Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	E	F	G	R	P	Q	R	V	A	Q	E	M	Q	K	E	I	A	L	I	L	Q	R	E	I	K	D	P	R	L	G	M	M	T	T	V	S	G	V	E	M	S	R	D	L	A	Y	A	K	V	Y	V	T	F	L	N	D	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	E	D	A	V	K	A	G	I	K	A	L	Q	E	A	S	G	F	I	R	S	L	L	G	K	A	M	R	L	R	I	V	P	E	L	T	F	F	Y	D	N	S	L	V	E	G	M	R	M	S	N	L	V	T	S	V	V	K	H	D
Secondary structure
SS confidence
Disorder		?																																																							?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.
Sequence		E	E	R	R	V	N	P	D	D	S	K	E	D
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 1kkg chain A Region: 1 - 108 Aligned: 108 Modelled: 108 Confidence: 100.0% Identity: 100% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 1jos chain A Region: 7 - 106 Aligned: 99 Modelled: 100 Confidence: 100.0% Identity: 71% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 2kzf chain A Region: 1 - 108 Aligned: 104 Modelled: 108 Confidence: 100.0% Identity: 36% PDB header:ribosomal protein Chain: A: PDB Molecule:ribosome-binding factor a; PDBTitle: solution nmr structure of the thermotoga maritima protein tm0855 a2 putative ribosome binding factor a Phyre2 PDB 2e7g chain A domain 1 Region: 3 - 117 Aligned: 113 Modelled: 115 Confidence: 100.0% Identity: 18% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 1pa4 chain A Region: 8 - 106 Aligned: 95 Modelled: 99 Confidence: 100.0% Identity: 20% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 2dyj chain A domain 1 Region: 8 - 102 Aligned: 88 Modelled: 95 Confidence: 100.0% Identity: 27% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 2qsi chain B Region: 81 - 119 Aligned: 39 Modelled: 39 Confidence: 12.4% Identity: 10% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative hydrogenase expression/formation protein hupg; PDBTitle: crystal structure of putative hydrogenase expression/formation protein2 hupg from rhodopseudomonas palustris cga009 Phyre2 PDB 3ere chain D Region: 2 - 129 Aligned: 115 Modelled: 123 Confidence: 9.6% Identity: 17% PDB header:dna binding protein/dna Chain: D: PDB Molecule:arginine repressor; PDBTitle: crystal structure of the arginine repressor protein from mycobacterium2 tuberculosis in complex with the dna operator Phyre2 PDB 1lr0 chain A Region: 9 - 94 Aligned: 85 Modelled: 86 Confidence: 9.2% Identity: 14% Fold: TolA/TonB C-terminal domain Superfamily: TolA/TonB C-terminal domain Family: TolA Phyre2 PDB 3kh0 chain A Region: 41 - 75 Aligned: 35 Modelled: 35 Confidence: 9.2% Identity: 20% PDB header:signaling protein Chain: A: PDB Molecule:ral guanine nucleotide dissociation stimulator; PDBTitle: crystal structure of the ras-association (ra) domain of2 ralgds Phyre2 PDB 1jmt chain A Region: 2 - 93 Aligned: 83 Modelled: 92 Confidence: 7.6% Identity: 19% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Splicing factor U2AF subunits Phyre2 PDB 3c1s chain A Region: 76 - 115 Aligned: 39 Modelled: 40 Confidence: 7.4% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:glutaredoxin-1; PDBTitle: crystal structure of grx1 in glutathionylated form Phyre2 PDB 2rgf chain A Region: 41 - 75 Aligned: 35 Modelled: 35 Confidence: 7.1% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ras-binding domain, RBD Phyre2 PDB 2jac chain A Region: 77 - 115 Aligned: 38 Modelled: 39 Confidence: 7.0% Identity: 16% PDB header:electron transport Chain: A: PDB Molecule:glutaredoxin-1; PDBTitle: glutaredoxin grx1p c30s mutant from yeast Phyre2 PDB 2b3a chain A domain 1 Region: 41 - 75 Aligned: 35 Modelled: 35 Confidence: 6.9% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ras-binding domain, RBD Phyre2 PDB 1ug8 chain A Region: 72 - 96 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 20% Fold: IF3-like Superfamily: R3H domain Family: R3H domain Phyre2 PDB 3fza chain A Region: 74 - 115 Aligned: 41 Modelled: 42 Confidence: 6.6% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:glutaredoxin; PDBTitle: crystal structure of poplar glutaredoxin s12 in complex with2 glutathione and beta-mercaptoethanol Phyre2 PDB 1lfd chain A Region: 41 - 75 Aligned: 35 Modelled: 35 Confidence: 6.4% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: Ras-binding domain, RBD Phyre2 PDB 1l0w chain A domain 2 Region: 70 - 90 Aligned: 21 Modelled: 21 Confidence: 6.4% Identity: 24% Fold: DCoH-like Superfamily: GAD domain-like Family: GAD domain Phyre2 PDB 3ipz chain A Region: 77 - 115 Aligned: 38 Modelled: 39 Confidence: 6.3% Identity: 11% PDB header:electron transport, oxidoreductase Chain: A: PDB Molecule:monothiol glutaredoxin-s14, chloroplastic; PDBTitle: crystal structure of arabidopsis monothiol glutaredoxin atgrxcp Phyre2 1 d1kkga_ 2 d1josa_ 3 c2kzfA_ 4 d2e7ga1 5 d1pa4a_ 6 d2dyja1 7 c2qsiB_ 8 c3ereD_ 9 d1lr0a_ 10 c3kh0A_ 11 d1jmta_ 12 c3c1sA_ 13 d2rgfa_ 14 c2jacA_ 15 d2b3aa1 16 d1ug8a_ 17 c3fzaA_ 18 d1lfda_ 19 d1l0wa2 20 c3ipzA_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 d1kkga_ 100.0 100 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 2 d1josa_ 100.0 71 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 3 c2kzfA_ 100.0 36 PDB header:ribosomal protein Chain: A: PDB Molecule:ribosome-binding factor a; PDBTitle: solution nmr structure of the thermotoga maritima protein tm0855 a2 putative ribosome binding factor a 4 d2e7ga1 100.0 18 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 5 d1pa4a_ 100.0 20 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 6 d2dyja1 100.0 27 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 7 c2qsiB_ 12.4 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative hydrogenase expression/formation protein hupg; PDBTitle: crystal structure of putative hydrogenase expression/formation protein2 hupg from rhodopseudomonas palustris cga009 8 c3ereD_ 9.6 17 PDB header:dna binding protein/dna Chain: D: PDB Molecule:arginine repressor; PDBTitle: crystal structure of the arginine repressor protein from mycobacterium2 tuberculosis in complex with the dna operator 9 d1lr0a_ 9.2 14 Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TolA 10 c3kh0A_ 9.2 20 PDB header:signaling protein Chain: A: PDB Molecule:ral guanine nucleotide dissociation stimulator; PDBTitle: crystal structure of the ras-association (ra) domain of2 ralgds 11 d1jmta_ 7.6 19 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Splicing factor U2AF subunits 12 c3c1sA_ 7.4 15 PDB header:oxidoreductase Chain: A: PDB Molecule:glutaredoxin-1; PDBTitle: crystal structure of grx1 in glutathionylated form 13 d2rgfa_ 7.1 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 14 c2jacA_ 7.0 16 PDB header:electron transport Chain: A: PDB Molecule:glutaredoxin-1; PDBTitle: glutaredoxin grx1p c30s mutant from yeast 15 d2b3aa1 6.9 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 16 d1ug8a_ 6.7 20 Fold:IF3-like Superfamily:R3H domain Family:R3H domain 17 c3fzaA_ 6.6 15 PDB header:oxidoreductase Chain: A: PDB Molecule:glutaredoxin; PDBTitle: crystal structure of poplar glutaredoxin s12 in complex with2 glutathione and beta-mercaptoethanol 18 d1lfda_ 6.4 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ras-binding domain, RBD 19 d1l0wa2 6.4 24 Fold:DCoH-like Superfamily:GAD domain-like Family:GAD domain 20 c3ipzA_ 6.3 11 PDB header:electron transport, oxidoreductase Chain: A: PDB Molecule:monothiol glutaredoxin-s14, chloroplastic; PDBTitle: crystal structure of arabidopsis monothiol glutaredoxin atgrxcp 21 d1xmka1 not modelled 6.3 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 22 c2gboB_ not modelled 6.2 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0358 protein ef2458; PDBTitle: protein of unknown function ef2458 from enterococcus faecalis 23 d2gboa1 not modelled 6.2 17 Fold:Open three-helical up-and-down bundle Superfamily:EF2458-like Family:EF2458-like 24 d1whxa_ not modelled 6.2 16 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 25 c3d5jB_ not modelled 5.8 13 PDB header:oxidoreductase Chain: B: PDB Molecule:glutaredoxin-2, mitochondrial; PDBTitle: structure of yeast grx2-c30s mutant with glutathionyl mixed2 disulfide 26 c3nm7D_ not modelled 5.7 19 PDB header:nucleic acid binding protein Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of borrelia burgdorferi pur-alpha 27 d1hska2 not modelled 5.2 17 Fold:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain Superfamily:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain Family:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain 28 d1ep7a_ not modelled 5.1 15 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Thioltransferase

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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