Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	P	L	I	L	S	I	F	A	L	F	L	A	G	C	T	H	S	Q	Q	S	M	V	D	T	F	R	A	S	L	F	D	N	Q	D	I	T	V	A	D	Q	Q	I	Q	A	L	P	Y	S	T	M	Y	L	R	L	N	E	G	Q
Secondary structure
SS confidence
Disorder		?	?	?	?														?	?	?															?	?	?	?	?	?					?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	I	F	V	V	L	G	Y	I	E	Q	E	Q	S	K	W	L	S	Q	D	N	A	M	L	V	T	H	N	G	R	L	L	K	T	V	K	L	N	N	N	L	L	E	V	T	N	S	G	Q	D	P	L	R	N	A	L	A	I	K	D
Secondary structure
SS confidence
Disorder																														?											?	?			?	?		?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	S	R	W	T	R	D	I	L	W	S	E	D	N	H	F	R	S	A	T	L	S	S	T	F	S	F	A	G	L	E	T	L	N	I	A	G	R	N	V	L	C	N	V	W	Q	E	E	V	T	S	T	R	P	E	K	Q	W	Q	N
Secondary structure
SS confidence
Disorder		?	?																									?	?	?	?						?																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.
Sequence		T	F	W	V	D	S	A	T	G	Q	V	R	Q	S	R	Q	M	L	G	A	G	V	I	P	V	E	M	T	F	L	K	P	A	P
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 2in5 chain A domain 1 Region: 18 - 214 Aligned: 194 Modelled: 197 Confidence: 100.0% Identity: 96% Fold: YmcC-like Superfamily: YmcC-like Family: YmcC-like Phyre2 PDB 1bml chain C domain 3 Region: 183 - 208 Aligned: 26 Modelled: 26 Confidence: 44.1% Identity: 27% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 2byo chain A domain 1 Region: 144 - 211 Aligned: 63 Modelled: 68 Confidence: 41.3% Identity: 16% Fold: LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily: Prokaryotic lipoproteins and lipoprotein localization factors Family: LppX-like Phyre2 PDB 3jsl chain A Region: 80 - 96 Aligned: 17 Modelled: 17 Confidence: 22.1% Identity: 18% PDB header:ligase Chain: A: PDB Molecule:dna ligase; PDBTitle: crystal structure of the adenylation domain of nad+-2 dependent dna ligase from staphylococcus aureus Phyre2 PDB 2x6v chain B Region: 80 - 104 Aligned: 25 Modelled: 25 Confidence: 18.5% Identity: 28% PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form Phyre2 PDB 1a0i chain A domain 1 Region: 84 - 103 Aligned: 20 Modelled: 20 Confidence: 18.4% Identity: 20% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: DNA ligase/mRNA capping enzyme postcatalytic domain Phyre2 PDB 3o0l chain B Region: 182 - 214 Aligned: 32 Modelled: 33 Confidence: 15.6% Identity: 25% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a pfam duf1425 family member (shew_1734) from2 shewanella sp. pv-4 at 1.81 a resolution Phyre2 PDB 3fzx chain A Region: 55 - 211 Aligned: 153 Modelled: 157 Confidence: 12.6% Identity: 12% PDB header:lipid binding protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of a putative exported protein with ymcc-like fold2 (bf2203) from bacteroides fragilis nctc 9343 at 2.22 a resolution Phyre2 PDB 1v9p chain A domain 3 Region: 80 - 96 Aligned: 17 Modelled: 17 Confidence: 12.5% Identity: 24% Fold: ATP-grasp Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain Family: Adenylation domain of NAD+-dependent DNA ligase Phyre2 PDB 1ogm chain X domain 1 Region: 50 - 94 Aligned: 44 Modelled: 45 Confidence: 12.4% Identity: 16% Fold: Dextranase, N-terminal domain Superfamily: Dextranase, N-terminal domain Family: Dextranase, N-terminal domain Phyre2 PDB 3kdv chain B Region: 75 - 123 Aligned: 49 Modelled: 49 Confidence: 12.2% Identity: 12% PDB header:dna binding protein Chain: B: PDB Molecule:dna damage response b protein; PDBTitle: crystal structure of dna damage response b (ddrb) from deinococcus2 geothermalis Phyre2 PDB 2v43 chain A Region: 41 - 206 Aligned: 142 Modelled: 151 Confidence: 11.8% Identity: 15% 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 2h8b chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 11.3% Identity: 57% PDB header:hormone/growth factor Chain: A: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 Phyre2 PDB 2k6t chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 11.3% Identity: 57% PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: solution structure of the relaxin-like factor Phyre2 PDB 2k6u chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 10.9% Identity: 57% PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: the solution structure of a conformationally restricted2 fully active derivative of the human relaxin-like factor3 (rlf) Phyre2 PDB 1h6f chain A Region: 80 - 104 Aligned: 25 Modelled: 25 Confidence: 9.5% Identity: 24% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: p53-like transcription factors Family: T-box Phyre2 PDB 3mlq chain E Region: 54 - 74 Aligned: 21 Modelled: 21 Confidence: 9.1% Identity: 19% PDB header:transferase/transcription Chain: E: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain Phyre2 PDB 1zbs chain A domain 2 Region: 14 - 46 Aligned: 33 Modelled: 31 Confidence: 9.0% Identity: 27% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: BadF/BadG/BcrA/BcrD-like Phyre2 PDB 3mlq chain H Region: 54 - 74 Aligned: 21 Modelled: 21 Confidence: 7.7% Identity: 19% PDB header:transferase/transcription Chain: H: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain Phyre2 PDB 1dgs chain A domain 3 Region: 80 - 96 Aligned: 17 Modelled: 17 Confidence: 7.2% Identity: 18% Fold: ATP-grasp Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain Family: Adenylation domain of NAD+-dependent DNA ligase Phyre2 1 d2in5a1 2 d1bmlc3 3 d2byoa1 4 c3jslA_ 5 c2x6vB_ 6 d1a0ia1 7 c3o0lB_ 8 c3fzxA_ 9 d1v9pa3 10 d1ogmx1 11 c3kdvB_ 12 c2v43A_ 13 c2h8bA_ 14 c2k6tA_ 15 c2k6uA_ 16 d1h6fa_ 17 c3mlqE_ 18 d1zbsa2 19 c3mlqH_ 20 d1dgsa3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d2in5a1 100.0 96 Fold:YmcC-like Superfamily:YmcC-like Family:YmcC-like 2 d1bmlc3 44.1 27 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 3 d2byoa1 41.3 16 Fold:LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily:Prokaryotic lipoproteins and lipoprotein localization factors Family:LppX-like 4 c3jslA_ 22.1 18 PDB header:ligase Chain: A: PDB Molecule:dna ligase; PDBTitle: crystal structure of the adenylation domain of nad+-2 dependent dna ligase from staphylococcus aureus 5 c2x6vB_ 18.5 28 PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form 6 d1a0ia1 18.4 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain 7 c3o0lB_ 15.6 25 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a pfam duf1425 family member (shew_1734) from2 shewanella sp. pv-4 at 1.81 a resolution 8 c3fzxA_ 12.6 12 PDB header:lipid binding protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of a putative exported protein with ymcc-like fold2 (bf2203) from bacteroides fragilis nctc 9343 at 2.22 a resolution 9 d1v9pa3 12.5 24 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 10 d1ogmx1 12.4 16 Fold:Dextranase, N-terminal domain Superfamily:Dextranase, N-terminal domain Family:Dextranase, N-terminal domain 11 c3kdvB_ 12.2 12 PDB header:dna binding protein Chain: B: PDB Molecule:dna damage response b protein; PDBTitle: crystal structure of dna damage response b (ddrb) from deinococcus2 geothermalis 12 c2v43A_ 11.8 15 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 13 c2h8bA_ 11.3 57 PDB header:hormone/growth factor Chain: A: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 14 c2k6tA_ 11.3 57 PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: solution structure of the relaxin-like factor 15 c2k6uA_ 10.9 57 PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: the solution structure of a conformationally restricted2 fully active derivative of the human relaxin-like factor3 (rlf) 16 d1h6fa_ 9.5 24 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:T-box 17 c3mlqE_ 9.1 19 PDB header:transferase/transcription Chain: E: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain 18 d1zbsa2 9.0 27 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:BadF/BadG/BcrA/BcrD-like 19 c3mlqH_ 7.7 19 PDB header:transferase/transcription Chain: H: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain 20 d1dgsa3 7.2 18 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 21 c3bacA_ not modelled 6.8 29 PDB header:ligase Chain: A: PDB Molecule:dna ligase; PDBTitle: structural basis for the inhibition of bacterial nad+2 dependent dna ligase 22 d1bhia_ not modelled 6.8 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 23 d2f1la2 not modelled 6.8 8 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:RimM N-terminal domain-like 24 d1b04a_ not modelled 6.5 18 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 25 d1azwa_ not modelled 5.9 21 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Proline iminopeptidase-like 26 d4tsva_ not modelled 5.9 17 Fold:TNF-like Superfamily:TNF-like Family:TNF-like 27 d1r57a_ not modelled 5.8 12 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-acetyl transferase, NAT 28 c3o44G_ not modelled 5.8 16 PDB header:toxin Chain: G: PDB Molecule:hemolysin; PDBTitle: crystal structure of the vibrio cholerae cytolysin (hlya) heptameric2 pore 29 c1c9lA_ not modelled 5.8 44 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin 30 d2cupa3 not modelled 5.8 44 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 31 d1a9xb1 not modelled 5.7 20 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Carbamoyl phosphate synthetase, small subunit N-terminal domain Family:Carbamoyl phosphate synthetase, small subunit N-terminal domain 32 c2j8pA_ not modelled 5.6 36 PDB header:nuclear protein Chain: A: PDB Molecule:cleavage stimulation factor 64 kda subunit; PDBTitle: nmr structure of c-terminal domain of human cstf-64 33 d1utca2 not modelled 5.5 44 Fold:7-bladed beta-propeller Superfamily:Clathrin heavy-chain terminal domain Family:Clathrin heavy-chain terminal domain 34 c3f6zB_ not modelled 5.4 14 PDB header:hydrolase Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of pseudomonas aeruginosa mlic in complex2 with hen egg white lysozyme 35 d3bl9a2 not modelled 5.4 24 Fold:mRNA decapping enzyme DcpS N-terminal domain Superfamily:mRNA decapping enzyme DcpS N-terminal domain Family:mRNA decapping enzyme DcpS N-terminal domain 36 d1vlra2 not modelled 5.3 18 Fold:mRNA decapping enzyme DcpS N-terminal domain Superfamily:mRNA decapping enzyme DcpS N-terminal domain Family:mRNA decapping enzyme DcpS N-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