Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	I	T	A	Q	S	V	Y	R	D	T	G	N	F	F	R	N	Q	F	M	T	I	L	L	V	S	L	L	C	A	F	I	T	V	V	L	G	H	V	F	S	P	S	D	A	Q	L	A	Q	L	N	D	G	V	P	V	S	G	S
Secondary structure
SS confidence
Disorder		?	?	?	?																																																		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	G	L	F	D	L	V	Q	N	M	S	P	E	Q	Q	Q	I	L	L	Q	A	S	A	A	S	T	F	S	G	L	I	G	N	A	I	L	A	G	G	V	I	L	I	I	Q	L	V	S	A	G	Q	R	V	S	A	L	R	A	I	G
Secondary structure
SS confidence
Disorder																					?	?	?																										?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	S	A	P	I	L	P	K	L	F	I	L	I	F	L	T	T	L	L	V	Q	I	G	I	M	L	V	V	V	P	G	I	I	M	A	I	L	L	A	L	A	P	V	M	L	V	Q	D	K	M	G	V	F	A	S	M	R	S	S	M
Secondary structure
SS confidence
Disorder																																																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	L	T	W	A	N	M	R	L	V	A	P	A	V	L	S	W	L	L	A	K	T	L	L	L	L	F	A	S	S	F	A	A	L	T	P	E	I	G	A	V	L	A	N	T	L	S	N	L	I	S	A	I	L	L	I	Y	L	F	R
Secondary structure
SS confidence
Disorder																																?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		L	Y	M	L	I	R	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 2kvl chain A Region: 177 - 195 Aligned: 19 Modelled: 19 Confidence: 23.2% Identity: 26% PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7 Phyre2 PDB 3hd7 chain A Region: 177 - 212 Aligned: 36 Modelled: 36 Confidence: 17.8% Identity: 8% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 1cii chain A Region: 185 - 234 Aligned: 50 Modelled: 50 Confidence: 13.5% Identity: 18% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 1k8r chain B Region: 173 - 182 Aligned: 10 Modelled: 10 Confidence: 9.5% Identity: 30% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ras-binding domain, RBD Phyre2 PDB 2hgc chain A domain 1 Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.0% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: YjcQ-like Phyre2 PDB 2hgc chain A Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.0% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yjcq protein; PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346. Phyre2 PDB 1k8k chain E Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 8.7% Identity: 8% Fold: Arp2/3 complex 21 kDa subunit ARPC3 Superfamily: Arp2/3 complex 21 kDa subunit ARPC3 Family: Arp2/3 complex 21 kDa subunit ARPC3 Phyre2 PDB 1rh5 chain C Region: 11 - 39 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 17% PDB header:protein transport Chain: C: PDB Molecule:secbeta; PDBTitle: the structure of a protein conducting channel Phyre2 PDB 1rh5 chain C Region: 11 - 39 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 17% Fold: Single transmembrane helix Superfamily: Sec-beta subunit Family: Sec-beta subunit Phyre2 PDB 3go5 chain A Region: 167 - 195 Aligned: 29 Modelled: 28 Confidence: 8.2% Identity: 0% PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution Phyre2 PDB 1pf4 chain A domain 2 Region: 173 - 216 Aligned: 44 Modelled: 44 Confidence: 8.2% Identity: 5% Fold: ABC transporter transmembrane region Superfamily: ABC transporter transmembrane region Family: ABC transporter transmembrane region Phyre2 PDB 1m45 chain B Region: 9 - 24 Aligned: 16 Modelled: 16 Confidence: 8.2% Identity: 6% PDB header:cell cycle protein Chain: B: PDB Molecule:iq2 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq2 of myo2p, a class v2 myosin Phyre2 PDB 1q2i chain A Region: 176 - 188 Aligned: 13 Modelled: 13 Confidence: 7.7% Identity: 0% PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells Phyre2 PDB 1unh chain D Region: 241 - 247 Aligned: 7 Modelled: 7 Confidence: 7.4% Identity: 71% PDB header:cell cycle Chain: D: PDB Molecule:cyclin-dependent kinase 5 activator 1; PDBTitle: structural mechanism for the inhibition of cdk5-p25 by2 roscovitine, aloisine and indirubin. Phyre2 PDB 1unl chain D Region: 241 - 247 Aligned: 7 Modelled: 7 Confidence: 7.4% Identity: 71% Fold: Cyclin-like Superfamily: Cyclin-like Family: Cyclin Phyre2 PDB 1kq8 chain A Region: 97 - 127 Aligned: 31 Modelled: 31 Confidence: 7.3% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 3 forkhead homolog 1; PDBTitle: solution structure of winged helix protein hfh-1 Phyre2 PDB 1kq8 chain A Region: 97 - 127 Aligned: 31 Modelled: 31 Confidence: 7.3% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Forkhead DNA-binding domain Phyre2 PDB 3jqo chain V Region: 183 - 201 Aligned: 19 Modelled: 14 Confidence: 7.0% Identity: 11% PDB header:transport protein Chain: V: PDB Molecule:traf protein; PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system Phyre2 PDB 4a1a chain M Region: 2 - 20 Aligned: 19 Modelled: 19 Confidence: 7.0% Identity: 5% PDB header:ribosome Chain: M: PDB Molecule:60s ribosomal protein l5; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. Phyre2 PDB 1zp0 chain D Region: 151 - 182 Aligned: 32 Modelled: 32 Confidence: 6.9% Identity: 13% PDB header:oxidoreductase Chain: D: PDB Molecule:small cytochrome binding protein; PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone Phyre2 1 c2kvlA_ 2 c3hd7A_ 3 c1ciiA_ 4 d1k8rb_ 5 d2hgca1 6 c2hgcA_ 7 d1k8ke_ 8 c1rh5C_ 9 d1rh5c_ 10 c3go5A_ 11 d1pf4a2 12 c1m45B_ 13 c1q2iA_ 14 c1unhD_ 15 d1unld_ 16 c1kq8A_ 17 d1kq8a_ 18 c3jqoV_ 19 c4a1aM_ 20 c1zp0D_ 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 53 54 55

Detailed template information

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

1 c2kvlA_ 23.2 26 PDB header:viral protein Chain: A: PDB Molecule:major outer capsid protein vp7; PDBTitle: nmr structure of the c-terminal domain of vp7 2 c3hd7A_ 17.8 8 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 3 c1ciiA_ 13.5 18 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 4 d1k8rb_ 9.5 30 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 5 d2hgca1 9.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:YjcQ-like 6 c2hgcA_ 9.0 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yjcq protein; PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346. 7 d1k8ke_ 8.7 8 Fold:Arp2/3 complex 21 kDa subunit ARPC3 Superfamily:Arp2/3 complex 21 kDa subunit ARPC3 Family:Arp2/3 complex 21 kDa subunit ARPC3 8 c1rh5C_ 8.6 17 PDB header:protein transport Chain: C: PDB Molecule:secbeta; PDBTitle: the structure of a protein conducting channel 9 d1rh5c_ 8.6 17 Fold:Single transmembrane helix Superfamily:Sec-beta subunit Family:Sec-beta subunit 10 c3go5A_ 8.2 0 PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution 11 d1pf4a2 8.2 5 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 12 c1m45B_ 8.2 6 PDB header:cell cycle protein Chain: B: PDB Molecule:iq2 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq2 of myo2p, a class v2 myosin 13 c1q2iA_ 7.7 0 PDB header:antitumor protein Chain: A: PDB Molecule:pnc27; PDBTitle: nmr solution structure of a peptide from the mdm-2 binding2 domain of the p53 protein that is selectively cytotoxic to3 cancer cells 14 c1unhD_ 7.4 71 PDB header:cell cycle Chain: D: PDB Molecule:cyclin-dependent kinase 5 activator 1; PDBTitle: structural mechanism for the inhibition of cdk5-p25 by2 roscovitine, aloisine and indirubin. 15 d1unld_ 7.4 71 Fold:Cyclin-like Superfamily:Cyclin-like Family:Cyclin 16 c1kq8A_ 7.3 19 PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 3 forkhead homolog 1; PDBTitle: solution structure of winged helix protein hfh-1 17 d1kq8a_ 7.3 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 18 c3jqoV_ 7.0 11 PDB header:transport protein Chain: V: PDB Molecule:traf protein; PDBTitle: crystal structure of the outer membrane complex of a type iv2 secretion system 19 c4a1aM_ 7.0 5 PDB header:ribosome Chain: M: PDB Molecule:60s ribosomal protein l5; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. 20 c1zp0D_ 6.9 13 PDB header:oxidoreductase Chain: D: PDB Molecule:small cytochrome binding protein; PDBTitle: crystal structure of mitochondrial respiratory complex ii2 bound with 3-nitropropionate and 2-thenoyltrifluoroacetone 21 d1cg5a_ not modelled 6.8 21 Fold:Globin-like Superfamily:Globin-like Family:Globins 22 c3mkuA_ not modelled 6.6 13 PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter 23 c1e17A_ not modelled 6.4 10 PDB header:dna binding domain Chain: A: PDB Molecule:afx; PDBTitle: solution structure of the dna binding domain of the human2 forkhead transcription factor afx (foxo4) 24 c3co7C_ not modelled 6.2 16 PDB header:transcription/dna Chain: C: PDB Molecule:forkhead box protein o1; PDBTitle: crystal structure of foxo1 dbd bound to dbe2 dna 25 d1myta_ not modelled 6.2 19 Fold:Globin-like Superfamily:Globin-like Family:Globins 26 d2fx0a2 not modelled 6.1 0 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 27 d1hdsa_ not modelled 6.1 7 Fold:Globin-like Superfamily:Globin-like Family:Globins 28 c2lkeA_ not modelled 5.9 30 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-m; PDBTitle: structures and interaction analyses of the integrin alpha-m beta-22 cytoplasmic tails 29 c3g73A_ not modelled 5.9 10 PDB header:transcription/dna Chain: A: PDB Molecule:forkhead box protein m1; PDBTitle: structure of the foxm1 dna binding 30 c1geaA_ not modelled 5.9 25 PDB header:neuropeptide Chain: A: PDB Molecule:pituitary adenylate cyclase activating PDBTitle: receptor-bound conformation of pacap21 31 c2ciuA_ not modelled 5.9 0 PDB header:protein transport Chain: A: PDB Molecule:import inner membrane translocase subunit tim21 PDBTitle: structure of the ims domain of the mitochondrial import2 protein tim21 from s. cerevisiae 32 c1n2dC_ not modelled 5.8 6 PDB header:cell cycle Chain: C: PDB Molecule:iq2 and iq3 motifs from myo2p, a class v myosin; PDBTitle: ternary complex of mlc1p bound to iq2 and iq3 of myo2p, a2 class v myosin 33 c2lkjA_ not modelled 5.6 33 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-m; PDBTitle: structures and interaction analyses of the integrin alpha-m beta-22 cytoplasmic tails 34 d2lhba_ not modelled 5.6 7 Fold:Globin-like Superfamily:Globin-like Family:Globins 35 d1d5va_ not modelled 5.6 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 36 c2wwbB_ not modelled 5.6 7 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome 37 c2rlwA_ not modelled 5.6 14 PDB header:toxin Chain: A: PDB Molecule:plnf; PDBTitle: three-dimensional structure of the two peptides that2 constitute the two-peptide bacteriocin plantaracin ef 38 c2qq4A_ not modelled 5.5 20 PDB header:metal binding protein Chain: A: PDB Molecule:iron-sulfur cluster biosynthesis protein iscu; PDBTitle: crystal structure of iron-sulfur cluster biosynthesis2 protein iscu (ttha1736) from thermus thermophilus hb8 39 c1yhuW_ not modelled 5.5 14 PDB header:oxygen storage/transport Chain: W: PDB Molecule:hemoglobin b1a chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits. 40 d3bpya1 not modelled 5.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 41 d1scta_ not modelled 5.5 23 Fold:Globin-like Superfamily:Globin-like Family:Globins 42 d2hfha_ not modelled 5.4 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 43 c2zs1D_ not modelled 5.4 8 PDB header:oxygen storage, oxygen transport Chain: D: PDB Molecule:extracellular giant hemoglobin major globin subunit b1; PDBTitle: structural basis for the heterotropic and homotropic interactions of2 invertebrate giant hemoglobin 44 d1sxja1 not modelled 5.4 9 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain 45 d1c17m_ not modelled 5.4 11 Fold:F1F0 ATP synthase subunit A Superfamily:F1F0 ATP synthase subunit A Family:F1F0 ATP synthase subunit A 46 c1g2cN_ not modelled 5.3 13 PDB header:viral protein Chain: N: PDB Molecule:fusion protein (f); PDBTitle: human respiratory syncytial virus fusion protein core 47 d2a07f1 not modelled 5.3 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 48 c2wukD_ not modelled 5.3 17 PDB header:cell cycle Chain: D: PDB Molecule:septum site-determining protein diviva; PDBTitle: diviva n-terminal domain, f17a mutant 49 c2nq2A_ not modelled 5.3 16 PDB header:metal transport Chain: A: PDB Molecule:hypothetical abc transporter permease protein PDBTitle: an inward-facing conformation of a putative metal-chelate2 type abc transporter. 50 d1hbra_ not modelled 5.3 0 Fold:Globin-like Superfamily:Globin-like Family:Globins 51 c2c0kB_ not modelled 5.3 11 PDB header:oxygen transport Chain: B: PDB Molecule:hemoglobin; PDBTitle: the structure of hemoglobin from the botfly gasterophilus2 intestinalis 52 c3gztF_ not modelled 5.2 28 PDB header:virus Chain: F: PDB Molecule:outer capsid glycoprotein vp7; PDBTitle: vp7 recoated rotavirus dlp 53 c3bjqA_ not modelled 5.2 14 PDB header:viral protein Chain: A: PDB Molecule:phage-related protein; PDBTitle: crystal structure of a phage-related protein (bb3626) from bordetella2 bronchiseptica rb50 at 2.05 a resolution 54 d2gdma_ not modelled 5.2 9 Fold:Globin-like Superfamily:Globin-like Family:Globins 55 c3h8aF_ not modelled 5.1 40 PDB header:lyase/protein binding Chain: F: PDB Molecule:rnase e; PDBTitle: crystal structure of e. coli enolase bound to its cognate rnase e2 recognition 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