	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 1jhf chain A domain 2 Region: 15 - 137 Aligned: 121 Modelled: 123 Confidence: 100.0% Identity: 33% Fold: LexA/Signal peptidase Superfamily: LexA/Signal peptidase Family: LexA-related Phyre2 PDB 1umu chain A Region: 32 - 136 Aligned: 105 Modelled: 105 Confidence: 100.0% Identity: 98% Fold: LexA/Signal peptidase Superfamily: LexA/Signal peptidase Family: LexA-related Phyre2 PDB 3k2z chain A Region: 14 - 138 Aligned: 123 Modelled: 125 Confidence: 99.9% Identity: 33% PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima Phyre2 PDB 1jhh chain B Region: 15 - 137 Aligned: 114 Modelled: 123 Confidence: 99.9% Identity: 32% PDB header:hydrolase Chain: B: PDB Molecule:lexa repressor; PDBTitle: lexa s119a mutant Phyre2 PDB 2hnf chain A Region: 10 - 134 Aligned: 122 Modelled: 125 Confidence: 99.9% Identity: 29% PDB header:viral protein Chain: A: PDB Molecule:repressor protein ci101-229dm-k192a; PDBTitle: structure of a hyper-cleavable monomeric fragment of phage2 lambda repressor containing the cleavage site region Phyre2 PDB 1f39 chain A Region: 49 - 136 Aligned: 86 Modelled: 88 Confidence: 99.8% Identity: 34% Fold: LexA/Signal peptidase Superfamily: LexA/Signal peptidase Family: LexA-related Phyre2 PDB 3bdn chain B Region: 6 - 135 Aligned: 125 Modelled: 130 Confidence: 99.7% Identity: 32% PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor Phyre2 PDB 2fjr chain B Region: 3 - 138 Aligned: 114 Modelled: 125 Confidence: 99.6% Identity: 10% PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 Phyre2 PDB 2fkd chain K Region: 68 - 138 Aligned: 66 Modelled: 71 Confidence: 98.7% Identity: 18% PDB header:transcription regulator Chain: K: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of the c-terminal domain of bacteriophage2 186 repressor Phyre2 PDB 1b12 chain A Region: 52 - 113 Aligned: 62 Modelled: 62 Confidence: 97.5% Identity: 21% Fold: LexA/Signal peptidase Superfamily: LexA/Signal peptidase Family: Type 1 signal peptidase Phyre2 PDB 1nnx chain A Region: 86 - 131 Aligned: 45 Modelled: 46 Confidence: 15.0% Identity: 18% Fold: OB-fold Superfamily: Hypothetical protein YgiW Family: Hypothetical protein YgiW Phyre2 PDB 1hr0 chain W Region: 66 - 87 Aligned: 22 Modelled: 22 Confidence: 14.9% Identity: 32% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1jt8 chain A Region: 66 - 93 Aligned: 28 Modelled: 28 Confidence: 14.6% Identity: 21% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1d7q chain A Region: 66 - 93 Aligned: 28 Modelled: 28 Confidence: 14.0% Identity: 18% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2uwq chain A Region: 58 - 66 Aligned: 8 Modelled: 9 Confidence: 10.5% Identity: 38% PDB header:apoptosis Chain: A: PDB Molecule:apoptosis-stimulating of p53 protein 2; PDBTitle: solution structure of aspp2 n-terminus Phyre2 PDB 2p84 chain A domain 1 Region: 60 - 129 Aligned: 55 Modelled: 55 Confidence: 10.1% Identity: 22% Fold: YopX-like Superfamily: YopX-like Family: YopX-like Phyre2 PDB 1ah9 chain A Region: 66 - 87 Aligned: 22 Modelled: 22 Confidence: 9.8% Identity: 32% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2oqk chain A Region: 66 - 87 Aligned: 22 Modelled: 22 Confidence: 9.1% Identity: 27% PDB header:translation Chain: A: PDB Molecule:putative translation initiation factor eif-1a; PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a Phyre2 PDB 2zpm chain A Region: 56 - 116 Aligned: 61 Modelled: 61 Confidence: 7.5% Identity: 11% PDB header:hydrolase Chain: A: PDB Molecule:regulator of sigma e protease; PDBTitle: crystal structure analysis of pdz domain b Phyre2 PDB 1zvp chain A domain 1 Region: 61 - 74 Aligned: 14 Modelled: 14 Confidence: 5.8% Identity: 14% Fold: Ferredoxin-like Superfamily: ACT-like Family: VC0802-like Phyre2 1 d1jhfa2 2 d1umua_ 3 c3k2zA_ 4 c1jhhB_ 5 c2hnfA_ 6 d1f39a_ 7 c3bdnB_ 8 c2fjrB_ 9 c2fkdK_ 10 d1b12a_ 11 d1nnxa_ 12 d1hr0w_ 13 d1jt8a_ 14 d1d7qa_ 15 c2uwqA_ 16 d2p84a1 17 d1ah9a_ 18 c2oqkA_ 19 c2zpmA_ 20 d1zvpa1 21

Detailed template information

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

1 d1jhfa2 100.0 33 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:LexA-related 2 d1umua_ 100.0 98 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:LexA-related 3 c3k2zA_ 99.9 33 PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima 4 c1jhhB_ 99.9 32 PDB header:hydrolase Chain: B: PDB Molecule:lexa repressor; PDBTitle: lexa s119a mutant 5 c2hnfA_ 99.9 29 PDB header:viral protein Chain: A: PDB Molecule:repressor protein ci101-229dm-k192a; PDBTitle: structure of a hyper-cleavable monomeric fragment of phage2 lambda repressor containing the cleavage site region 6 d1f39a_ 99.8 34 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:LexA-related 7 c3bdnB_ 99.7 32 PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor 8 c2fjrB_ 99.6 10 PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 9 c2fkdK_ 98.7 18 PDB header:transcription regulator Chain: K: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of the c-terminal domain of bacteriophage2 186 repressor 10 d1b12a_ 97.5 21 Fold:LexA/Signal peptidase Superfamily:LexA/Signal peptidase Family:Type 1 signal peptidase 11 d1nnxa_ 15.0 18 Fold:OB-fold Superfamily:Hypothetical protein YgiW Family:Hypothetical protein YgiW 12 d1hr0w_ 14.9 32 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 13 d1jt8a_ 14.6 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 14 d1d7qa_ 14.0 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 15 c2uwqA_ 10.5 38 PDB header:apoptosis Chain: A: PDB Molecule:apoptosis-stimulating of p53 protein 2; PDBTitle: solution structure of aspp2 n-terminus 16 d2p84a1 10.1 22 Fold:YopX-like Superfamily:YopX-like Family:YopX-like 17 d1ah9a_ 9.8 32 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 18 c2oqkA_ 9.1 27 PDB header:translation Chain: A: PDB Molecule:putative translation initiation factor eif-1a; PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a 19 c2zpmA_ 7.5 11 PDB header:hydrolase Chain: A: PDB Molecule:regulator of sigma e protease; PDBTitle: crystal structure analysis of pdz domain b 20 d1zvpa1 5.8 14 Fold:Ferredoxin-like Superfamily:ACT-like Family:VC0802-like 21 d2vgna1 not modelled 5.3 14 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-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