Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	V	I	A	I	I	A	I	V	I	I	V	I	I	L	N	K	T	G	V	S	D	S	L	T	A	L	T	L	A	T	V	A	A	L	L	T	G	G	G	A	A	G	A	A	S	V	A	L	T	P	F	V	G	V	P	V	G	I
Secondary structure
SS confidence
Disorder		?	?	?														?																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.
Sequence		F	V	G	I	Y	V	F	A	K	V	V	R	L	I	S	G	K	K
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 1cii chain A Region: 36 - 75 Aligned: 40 Modelled: 40 Confidence: 64.1% Identity: 20% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 3aqp chain B Region: 12 - 77 Aligned: 66 Modelled: 66 Confidence: 22.1% Identity: 27% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 1qg9 chain A Region: 61 - 78 Aligned: 18 Modelled: 16 Confidence: 18.9% Identity: 28% PDB header:transmembrane channel Chain: A: PDB Molecule:protein (sodium channel protein, brain ii alpha PDBTitle: second repeat (is2mic) from voltage-gated sodium channel Phyre2 PDB 1a8r chain A Region: 50 - 77 Aligned: 28 Modelled: 28 Confidence: 18.0% Identity: 14% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: GTP cyclohydrolase I Phyre2 PDB 1wpl chain A Region: 50 - 77 Aligned: 28 Modelled: 28 Confidence: 16.3% Identity: 39% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: GTP cyclohydrolase I Phyre2 PDB 1is7 chain F Region: 50 - 77 Aligned: 28 Modelled: 28 Confidence: 14.7% Identity: 39% PDB header:hydrolase/protein binding Chain: F: PDB Molecule:gtp cyclohydrolase i; PDBTitle: crystal structure of rat gtpchi/gfrp stimulatory complex Phyre2 PDB 3jzd chain A Region: 22 - 78 Aligned: 56 Modelled: 57 Confidence: 13.1% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:iron-containing alcohol dehydrogenase; PDBTitle: crystal structure of putative alcohol dehedrogenase (yp_298327.1) from2 ralstonia eutropha jmp134 at 2.10 a resolution Phyre2 PDB 1jo5 chain A Region: 60 - 76 Aligned: 17 Modelled: 17 Confidence: 13.1% Identity: 18% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1wur chain A domain 1 Region: 50 - 77 Aligned: 28 Modelled: 28 Confidence: 12.8% Identity: 39% Fold: T-fold Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like Family: GTP cyclohydrolase I Phyre2 PDB 1wm9 chain D Region: 50 - 77 Aligned: 28 Modelled: 28 Confidence: 12.8% Identity: 39% PDB header:hydrolase Chain: D: PDB Molecule:gtp cyclohydrolase i; PDBTitle: structure of gtp cyclohydrolase i from thermus thermophilus hb8 Phyre2 PDB 1ztd chain A domain 1 Region: 47 - 59 Aligned: 13 Modelled: 13 Confidence: 12.1% Identity: 62% Fold: RNase III domain-like Superfamily: RNase III domain-like Family: PF0609-like Phyre2 PDB 2xzm chain O Region: 9 - 30 Aligned: 22 Modelled: 22 Confidence: 9.7% Identity: 27% PDB header:ribosome Chain: O: PDB Molecule:rps13e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 1rh1 chain A domain 2 Region: 32 - 61 Aligned: 30 Modelled: 30 Confidence: 9.6% Identity: 20% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 2ari chain A Region: 40 - 51 Aligned: 12 Modelled: 12 Confidence: 9.4% Identity: 58% PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 Phyre2 PDB 1h2d chain A Region: 20 - 56 Aligned: 37 Modelled: 37 Confidence: 9.2% Identity: 30% PDB header:virus/viral protein Chain: A: PDB Molecule:matrix protein vp40; PDBTitle: ebola virus matrix protein vp40 n-terminal domain in2 complex with rna (low-resolution vp40[31-212] variant). Phyre2 PDB 1h2c chain A Region: 32 - 56 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 28% Fold: EV matrix protein Superfamily: EV matrix protein Family: EV matrix protein Phyre2 PDB 3izb chain O Region: 9 - 30 Aligned: 22 Modelled: 22 Confidence: 8.6% Identity: 14% PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1cii chain A domain 1 Region: 32 - 75 Aligned: 44 Modelled: 44 Confidence: 7.6% Identity: 18% Fold: Toxins' membrane translocation domains Superfamily: Colicin Family: Colicin Phyre2 PDB 1wrg chain A Region: 60 - 76 Aligned: 17 Modelled: 17 Confidence: 7.1% Identity: 29% PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum Phyre2 PDB 2i88 chain A Region: 32 - 77 Aligned: 46 Modelled: 46 Confidence: 6.9% Identity: 15% PDB header:membrane protein Chain: A: PDB Molecule:colicin-e1; PDBTitle: crystal structure of the channel-forming domain of colicin2 e1 Phyre2 1 c1ciiA_ 2 c3aqpB_ 3 c1qg9A_ 4 d1a8ra_ 5 d1wpla_ 6 c1is7F_ 7 c3jzdA_ 8 d1jo5a_ 9 d1wura1 10 c1wm9D_ 11 d1ztda1 12 c2xzmO_ 13 d1rh1a2 14 c2ariA_ 15 c1h2dA_ 16 d1h2ca_ 17 c3izbO_ 18 d1ciia1 19 c1wrgA_ 20 c2i88A_ 21

Detailed template information

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

1 c1ciiA_ 64.1 20 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 2 c3aqpB_ 22.1 27 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 3 c1qg9A_ 18.9 28 PDB header:transmembrane channel Chain: A: PDB Molecule:protein (sodium channel protein, brain ii alpha PDBTitle: second repeat (is2mic) from voltage-gated sodium channel 4 d1a8ra_ 18.0 14 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 5 d1wpla_ 16.3 39 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 6 c1is7F_ 14.7 39 PDB header:hydrolase/protein binding Chain: F: PDB Molecule:gtp cyclohydrolase i; PDBTitle: crystal structure of rat gtpchi/gfrp stimulatory complex 7 c3jzdA_ 13.1 14 PDB header:oxidoreductase Chain: A: PDB Molecule:iron-containing alcohol dehydrogenase; PDBTitle: crystal structure of putative alcohol dehedrogenase (yp_298327.1) from2 ralstonia eutropha jmp134 at 2.10 a resolution 8 d1jo5a_ 13.1 18 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 9 d1wura1 12.8 39 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:GTP cyclohydrolase I 10 c1wm9D_ 12.8 39 PDB header:hydrolase Chain: D: PDB Molecule:gtp cyclohydrolase i; PDBTitle: structure of gtp cyclohydrolase i from thermus thermophilus hb8 11 d1ztda1 12.1 62 Fold:RNase III domain-like Superfamily:RNase III domain-like Family:PF0609-like 12 c2xzmO_ 9.7 27 PDB header:ribosome Chain: O: PDB Molecule:rps13e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 13 d1rh1a2 9.6 20 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 14 c2ariA_ 9.4 58 PDB header:viral protein Chain: A: PDB Molecule:envelope polyprotein gp160; PDBTitle: solution structure of micelle-bound fusion domain of hiv-12 gp41 15 c1h2dA_ 9.2 30 PDB header:virus/viral protein Chain: A: PDB Molecule:matrix protein vp40; PDBTitle: ebola virus matrix protein vp40 n-terminal domain in2 complex with rna (low-resolution vp40[31-212] variant). 16 d1h2ca_ 9.0 28 Fold:EV matrix protein Superfamily:EV matrix protein Family:EV matrix protein 17 c3izbO_ 8.6 14 PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 18 d1ciia1 7.6 18 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 19 c1wrgA_ 7.1 29 PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum 20 c2i88A_ 6.9 15 PDB header:membrane protein Chain: A: PDB Molecule:colicin-e1; PDBTitle: crystal structure of the channel-forming domain of colicin2 e1 21 d2vv5a3 not modelled 5.8 29 Fold:Mechanosensitive channel protein MscS (YggB), transmembrane region Superfamily:Mechanosensitive channel protein MscS (YggB), transmembrane region Family:Mechanosensitive channel protein MscS (YggB), transmembrane region

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