Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	Y	T	F	D	F	D	E	I	E	S	Q	E	D	F	Y	R	D	F	S	Q	T	F	G	L	A	K	D	K	V	R	D	L	D	S	L	W	D	V	L	M	N	D	V	L	P	L	P	L	E	I	E	F	V	H	L	G	E
Secondary structure
SS confidence
Disorder		?	?																																																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90
Sequence		K	T	R	R	R	F	G	A	L	I	L	L	F	D	E	A	E	E	E	L	E	G	H	L	R	F	N	V	R	H
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 2cx6 chain A domain 1 Region: 1 - 90 Aligned: 90 Modelled: 89 Confidence: 100.0% Identity: 98% Fold: Barstar-like Superfamily: Barstar-related Family: Barstar-related Phyre2 PDB 1ay7 chain B Region: 2 - 82 Aligned: 80 Modelled: 81 Confidence: 99.9% Identity: 24% Fold: Barstar-like Superfamily: Barstar-related Family: Barstar-related Phyre2 PDB 1sb7 chain A Region: 2 - 32 Aligned: 31 Modelled: 31 Confidence: 68.7% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase d; PDBTitle: crystal structure of the e.coli pseudouridine synthase trud Phyre2 PDB 1szw chain A Region: 2 - 32 Aligned: 31 Modelled: 31 Confidence: 68.2% Identity: 16% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: tRNA pseudouridine synthase TruD Phyre2 PDB 3nme chain A Region: 37 - 57 Aligned: 20 Modelled: 21 Confidence: 24.0% Identity: 10% PDB header:hydrolase Chain: A: PDB Molecule:sex4 glucan phosphatase; PDBTitle: structure of a plant phosphatase Phyre2 PDB 2aho chain B domain 1 Region: 12 - 45 Aligned: 32 Modelled: 34 Confidence: 23.6% Identity: 6% Fold: SAM domain-like Superfamily: eIF2alpha middle domain-like Family: eIF2alpha middle domain-like Phyre2 PDB 1nks chain A Region: 1 - 30 Aligned: 30 Modelled: 30 Confidence: 21.2% Identity: 7% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nucleotide and nucleoside kinases Phyre2 PDB 2c0k chain B Region: 14 - 42 Aligned: 29 Modelled: 29 Confidence: 18.9% Identity: 10% PDB header:oxygen transport Chain: B: PDB Molecule:hemoglobin; PDBTitle: the structure of hemoglobin from the botfly gasterophilus2 intestinalis Phyre2 PDB 1z2z chain B Region: 2 - 32 Aligned: 31 Modelled: 31 Confidence: 18.5% Identity: 13% PDB header:lyase Chain: B: PDB Molecule:probable trna pseudouridine synthase d; PDBTitle: crystal structure of the putative trna pseudouridine2 synthase d (trud) from methanosarcina mazei, northeast3 structural genomics target mar1 Phyre2 PDB 3da5 chain A Region: 32 - 42 Aligned: 11 Modelled: 11 Confidence: 18.5% Identity: 45% PDB header:rna binding protein Chain: A: PDB Molecule:argonaute; PDBTitle: crystal structure of piwi/argonaute/zwille(paz) domain from2 thermococcus thioreducens Phyre2 PDB 1vpy chain A Region: 25 - 75 Aligned: 51 Modelled: 44 Confidence: 17.9% Identity: 10% Fold: TIM beta/alpha-barrel Superfamily: TM1631-like Family: TM1631-like Phyre2 PDB 2dnf chain A Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 17.4% Identity: 4% PDB header:protein binding Chain: A: PDB Molecule:doublecortin domain-containing protein 2; PDBTitle: solution structure of rsgi ruh-062, a dcx domain from human Phyre2 PDB 3f1x chain A Region: 6 - 33 Aligned: 28 Modelled: 28 Confidence: 16.7% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:serine acetyltransferase; PDBTitle: three dimensional structure of the serine acetyltransferase from2 bacteroides vulgatus, northeast structural genomics consortium target3 bvr62. Phyre2 PDB 2zpm chain A Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 14.5% Identity: 10% PDB header:hydrolase Chain: A: PDB Molecule:regulator of sigma e protease; PDBTitle: crystal structure analysis of pdz domain b Phyre2 PDB 2hga chain A domain 1 Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 12.7% Identity: 5% Fold: PDZ domain-like Superfamily: PDZ domain-like Family: MTH1368 C-terminal domain-like Phyre2 PDB 2k5c chain A Region: 11 - 35 Aligned: 25 Modelled: 25 Confidence: 12.5% Identity: 16% PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 Phyre2 PDB 1gg3 chain A domain 3 Region: 2 - 32 Aligned: 31 Modelled: 31 Confidence: 12.2% Identity: 10% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: First domain of FERM Phyre2 PDB 2grj chain H Region: 1 - 28 Aligned: 28 Modelled: 27 Confidence: 11.7% Identity: 4% PDB header:transferase Chain: H: PDB Molecule:dephospho-coa kinase; PDBTitle: crystal structure of dephospho-coa kinase (ec 2.7.1.24)2 (dephosphocoenzyme a kinase) (tm1387) from thermotoga maritima at3 2.60 a resolution Phyre2 PDB 1y14 chain B domain 2 Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 11.6% Identity: 0% Fold: Dodecin subunit-like Superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE) Family: N-terminal, heterodimerisation domain of RBP7 (RpoE) Phyre2 PDB 2c4v chain A domain 1 Region: 1 - 87 Aligned: 75 Modelled: 87 Confidence: 10.4% Identity: 15% Fold: Flavodoxin-like Superfamily: Type II 3-dehydroquinate dehydratase Family: Type II 3-dehydroquinate dehydratase Phyre2 1 d2cx6a1 2 d1ay7b_ 3 c1sb7A_ 4 d1szwa_ 5 c3nmeA_ 6 d2ahob1 7 d1nksa_ 8 c2c0kB_ 9 c1z2zB_ 10 c3da5A_ 11 d1vpya_ 12 c2dnfA_ 13 c3f1xA_ 14 c2zpmA_ 15 d2hgaa1 16 c2k5cA_ 17 d1gg3a3 18 c2grjH_ 19 d1y14b2 20 d2c4va1 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

Detailed template information

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

1 d2cx6a1 100.0 98 Fold:Barstar-like Superfamily:Barstar-related Family:Barstar-related 2 d1ay7b_ 99.9 24 Fold:Barstar-like Superfamily:Barstar-related Family:Barstar-related 3 c1sb7A_ 68.7 16 PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase d; PDBTitle: crystal structure of the e.coli pseudouridine synthase trud 4 d1szwa_ 68.2 16 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:tRNA pseudouridine synthase TruD 5 c3nmeA_ 24.0 10 PDB header:hydrolase Chain: A: PDB Molecule:sex4 glucan phosphatase; PDBTitle: structure of a plant phosphatase 6 d2ahob1 23.6 6 Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like 7 d1nksa_ 21.2 7 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases 8 c2c0kB_ 18.9 10 PDB header:oxygen transport Chain: B: PDB Molecule:hemoglobin; PDBTitle: the structure of hemoglobin from the botfly gasterophilus2 intestinalis 9 c1z2zB_ 18.5 13 PDB header:lyase Chain: B: PDB Molecule:probable trna pseudouridine synthase d; PDBTitle: crystal structure of the putative trna pseudouridine2 synthase d (trud) from methanosarcina mazei, northeast3 structural genomics target mar1 10 c3da5A_ 18.5 45 PDB header:rna binding protein Chain: A: PDB Molecule:argonaute; PDBTitle: crystal structure of piwi/argonaute/zwille(paz) domain from2 thermococcus thioreducens 11 d1vpya_ 17.9 10 Fold:TIM beta/alpha-barrel Superfamily:TM1631-like Family:TM1631-like 12 c2dnfA_ 17.4 4 PDB header:protein binding Chain: A: PDB Molecule:doublecortin domain-containing protein 2; PDBTitle: solution structure of rsgi ruh-062, a dcx domain from human 13 c3f1xA_ 16.7 14 PDB header:transferase Chain: A: PDB Molecule:serine acetyltransferase; PDBTitle: three dimensional structure of the serine acetyltransferase from2 bacteroides vulgatus, northeast structural genomics consortium target3 bvr62. 14 c2zpmA_ 14.5 10 PDB header:hydrolase Chain: A: PDB Molecule:regulator of sigma e protease; PDBTitle: crystal structure analysis of pdz domain b 15 d2hgaa1 12.7 5 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:MTH1368 C-terminal domain-like 16 c2k5cA_ 12.5 16 PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 17 d1gg3a3 12.2 10 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 18 c2grjH_ 11.7 4 PDB header:transferase Chain: H: PDB Molecule:dephospho-coa kinase; PDBTitle: crystal structure of dephospho-coa kinase (ec 2.7.1.24)2 (dephosphocoenzyme a kinase) (tm1387) from thermotoga maritima at3 2.60 a resolution 19 d1y14b2 11.6 0 Fold:Dodecin subunit-like Superfamily:N-terminal, heterodimerisation domain of RBP7 (RpoE) Family:N-terminal, heterodimerisation domain of RBP7 (RpoE) 20 d2c4va1 10.4 15 Fold:Flavodoxin-like Superfamily:Type II 3-dehydroquinate dehydratase Family:Type II 3-dehydroquinate dehydratase 21 d1sota1 not modelled 9.6 14 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:HtrA-like serine proteases 22 d1ky9b2 not modelled 9.5 5 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:HtrA-like serine proteases 23 d1wuda1 not modelled 9.3 11 Fold:SAM domain-like Superfamily:HRDC-like Family:HRDC domain from helicases 24 d2ciwa2 not modelled 9.1 11 Fold:EF Hand-like Superfamily:Cloroperoxidase Family:Cloroperoxidase 25 c3q3uA_ not modelled 9.0 22 PDB header:oxidoreductase Chain: A: PDB Molecule:lignin peroxidase; PDBTitle: trametes cervina lignin peroxidase 26 d2zpya3 not modelled 8.9 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 27 c2p3wB_ not modelled 8.4 5 PDB header:protein binding Chain: B: PDB Molecule:probable serine protease htra3; PDBTitle: crystal structure of the htra3 pdz domain bound to a phage-derived2 ligand (fgrwv) 28 c2xxsA_ not modelled 8.4 11 PDB header:protein binding Chain: A: PDB Molecule:protein mxig; PDBTitle: solution structure of the n-terminal domain of the shigella2 type iii secretion protein mxig 29 c3i18A_ not modelled 7.6 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lmo2051 protein; PDBTitle: crystal structure of the pdz domain of the sdrc-like protein2 (lmo2051) from listeria monocytogenes, northeast structural3 genomics consortium target lmr166b 30 d2e1fa1 not modelled 7.6 6 Fold:SAM domain-like Superfamily:HRDC-like Family:HRDC domain from helicases 31 c2kl1A_ not modelled 7.5 19 PDB header:protein binding Chain: A: PDB Molecule:ylbl protein; PDBTitle: solution structure of gtr34c from geobacillus thermodenitrificans.2 northeast structural genomics consortium target gtr34c 32 c2x7jA_ not modelled 7.2 13 PDB header:transferase Chain: A: PDB Molecule:2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene PDBTitle: structure of the menaquinone biosynthesis protein mend from2 bacillus subtilis 33 d1ni2a3 not modelled 7.1 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 34 d2z9ia1 not modelled 6.9 14 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:HtrA-like serine proteases 35 c2o42B_ not modelled 6.9 19 PDB header:apoptosis inhibitor Chain: B: PDB Molecule:m11l protein; PDBTitle: crystal structure of m11l, bcl-2 homolog from myxoma virus 36 c3bq9A_ not modelled 6.8 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted rossmann fold nucleotide-binding domain- PDBTitle: crystal structure of predicted nucleotide-binding protein from2 idiomarina baltica os145 37 d1itha_ not modelled 6.6 15 Fold:Globin-like Superfamily:Globin-like Family:Globins 38 d1ef1a3 not modelled 6.6 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 39 c1yz7A_ not modelled 6.6 9 PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 alpha PDBTitle: crystal structure of a c-terminal segment of the alpha2 subunit of aif2 from pyrococcus abyssi 40 d1sxja1 not modelled 6.5 0 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain 41 d1ukza_ not modelled 6.5 0 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases 42 d2r8oa2 not modelled 6.5 15 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:TK-like PP module 43 c3u8zD_ not modelled 5.8 17 PDB header:signaling protein Chain: D: PDB Molecule:merlin; PDBTitle: human merlin ferm domain 44 c2joaA_ not modelled 5.8 14 PDB header:protein binding Chain: A: PDB Molecule:serine protease htra1; PDBTitle: htra1 bound to an optimized peptide: nmr assignment of pdz2 domain and ligand resonances 45 c2q9rA_ not modelled 5.7 26 PDB header:unknown function Chain: A: PDB Molecule:protein of unknown function; PDBTitle: crystal structure of a duf416 family protein (sbal_3149) from2 shewanella baltica os155 at 1.91 a resolution 46 d1yyda1 not modelled 5.5 17 Fold:Heme-dependent peroxidases Superfamily:Heme-dependent peroxidases Family:CCP-like 47 d2e39a1 not modelled 5.5 22 Fold:Heme-dependent peroxidases Superfamily:Heme-dependent peroxidases Family:CCP-like 48 d1tw9a2 not modelled 5.4 20 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 49 d1orjb_ not modelled 5.2 18 Fold:Four-helical up-and-down bundle Superfamily:Flagellar export chaperone FliS Family:Flagellar export chaperone FliS 50 d2i6va1 not modelled 5.2 5 Fold:PDZ domain-like Superfamily:PDZ domain-like Family:EpsC C-terminal domain-like 51 d3c8ya2 not modelled 5.1 8 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin domains from multidomain proteins 52 c2vvyC_ not modelled 5.1 32 PDB header:viral protein Chain: C: PDB Molecule:protein b15; PDBTitle: structure of vaccinia virus protein b14 53 d1glqa2 not modelled 5.0 12 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 54 c2z5sN_ not modelled 5.0 8 PDB header:cell cycle Chain: N: PDB Molecule:mdm4 protein; PDBTitle: molecular basis for the inhibition of p53 by mdmx

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