Secondary structure and disorder prediction

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Sequence		M	R	E	Y	P	N	G	E	K	T	H	L	T	V	M	A	A	G	F	P	S	L	T	G	D	H	K	V	I	Y	V	A	A	D	R	H	V	T	S	E	E	I	L	E	A	A	I	R	L	L	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 1khb chain A domain 1 Region: 5 - 24 Aligned: 17 Modelled: 20 Confidence: 42.8% Identity: 65% Fold: PEP carboxykinase-like Superfamily: PEP carboxykinase-like Family: PEP carboxykinase C-terminal domain Phyre2 PDB 2qey chain A Region: 5 - 24 Aligned: 17 Modelled: 20 Confidence: 24.5% Identity: 53% PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase, cytosolic [gtp]; PDBTitle: rat cytosolic pepck in complex with gtp Phyre2 PDB 1pn0 chain A domain 3 Region: 24 - 51 Aligned: 28 Modelled: 28 Confidence: 14.5% Identity: 18% Fold: FAD-linked reductases, C-terminal domain Superfamily: FAD-linked reductases, C-terminal domain Family: PHBH-like Phyre2 PDB 2gfn chain A domain 1 Region: 33 - 50 Aligned: 18 Modelled: 18 Confidence: 8.5% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Tetracyclin repressor-like, N-terminal domain Phyre2 PDB 3bru chain A Region: 34 - 50 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 18% PDB header:transcription Chain: A: PDB Molecule:regulatory protein, tetr family; PDBTitle: crystal structure of regulatory protein tetr from rhodobacter2 sphaeroides Phyre2 PDB 2g7l chain A domain 1 Region: 37 - 50 Aligned: 14 Modelled: 13 Confidence: 7.1% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Tetracyclin repressor-like, N-terminal domain Phyre2 PDB 2zci chain D Region: 5 - 24 Aligned: 17 Modelled: 20 Confidence: 7.1% Identity: 53% PDB header:signaling protein, lyase Chain: D: PDB Molecule:phosphoenolpyruvate carboxykinase [gtp]; PDBTitle: structure of a gtp-dependent bacterial pep-carboxykinase2 from corynebacterium glutamicum Phyre2 PDB 2g7l chain A Region: 37 - 50 Aligned: 14 Modelled: 13 Confidence: 6.5% Identity: 21% PDB header:transcription Chain: A: PDB Molecule:tetr-family transcriptional regulator; PDBTitle: crystal structure of putative transcription regulator sco7704 from2 streptomyces coelicor Phyre2 PDB 3h4c chain A Region: 35 - 49 Aligned: 15 Modelled: 15 Confidence: 6.0% Identity: 33% PDB header:transcription Chain: A: PDB Molecule:transcription factor tfiib-like; PDBTitle: structure of the c-terminal domain of transcription factor iib from2 trypanosoma brucei Phyre2 PDB 1rqt chain A Region: 37 - 45 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 44% PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli Phyre2 PDB 1rqt chain A Region: 37 - 45 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 44% Fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Phyre2 PDB 1rqt chain B Region: 37 - 45 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 44% PDB header:ribosome Chain: B: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli Phyre2 PDB 1c4p chain C Region: 20 - 50 Aligned: 31 Modelled: 31 Confidence: 5.1% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 1bjz chain A Region: 37 - 50 Aligned: 14 Modelled: 14 Confidence: 5.1% Identity: 36% PDB header:transcription regulation Chain: A: PDB Molecule:tetracycline repressor; PDBTitle: tetracycline chelated mg2+-ion initiates helix unwinding for tet2 repressor induction Phyre2 PDB 2id3 chain A domain 1 Region: 38 - 50 Aligned: 13 Modelled: 13 Confidence: 5.0% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Tetracyclin repressor-like, N-terminal domain Phyre2 1 d1khba1 2 c2qeyA_ 3 d1pn0a3 4 d2gfna1 5 c3bruA_ 6 d2g7la1 7 c2zciD_ 8 c2g7lA_ 9 c3h4cA_ 10 c1rqtA_ 11 d1rqta_ 12 c1rqtB_ 13 d1c4pc_ 14 c1bjzA_ 15 d2id3a1

Detailed template information

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

1 d1khba1 42.8 65 Fold:PEP carboxykinase-like Superfamily:PEP carboxykinase-like Family:PEP carboxykinase C-terminal domain 2 c2qeyA_ 24.5 53 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase, cytosolic [gtp]; PDBTitle: rat cytosolic pepck in complex with gtp 3 d1pn0a3 14.5 18 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:PHBH-like 4 d2gfna1 8.5 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 5 c3bruA_ 7.4 18 PDB header:transcription Chain: A: PDB Molecule:regulatory protein, tetr family; PDBTitle: crystal structure of regulatory protein tetr from rhodobacter2 sphaeroides 6 d2g7la1 7.1 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 7 c2zciD_ 7.1 53 PDB header:signaling protein, lyase Chain: D: PDB Molecule:phosphoenolpyruvate carboxykinase [gtp]; PDBTitle: structure of a gtp-dependent bacterial pep-carboxykinase2 from corynebacterium glutamicum 8 c2g7lA_ 6.5 21 PDB header:transcription Chain: A: PDB Molecule:tetr-family transcriptional regulator; PDBTitle: crystal structure of putative transcription regulator sco7704 from2 streptomyces coelicor 9 c3h4cA_ 6.0 33 PDB header:transcription Chain: A: PDB Molecule:transcription factor tfiib-like; PDBTitle: structure of the c-terminal domain of transcription factor iib from2 trypanosoma brucei 10 c1rqtA_ 5.4 44 PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli 11 d1rqta_ 5.4 44 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 12 c1rqtB_ 5.4 44 PDB header:ribosome Chain: B: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli 13 d1c4pc_ 5.1 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 14 c1bjzA_ 5.1 36 PDB header:transcription regulation Chain: A: PDB Molecule:tetracycline repressor; PDBTitle: tetracycline chelated mg2+-ion initiates helix unwinding for tet2 repressor induction 15 d2id3a1 5.0 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, 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