Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	I	A	I	T	C	A	L	L	S	S	L	V	A	S	S	V	W	A	D	A	A	S	D	L	K	S	R	L	D	K	V	S	S	F	H	A	S	F	T	Q	K	V	T	D	G	S	G	A	A	V	Q	E	G	Q	G	D	L
Secondary structure
SS confidence
Disorder		?	?														?	?	?	?	?	?	?														?											?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	V	K	R	P	N	L	F	N	W	H	M	T	Q	P	D	E	S	I	L	V	S	D	G	K	T	L	W	F	Y	N	P	F	V	E	Q	A	T	A	T	W	L	K	D	A	T	G	N	T	P	F	M	L	I	A	R	N	Q	S	S
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?	?	?	?					?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	W	Q	Q	Y	N	I	K	Q	N	G	D	D	F	V	L	T	P	K	A	S	N	G	N	L	K	Q	F	T	I	N	V	G	R	D	G	T	I	H	Q	F	S	A	V	E	Q	D	D	Q	R	S	S	Y	Q	L	K	S	Q	Q	N
Secondary structure
SS confidence
Disorder		?	?																			?		?																																			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.
Sequence		G	A	V	D	A	A	K	F	T	F	T	P	P	Q	G	V	T	V	D	D	Q	R	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 1iwl chain A Region: 22 - 203 Aligned: 177 Modelled: 182 Confidence: 100.0% Identity: 99% Fold: LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily: Prokaryotic lipoproteins and lipoprotein localization factors Family: Outer-membrane lipoproteins carrier protein LolA Phyre2 PDB 2w7q chain B Region: 21 - 201 Aligned: 174 Modelled: 181 Confidence: 100.0% Identity: 35% PDB header:protein transport Chain: B: PDB Molecule:outer-membrane lipoprotein carrier protein; PDBTitle: structure of pseudomonas aeruginosa lola Phyre2 PDB 3buu chain B Region: 17 - 189 Aligned: 170 Modelled: 173 Confidence: 99.7% Identity: 14% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized lola superfamily protein ne2245; PDBTitle: crystal structure of lola superfamily protein ne2245 from2 nitrosomonas europaea Phyre2 PDB 3bk5 chain A Region: 24 - 189 Aligned: 166 Modelled: 166 Confidence: 99.2% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative outer membrane lipoprotein-sorting protein; PDBTitle: crystal structure of putative outer membrane lipoprotein-sorting2 protein domain from vibrio parahaemolyticus Phyre2 PDB 2v43 chain A Region: 19 - 187 Aligned: 160 Modelled: 169 Confidence: 99.0% Identity: 10% PDB header:regulator Chain: A: PDB Molecule:sigma-e factor regulatory protein rseb; PDBTitle: crystal structure of rseb: a sensor for periplasmic stress2 response in e. coli Phyre2 PDB 2yzy chain A Region: 66 - 201 Aligned: 118 Modelled: 121 Confidence: 98.2% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein ttha1012; PDBTitle: crystal structure of uncharacterized conserved protein from thermus2 thermophilus hb8 Phyre2 PDB 3mha chain B Region: 18 - 177 Aligned: 158 Modelled: 159 Confidence: 58.3% Identity: 13% PDB header:lipid binding protein Chain: B: PDB Molecule:lipoprotein lprg; PDBTitle: crystal structure of lprg from mycobacterium tuberculosis bound to pim Phyre2 PDB 2byo chain A domain 1 Region: 18 - 177 Aligned: 160 Modelled: 160 Confidence: 25.7% Identity: 9% Fold: LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily: Prokaryotic lipoproteins and lipoprotein localization factors Family: LppX-like Phyre2 PDB 3gf5 chain A Region: 189 - 203 Aligned: 15 Modelled: 15 Confidence: 13.1% Identity: 27% PDB header:structural protein Chain: A: PDB Molecule:major vault protein; PDBTitle: crystal structure of the p21 r1-r7 n-terminal domain of murine mvp Phyre2 PDB 3r2c chain J Region: 185 - 199 Aligned: 15 Modelled: 15 Confidence: 11.5% Identity: 33% PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna Phyre2 PDB 2f9j chain P Region: 180 - 198 Aligned: 19 Modelled: 19 Confidence: 9.3% Identity: 21% PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 Phyre2 PDB 2jna chain A domain 1 Region: 1 - 22 Aligned: 22 Modelled: 22 Confidence: 9.1% Identity: 41% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 1o5u chain A Region: 60 - 101 Aligned: 40 Modelled: 42 Confidence: 8.8% Identity: 18% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Hypothetical protein TM1112 Phyre2 PDB 1qub chain A domain 5 Region: 76 - 91 Aligned: 16 Modelled: 16 Confidence: 7.2% Identity: 13% Fold: Complement control module/SCR domain Superfamily: Complement control module/SCR domain Family: Complement control module/SCR domain Phyre2 PDB 1c1z chain A domain 5 Region: 76 - 91 Aligned: 16 Modelled: 16 Confidence: 7.1% Identity: 13% Fold: Complement control module/SCR domain Superfamily: Complement control module/SCR domain Family: Complement control module/SCR domain Phyre2 PDB 1yrr chain A domain 1 Region: 191 - 201 Aligned: 11 Modelled: 11 Confidence: 7.1% Identity: 9% Fold: Composite domain of metallo-dependent hydrolases Superfamily: Composite domain of metallo-dependent hydrolases Family: N-acetylglucosamine-6-phosphate deacetylase, NagA Phyre2 PDB 1gwm chain A Region: 132 - 197 Aligned: 64 Modelled: 66 Confidence: 6.1% Identity: 11% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 29 carbohydrate binding module, CBM29 Phyre2 PDB 1zak chain A domain 2 Region: 189 - 201 Aligned: 13 Modelled: 13 Confidence: 5.8% Identity: 15% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 2ky8 chain A Region: 180 - 194 Aligned: 15 Modelled: 15 Confidence: 5.7% Identity: 33% PDB header:transcription/dna Chain: A: PDB Molecule:methyl-cpg-binding domain protein 2; PDBTitle: solution structure and dynamic analysis of chicken mbd2 methyl binding2 domain bound to a target methylated dna sequence Phyre2 PDB 1iwm chain A Region: 19 - 177 Aligned: 158 Modelled: 159 Confidence: 5.6% Identity: 10% Fold: LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily: Prokaryotic lipoproteins and lipoprotein localization factors Family: Outer membrane lipoprotein receptor LolB Phyre2 1 d1iwla_ 2 c2w7qB_ 3 c3buuB_ 4 c3bk5A_ 5 c2v43A_ 6 c2yzyA_ 7 c3mhaB_ 8 d2byoa1 9 c3gf5A_ 10 c3r2cJ_ 11 c2f9jP_ 12 d2jnaa1 13 d1o5ua_ 14 d1quba5 15 d1c1za5 16 d1yrra1 17 d1gwma_ 18 d1zaka2 19 c2ky8A_ 20 d1iwma_

Detailed template information

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

1 d1iwla_ 100.0 99 Fold:LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily:Prokaryotic lipoproteins and lipoprotein localization factors Family:Outer-membrane lipoproteins carrier protein LolA 2 c2w7qB_ 100.0 35 PDB header:protein transport Chain: B: PDB Molecule:outer-membrane lipoprotein carrier protein; PDBTitle: structure of pseudomonas aeruginosa lola 3 c3buuB_ 99.7 14 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized lola superfamily protein ne2245; PDBTitle: crystal structure of lola superfamily protein ne2245 from2 nitrosomonas europaea 4 c3bk5A_ 99.2 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative outer membrane lipoprotein-sorting protein; PDBTitle: crystal structure of putative outer membrane lipoprotein-sorting2 protein domain from vibrio parahaemolyticus 5 c2v43A_ 99.0 10 PDB header:regulator Chain: A: PDB Molecule:sigma-e factor regulatory protein rseb; PDBTitle: crystal structure of rseb: a sensor for periplasmic stress2 response in e. coli 6 c2yzyA_ 98.2 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein ttha1012; PDBTitle: crystal structure of uncharacterized conserved protein from thermus2 thermophilus hb8 7 c3mhaB_ 58.3 13 PDB header:lipid binding protein Chain: B: PDB Molecule:lipoprotein lprg; PDBTitle: crystal structure of lprg from mycobacterium tuberculosis bound to pim 8 d2byoa1 25.7 9 Fold:LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily:Prokaryotic lipoproteins and lipoprotein localization factors Family:LppX-like 9 c3gf5A_ 13.1 27 PDB header:structural protein Chain: A: PDB Molecule:major vault protein; PDBTitle: crystal structure of the p21 r1-r7 n-terminal domain of murine mvp 10 c3r2cJ_ 11.5 33 PDB header:transcription/rna Chain: J: PDB Molecule:30s ribosomal protein s10; PDBTitle: crystal structure of antitermination factors nusb and nuse in complex2 with boxa rna 11 c2f9jP_ 9.3 21 PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 12 d2jnaa1 9.1 41 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 13 d1o5ua_ 8.8 18 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Hypothetical protein TM1112 14 d1quba5 7.2 13 Fold:Complement control module/SCR domain Superfamily:Complement control module/SCR domain Family:Complement control module/SCR domain 15 d1c1za5 7.1 13 Fold:Complement control module/SCR domain Superfamily:Complement control module/SCR domain Family:Complement control module/SCR domain 16 d1yrra1 7.1 9 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:N-acetylglucosamine-6-phosphate deacetylase, NagA 17 d1gwma_ 6.1 11 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 29 carbohydrate binding module, CBM29 18 d1zaka2 5.8 15 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 19 c2ky8A_ 5.7 33 PDB header:transcription/dna Chain: A: PDB Molecule:methyl-cpg-binding domain protein 2; PDBTitle: solution structure and dynamic analysis of chicken mbd2 methyl binding2 domain bound to a target methylated dna sequence 20 d1iwma_ 5.6 10 Fold:LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily:Prokaryotic lipoproteins and lipoprotein localization factors Family:Outer membrane lipoprotein receptor LolB

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