Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	D	T	T	E	L	V	D	L	A	V	I	F	P	D	L	E	I	E	L	K	Y	A	C	A	D	N	I	T	G	K	A	I	Y	Q	Q	A	R	C	L	L	H	K	D	A	I	T	A	L	A	K	S	I	S	I	A	Q	L	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	Q	L	V	I	Y	D	A	Y	R	P	Q	Q	A	Q	A	M	L	W	Q	A	C	P	D	P	Q	Y	V	V	D	V	T	V	G	S	N	H	S	R	G	T	A	I	D	L	T	L	R	D	E	H	G	N	I	L	D	M	G	A
Secondary structure
SS confidence
Disorder																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	F	D	E	M	H	E	R	S	H	A	Y	H	P	S	V	P	P	A	A	Q	R	N	R	L	L	L	N	A	I	M	T	G	G	G	F	V	G	I	S	S	E	W	W	H	F	E	L	P	Q	A	A	S	Y	P	L	L	A	D	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.
Sequence		F	S	C	F	I	S	P	G	T	Q	H	V	S
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 1r44 chain A Region: 6 - 182 Aligned: 176 Modelled: 177 Confidence: 100.0% Identity: 36% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: VanX-like Phyre2 PDB 2vo9 chain A domain 1 Region: 40 - 173 Aligned: 115 Modelled: 115 Confidence: 99.8% Identity: 25% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: VanY-like Phyre2 PDB 2vo9 chain C Region: 40 - 173 Aligned: 115 Modelled: 115 Confidence: 99.8% Identity: 25% PDB header:hydrolase Chain: C: PDB Molecule:l-alanyl-d-glutamate peptidase; PDBTitle: crystal structure of the enzymatically active domain of the2 listeria monocytogenes bacteriophage 500 endolysin ply500 Phyre2 PDB 3d1m chain A domain 1 Region: 22 - 118 Aligned: 81 Modelled: 81 Confidence: 95.8% Identity: 19% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: Hedgehog (development protein), N-terminal signaling domain Phyre2 PDB 1lbu chain A domain 2 Region: 42 - 116 Aligned: 64 Modelled: 75 Confidence: 95.6% Identity: 20% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: Muramoyl-pentapeptide carboxypeptidase Phyre2 PDB 1lbu chain A Region: 41 - 106 Aligned: 55 Modelled: 66 Confidence: 95.5% Identity: 22% PDB header:hydrolase Chain: A: PDB Molecule:muramoyl-pentapeptide carboxypeptidase; PDBTitle: hydrolase metallo (zn) dd-peptidase Phyre2 PDB 3m1n chain B Region: 41 - 118 Aligned: 62 Modelled: 62 Confidence: 94.9% Identity: 19% PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain Phyre2 PDB 2ibg chain E domain 1 Region: 41 - 118 Aligned: 62 Modelled: 62 Confidence: 93.4% Identity: 18% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: Hedgehog (development protein), N-terminal signaling domain Phyre2 PDB 1tzp chain A Region: 37 - 114 Aligned: 64 Modelled: 64 Confidence: 79.7% Identity: 20% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: MepA-like Phyre2 PDB 1esw chain A Region: 147 - 193 Aligned: 47 Modelled: 47 Confidence: 33.7% Identity: 13% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1nwb chain A Region: 42 - 105 Aligned: 42 Modelled: 42 Confidence: 26.5% Identity: 17% Fold: HesB-like domain Superfamily: HesB-like domain Family: HesB-like domain Phyre2 PDB 2k4z chain A Region: 42 - 67 Aligned: 26 Modelled: 26 Confidence: 26.4% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dsrr; PDBTitle: solution nmr structure of allochromatium vinosum dsrr:2 northeast structural genomics consortium target op5 Phyre2 PDB 2j07 chain A domain 2 Region: 46 - 127 Aligned: 81 Modelled: 82 Confidence: 25.2% Identity: 10% Fold: Cryptochrome/photolyase, N-terminal domain Superfamily: Cryptochrome/photolyase, N-terminal domain Family: Cryptochrome/photolyase, N-terminal domain Phyre2 PDB 2apn chain A Region: 42 - 67 Aligned: 26 Modelled: 26 Confidence: 21.9% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure Phyre2 PDB 1x1n chain A domain 1 Region: 147 - 193 Aligned: 47 Modelled: 47 Confidence: 20.7% Identity: 9% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 3kyz chain A Region: 165 - 182 Aligned: 18 Modelled: 18 Confidence: 19.8% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:sensor protein pfes; PDBTitle: the crystal structure of the sensor domain of two-component2 sensor pfes from pseudomonas aeruginosa pa01 Phyre2 PDB 1bhu chain A Region: 165 - 193 Aligned: 29 Modelled: 29 Confidence: 19.3% Identity: 31% Fold: gamma-Crystallin-like Superfamily: gamma-Crystallin-like Family: Streptomyces metalloproteinase inhibitor, SMPI Phyre2 PDB 1xpj chain A Region: 38 - 69 Aligned: 28 Modelled: 32 Confidence: 18.9% Identity: 29% Fold: HAD-like Superfamily: HAD-like Family: Hypothetical protein VC0232 Phyre2 PDB 2d8z chain A domain 1 Region: 154 - 165 Aligned: 12 Modelled: 12 Confidence: 18.2% Identity: 33% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 3aq3 chain A Region: 118 - 189 Aligned: 64 Modelled: 72 Confidence: 16.8% Identity: 22% PDB header:toxin Chain: A: PDB Molecule:6b protein; PDBTitle: molecular insights into plant cell proliferation disturbance by2 agrobacterium protein 6b Phyre2 1 d1r44a_ 2 d2vo9a1 3 c2vo9C_ 4 d3d1ma1 5 d1lbua2 6 c1lbuA_ 7 c3m1nB_ 8 d2ibge1 9 d1tzpa_ 10 d1eswa_ 11 d1nwba_ 12 c2k4zA_ 13 d2j07a2 14 c2apnA_ 15 d1x1na1 16 c3kyzA_ 17 d1bhua_ 18 d1xpja_ 19 d2d8za1 20 c3aq3A_ 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 56 57 58 59

Detailed template information

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

1 d1r44a_ 100.0 36 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:VanX-like 2 d2vo9a1 99.8 25 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:VanY-like 3 c2vo9C_ 99.8 25 PDB header:hydrolase Chain: C: PDB Molecule:l-alanyl-d-glutamate peptidase; PDBTitle: crystal structure of the enzymatically active domain of the2 listeria monocytogenes bacteriophage 500 endolysin ply500 4 d3d1ma1 95.8 19 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain 5 d1lbua2 95.6 20 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Muramoyl-pentapeptide carboxypeptidase 6 c1lbuA_ 95.5 22 PDB header:hydrolase Chain: A: PDB Molecule:muramoyl-pentapeptide carboxypeptidase; PDBTitle: hydrolase metallo (zn) dd-peptidase 7 c3m1nB_ 94.9 19 PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain 8 d2ibge1 93.4 18 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain 9 d1tzpa_ 79.7 20 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:MepA-like 10 d1eswa_ 33.7 13 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 11 d1nwba_ 26.5 17 Fold:HesB-like domain Superfamily:HesB-like domain Family:HesB-like domain 12 c2k4zA_ 26.4 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dsrr; PDBTitle: solution nmr structure of allochromatium vinosum dsrr:2 northeast structural genomics consortium target op5 13 d2j07a2 25.2 10 Fold:Cryptochrome/photolyase, N-terminal domain Superfamily:Cryptochrome/photolyase, N-terminal domain Family:Cryptochrome/photolyase, N-terminal domain 14 c2apnA_ 21.9 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure 15 d1x1na1 20.7 9 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 16 c3kyzA_ 19.8 11 PDB header:transferase Chain: A: PDB Molecule:sensor protein pfes; PDBTitle: the crystal structure of the sensor domain of two-component2 sensor pfes from pseudomonas aeruginosa pa01 17 d1bhua_ 19.3 31 Fold:gamma-Crystallin-like Superfamily:gamma-Crystallin-like Family:Streptomyces metalloproteinase inhibitor, SMPI 18 d1xpja_ 18.9 29 Fold:HAD-like Superfamily:HAD-like Family:Hypothetical protein VC0232 19 d2d8za1 18.2 33 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 20 c3aq3A_ 16.8 22 PDB header:toxin Chain: A: PDB Molecule:6b protein; PDBTitle: molecular insights into plant cell proliferation disturbance by2 agrobacterium protein 6b 21 d2cura2 not modelled 16.6 25 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 22 c3d2hA_ not modelled 14.3 6 PDB header:oxidoreductase Chain: A: PDB Molecule:berberine bridge-forming enzyme; PDBTitle: structure of berberine bridge enzyme from eschscholzia californica,2 monoclinic crystal form 23 d1n8ja_ not modelled 14.0 14 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 24 c2ipiD_ not modelled 13.6 8 PDB header:oxidoreductase Chain: D: PDB Molecule:aclacinomycin oxidoreductase (aknox); PDBTitle: crystal structure of aclacinomycin oxidoreductase 25 d2nlya1 not modelled 11.1 17 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:Divergent polysaccharide deacetylase 26 d2qn6b1 not modelled 9.3 20 Fold:Ferredoxin-like Superfamily:eIF-2-alpha, C-terminal domain Family:eIF-2-alpha, C-terminal domain 27 c3fwaA_ not modelled 9.1 6 PDB header:flavoprotein Chain: A: PDB Molecule:reticuline oxidase; PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline 28 d2pp6a1 not modelled 9.1 13 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:gpFII-like 29 c3kebB_ not modelled 9.0 10 PDB header:oxidoreductase Chain: B: PDB Molecule:probable thiol peroxidase; PDBTitle: thiol peroxidase from chromobacterium violaceum 30 d1vk9a_ not modelled 8.3 25 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Hypothetical protein TM1506 31 d2r4qa1 not modelled 8.3 28 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:PTS system IIB component-like Family:PTS system, Fructose specific IIB subunit-like 32 c2ov2O_ not modelled 8.2 27 PDB header:protein binding/transferase Chain: O: PDB Molecule:serine/threonine-protein kinase pak 4; PDBTitle: the crystal structure of the human rac3 in complex with the crib2 domain of human p21-activated kinase 4 (pak4) 33 c3lklB_ not modelled 8.0 16 PDB header:transport protein Chain: B: PDB Molecule:antisigma-factor antagonist stas; PDBTitle: crystal structure of the c-terminal domain of anti-sigma factor2 antagonist stas from rhodobacter sphaeroides 34 d1np7a2 not modelled 7.8 11 Fold:Cryptochrome/photolyase, N-terminal domain Superfamily:Cryptochrome/photolyase, N-terminal domain Family:Cryptochrome/photolyase, N-terminal domain 35 c3o2iB_ not modelled 7.6 31 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of a functionally unknown protein from2 leptospirillum sp. group ii uba 36 d1tz7a1 not modelled 7.5 7 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 37 c1dxyA_ not modelled 7.4 21 PDB header:oxidoreductase Chain: A: PDB Molecule:d-2-hydroxyisocaproate dehydrogenase; PDBTitle: structure of d-2-hydroxyisocaproate dehydrogenase 38 c2h31A_ not modelled 7.2 16 PDB header:ligase, lyase Chain: A: PDB Molecule:multifunctional protein ade2; PDBTitle: crystal structure of human paics, a bifunctional carboxylase and2 synthetase in purine biosynthesis 39 d2r48a1 not modelled 7.0 28 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:PTS system IIB component-like Family:PTS system, Fructose specific IIB subunit-like 40 c2kyrA_ not modelled 6.7 33 PDB header:transferase Chain: A: PDB Molecule:fructose-like phosphotransferase enzyme iib component 1; PDBTitle: solution structure of enzyme iib subunit of pts system from2 escherichia coli k12. northeast structural genomics consortium target3 er315/ontario center for structural proteomics target ec0544 41 d1lvaa3 not modelled 6.5 4 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal fragment of elongation factor SelB 42 c1s1iS_ not modelled 6.2 26 PDB header:ribosome Chain: S: PDB Molecule:60s ribosomal protein l24-a; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 43 c2zkru_ not modelled 6.2 26 PDB header:ribosomal protein/rna Chain: U: PDB Molecule:rna expansion segment es41; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 44 d1j4aa1 not modelled 6.1 25 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain 45 c1ybaC_ not modelled 6.1 22 PDB header:oxidoreductase Chain: C: PDB Molecule:d-3-phosphoglycerate dehydrogenase; PDBTitle: the active form of phosphoglycerate dehydrogenase 46 c3fzeA_ not modelled 5.7 23 PDB header:protein binding Chain: A: PDB Molecule:protein ste5; PDBTitle: structure of the 'minimal scaffold' (ms) domain of ste52 that cocatalyzes fus3 phosphorylation by ste7 47 d1yj5a1 not modelled 5.7 25 Fold:HAD-like Superfamily:HAD-like Family:phosphatase domain of polynucleotide kinase 48 d1owla2 not modelled 5.5 17 Fold:Cryptochrome/photolyase, N-terminal domain Superfamily:Cryptochrome/photolyase, N-terminal domain Family:Cryptochrome/photolyase, N-terminal domain 49 c3izcZ_ not modelled 5.5 26 PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein rpl24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 50 c3lloA_ not modelled 5.5 13 PDB header:motor protein Chain: A: PDB Molecule:prestin; PDBTitle: crystal structure of the stas domain of motor protein prestin (anion2 transporter slc26a5) 51 c4a1eT_ not modelled 5.5 21 PDB header:ribosome Chain: T: PDB Molecule:rpl24; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 52 d2naca1 not modelled 5.5 15 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain 53 c3iz5Z_ not modelled 5.4 21 PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein l24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 54 d2i0ka2 not modelled 5.4 11 Fold:FAD-binding/transporter-associated domain-like Superfamily:FAD-binding/transporter-associated domain-like Family:FAD-linked oxidases, N-terminal domain 55 c3isyA_ not modelled 5.3 21 PDB header:protein binding Chain: A: PDB Molecule:intracellular proteinase inhibitor; PDBTitle: crystal structure of an intracellular proteinase inhibitor (ipi,2 bsu11130) from bacillus subtilis at 2.61 a resolution 56 c3d8uA_ not modelled 5.3 14 PDB header:transcription regulator Chain: A: PDB Molecule:purr transcriptional regulator; PDBTitle: the crystal structure of a purr family transcriptional regulator from2 vibrio parahaemolyticus rimd 2210633 57 c1vkzA_ not modelled 5.2 9 PDB header:ligase Chain: A: PDB Molecule:phosphoribosylamine--glycine ligase; PDBTitle: crystal structure of phosphoribosylamine--glycine ligase (tm1250) from2 thermotoga maritima at 2.30 a resolution 58 d1vqou1 not modelled 5.2 25 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Ribosomal protein L24e 59 d1dnpa2 not modelled 5.1 13 Fold:Cryptochrome/photolyase, N-terminal domain Superfamily:Cryptochrome/photolyase, N-terminal domain Family:Cryptochrome/photolyase, 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