Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	I	N	Q	P	A	V	A	G	T	L	E	S	G	D	V	M	I	R	I	A	P	L	D	T	Q	D	I	D	L	Q	I	N	S	S	V	E	K	Q	F	G	D	A	I	R	T	T	I	L	D	V	L	A	R	Y	N	V	R	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.
Sequence		V	Q	L	N	V	D	D	K	G	A	L	D	C	I	L	R	A	R	L	E	A	L	L	A	R	A	S	G	I	P	A	L	P	W	E	D	C	Q
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 1ufw chain A Region: 23 - 71 Aligned: 47 Modelled: 49 Confidence: 56.6% Identity: 23% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 2dy1 chain A domain 3 Region: 16 - 67 Aligned: 52 Modelled: 52 Confidence: 51.1% Identity: 29% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Translational machinery components Phyre2 PDB 2dnr chain A Region: 23 - 67 Aligned: 43 Modelled: 45 Confidence: 41.8% Identity: 19% PDB header:rna binding protein Chain: A: PDB Molecule:synaptojanin-1; PDBTitle: solution structure of rna binding domain in synaptojanin 1 Phyre2 PDB 2bv3 chain A domain 3 Region: 10 - 67 Aligned: 58 Modelled: 58 Confidence: 37.4% Identity: 21% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Translational machinery components Phyre2 PDB 1vbk chain A Region: 30 - 66 Aligned: 37 Modelled: 37 Confidence: 32.3% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ph1313; PDBTitle: crystal structure of ph1313 from pyrococcus horikoshii ot3 Phyre2 PDB 1mg7 chain A domain 1 Region: 32 - 73 Aligned: 41 Modelled: 42 Confidence: 25.6% Identity: 12% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Early switch protein XOL-1, N-terminal domain Phyre2 PDB 1vbk chain A domain 2 Region: 30 - 66 Aligned: 37 Modelled: 37 Confidence: 24.1% Identity: 14% Fold: THUMP domain Superfamily: THUMP domain-like Family: THUMP domain Phyre2 PDB 2nsc chain A Region: 35 - 55 Aligned: 21 Modelled: 21 Confidence: 22.1% Identity: 19% PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima Phyre2 PDB 1am7 chain A Region: 67 - 93 Aligned: 27 Modelled: 27 Confidence: 21.1% Identity: 37% Fold: Lysozyme-like Superfamily: Lysozyme-like Family: Lambda lysozyme Phyre2 PDB 1mg7 chain B Region: 41 - 73 Aligned: 32 Modelled: 33 Confidence: 20.0% Identity: 13% PDB header:gene regulation Chain: B: PDB Molecule:early switch protein xol-1 2.2k splice form; PDBTitle: crystal structure of xol-1 Phyre2 PDB 3jvn chain A Region: 41 - 70 Aligned: 30 Modelled: 30 Confidence: 15.6% Identity: 27% PDB header:transferase Chain: A: PDB Molecule:acetyltransferase; PDBTitle: crystal structure of the acetyltransferase vf_1542 from vibrio2 fischeri, northeast structural genomics consortium target vfr136 Phyre2 PDB 1uwd chain A Region: 21 - 71 Aligned: 51 Modelled: 51 Confidence: 15.4% Identity: 10% Fold: Alpha-lytic protease prodomain-like Superfamily: Fe-S cluster assembly (FSCA) domain-like Family: PaaD-like Phyre2 PDB 2cu6 chain A domain 1 Region: 19 - 65 Aligned: 44 Modelled: 47 Confidence: 14.0% Identity: 14% Fold: Alpha-lytic protease prodomain-like Superfamily: Fe-S cluster assembly (FSCA) domain-like Family: PaaD-like Phyre2 PDB 3gty chain X Region: 35 - 55 Aligned: 21 Modelled: 21 Confidence: 12.8% Identity: 19% PDB header:chaperone/ribosomal protein Chain: X: PDB Molecule:trigger factor; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone Phyre2 PDB 3ffv chain A Region: 10 - 32 Aligned: 22 Modelled: 23 Confidence: 12.7% Identity: 18% PDB header:protein binding Chain: A: PDB Molecule:protein syd; PDBTitle: crystal structure analysis of syd Phyre2 PDB 2nn6 chain H domain 2 Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 12.7% Identity: 25% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 1tte chain A domain 1 Region: 46 - 61 Aligned: 16 Modelled: 16 Confidence: 10.5% Identity: 31% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 1win chain A Region: 39 - 67 Aligned: 29 Modelled: 29 Confidence: 10.2% Identity: 17% Fold: EF-Ts domain-like Superfamily: Band 7/SPFH domain Family: Band 7/SPFH domain Phyre2 PDB 2zkq chain I Region: 10 - 86 Aligned: 75 Modelled: 77 Confidence: 9.6% Identity: 15% PDB header:ribosomal protein/rna Chain: I: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1reg chain X Region: 49 - 60 Aligned: 12 Modelled: 12 Confidence: 9.2% Identity: 17% Fold: Ferredoxin-like Superfamily: Translational regulator protein regA Family: Translational regulator protein regA Phyre2 1 d1ufwa_ 2 d2dy1a3 3 c2dnrA_ 4 d2bv3a3 5 c1vbkA_ 6 d1mg7a1 7 d1vbka2 8 c2nscA_ 9 d1am7a_ 10 c1mg7B_ 11 c3jvnA_ 12 d1uwda_ 13 d2cu6a1 14 c3gtyX_ 15 c3ffvA_ 16 d2nn6h2 17 d1ttea1 18 d1wina_ 19 c2zkqi_ 20 d1regx_ 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 51 52

Detailed template information

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

1 d1ufwa_ 56.6 23 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 2 d2dy1a3 51.1 29 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 3 c2dnrA_ 41.8 19 PDB header:rna binding protein Chain: A: PDB Molecule:synaptojanin-1; PDBTitle: solution structure of rna binding domain in synaptojanin 1 4 d2bv3a3 37.4 21 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 5 c1vbkA_ 32.3 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ph1313; PDBTitle: crystal structure of ph1313 from pyrococcus horikoshii ot3 6 d1mg7a1 25.6 12 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Early switch protein XOL-1, N-terminal domain 7 d1vbka2 24.1 14 Fold:THUMP domain Superfamily:THUMP domain-like Family:THUMP domain 8 c2nscA_ 22.1 19 PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima 9 d1am7a_ 21.1 37 Fold:Lysozyme-like Superfamily:Lysozyme-like Family:Lambda lysozyme 10 c1mg7B_ 20.0 13 PDB header:gene regulation Chain: B: PDB Molecule:early switch protein xol-1 2.2k splice form; PDBTitle: crystal structure of xol-1 11 c3jvnA_ 15.6 27 PDB header:transferase Chain: A: PDB Molecule:acetyltransferase; PDBTitle: crystal structure of the acetyltransferase vf_1542 from vibrio2 fischeri, northeast structural genomics consortium target vfr136 12 d1uwda_ 15.4 10 Fold:Alpha-lytic protease prodomain-like Superfamily:Fe-S cluster assembly (FSCA) domain-like Family:PaaD-like 13 d2cu6a1 14.0 14 Fold:Alpha-lytic protease prodomain-like Superfamily:Fe-S cluster assembly (FSCA) domain-like Family:PaaD-like 14 c3gtyX_ 12.8 19 PDB header:chaperone/ribosomal protein Chain: X: PDB Molecule:trigger factor; PDBTitle: promiscuous substrate recognition in folding and assembly activities2 of the trigger factor chaperone 15 c3ffvA_ 12.7 18 PDB header:protein binding Chain: A: PDB Molecule:protein syd; PDBTitle: crystal structure analysis of syd 16 d2nn6h2 12.7 25 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 17 d1ttea1 10.5 31 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 18 d1wina_ 10.2 17 Fold:EF-Ts domain-like Superfamily:Band 7/SPFH domain Family:Band 7/SPFH domain 19 c2zkqi_ 9.6 15 PDB header:ribosomal protein/rna Chain: I: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 20 d1regx_ 9.2 17 Fold:Ferredoxin-like Superfamily:Translational regulator protein regA Family:Translational regulator protein regA 21 d1z7ma1 not modelled 9.1 9 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 22 d1yd9a1 not modelled 8.8 15 Fold:Macro domain-like Superfamily:Macro domain-like Family:Macro domain 23 c1fwlD_ not modelled 8.7 13 PDB header:transferase Chain: D: PDB Molecule:homoserine kinase; PDBTitle: crystal structure of homoserine kinase 24 d1puga_ not modelled 8.4 18 Fold:YbaB-like Superfamily:YbaB-like Family:YbaB-like 25 d1dwka2 not modelled 8.3 7 Fold:Cyanase C-terminal domain Superfamily:Cyanase C-terminal domain Family:Cyanase C-terminal domain 26 d1w1oa1 not modelled 8.1 16 Fold:Ferredoxin-like Superfamily:FAD-linked oxidases, C-terminal domain Family:Cytokinin dehydrogenase 1 27 c3m0zD_ not modelled 7.6 13 PDB header:lyase Chain: D: PDB Molecule:putative aldolase; PDBTitle: crystal structure of putative aldolase from klebsiella2 pneumoniae. 28 c2kq1A_ not modelled 7.5 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:bh0266 protein; PDBTitle: solution structure of protein bh0266 from bacillus2 halodurans. northeast structural genomics consortium target3 bhr97a 29 c1zr5B_ not modelled 7.2 14 PDB header:gene regulation Chain: B: PDB Molecule:h2afy protein; PDBTitle: crystal structure of the macro-domain of human core histone variant2 macroh2a1.2 30 d1t11a2 not modelled 6.9 32 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 31 c1ybxA_ not modelled 6.6 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: conserved hypothetical protein cth-383 from clostridium thermocellum 32 c3lnoA_ not modelled 6.5 19 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of domain of unknown function duf59 from2 bacillus anthracis 33 d1p97a_ not modelled 6.5 17 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Hypoxia-inducible factor Hif2a, C-terminal domain 34 c2jo7A_ not modelled 6.5 63 PDB header:surface active protein Chain: A: PDB Molecule:glycosylphosphatidylinositol-anchored merozoite PDBTitle: solution structure of the adhesion protein bd37 from2 babesia divergens 35 d1p42a1 not modelled 6.4 30 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC 36 c1usvB_ not modelled 6.3 15 PDB header:chaperone Chain: B: PDB Molecule:aha1; PDBTitle: the structure of the complex between aha1 and hsp90 37 c3ew5B_ not modelled 6.2 11 PDB header:rna binding protein Chain: B: PDB Molecule:macro domain of non-structural protein 3; PDBTitle: structure of the tetragonal crystal form of x (adrp) domain2 from fcov 38 d1o75a3 not modelled 6.1 29 Fold:Tp47 lipoprotein, N-terminal domain Superfamily:Tp47 lipoprotein, N-terminal domain Family:Tp47 lipoprotein, N-terminal domain 39 c3h0gO_ not modelled 6.0 23 PDB header:transcription Chain: O: PDB Molecule:dna-directed rna polymerase ii subunit rpb3; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 40 d2q3la1 not modelled 5.9 8 Fold:SpoIIaa-like Superfamily:SpoIIaa-like Family:Sfri0576-like 41 d1y14b2 not modelled 5.9 18 Fold:Dodecin subunit-like Superfamily:N-terminal, heterodimerisation domain of RBP7 (RpoE) Family:N-terminal, heterodimerisation domain of RBP7 (RpoE) 42 c3q71A_ not modelled 5.8 14 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 14; PDBTitle: human parp14 (artd8) - macro domain 2 in complex with adenosine-5-2 diphosphoribose 43 c2rpbA_ not modelled 5.7 11 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein 44 c1ta9A_ not modelled 5.6 11 PDB header:oxidoreductase Chain: A: PDB Molecule:glycerol dehydrogenase; PDBTitle: crystal structure of glycerol dehydrogenase from schizosaccharomyces2 pombe 45 d1v54g_ not modelled 5.5 25 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIa Family:Mitochondrial cytochrome c oxidase subunit VIa 46 d1u0ua2 not modelled 5.4 11 Fold:Thiolase-like Superfamily:Thiolase-like Family:Chalcone synthase-like 47 d1ee0a2 not modelled 5.4 11 Fold:Thiolase-like Superfamily:Thiolase-like Family:Chalcone synthase-like 48 d1usub_ not modelled 5.4 15 Fold:Aha1/BPI domain-like Superfamily:Activator of Hsp90 ATPase, Aha1 Family:Activator of Hsp90 ATPase, Aha1 49 c3imkA_ not modelled 5.3 40 PDB header:metal binding protein Chain: A: PDB Molecule:putative molybdenum carrier protein; PDBTitle: crystal structure of putative molybdenum carrier protein (yp_461806.1)2 from syntrophus aciditrophicus sb at 1.45 a resolution 50 d2ba0a2 not modelled 5.3 17 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 51 d1mxaa3 not modelled 5.2 40 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 52 d1wuda1 not modelled 5.1 13 Fold:SAM domain-like Superfamily:HRDC-like Family:HRDC domain from helicases

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