Secondary structure and disorder prediction

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Sequence		M	E	L	K	K	L	M	E	H	I	S	I	T	P	D	Y	R	Q	A	W	K	V	V	H	K	L	S	D	I	L	L	L	T	I	C	A	V	I	S	G	A	E	G	W	E	D	I	E	D	F	G	E	T	H	L	D	F	L	K	Q
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.
Sequence		Y	G	D	F	E	N	G	I	P	V	H	D	T	I	A	R	V	V	S	Q	G	K	I	T
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 2kvc chain A Region: 47 - 74 Aligned: 26 Modelled: 28 Confidence: 48.5% Identity: 23% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a Phyre2 PDB 3ol4 chain B Region: 49 - 74 Aligned: 24 Modelled: 26 Confidence: 48.4% Identity: 25% PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c Phyre2 PDB 1pdn chain C Region: 52 - 78 Aligned: 27 Modelled: 27 Confidence: 34.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 3bpy chain A domain 1 Region: 17 - 82 Aligned: 66 Modelled: 66 Confidence: 30.1% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Forkhead DNA-binding domain Phyre2 PDB 2lky chain A Region: 50 - 74 Aligned: 23 Modelled: 25 Confidence: 23.9% Identity: 22% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of msmeg_1053, the second duf3349 annotated protein2 in the genome of mycobacterium smegmatis, seattle structural genomics3 center for infectious disease target mysma.17112.b Phyre2 PDB 1e17 chain A Region: 17 - 82 Aligned: 66 Modelled: 66 Confidence: 21.4% Identity: 12% PDB header:dna binding domain Chain: A: PDB Molecule:afx; PDBTitle: solution structure of the dna binding domain of the human2 forkhead transcription factor afx (foxo4) Phyre2 PDB 3hef chain B Region: 30 - 76 Aligned: 32 Modelled: 32 Confidence: 19.5% Identity: 25% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 2fna chain A domain 1 Region: 31 - 81 Aligned: 39 Modelled: 46 Confidence: 18.0% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Helicase DNA-binding domain Phyre2 PDB 3co7 chain C Region: 17 - 82 Aligned: 66 Modelled: 66 Confidence: 17.7% Identity: 14% PDB header:transcription/dna Chain: C: PDB Molecule:forkhead box protein o1; PDBTitle: crystal structure of foxo1 dbd bound to dbe2 dna Phyre2 PDB 1pm6 chain A Region: 54 - 83 Aligned: 26 Modelled: 30 Confidence: 13.1% Identity: 15% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 2ezi chain A Region: 68 - 83 Aligned: 16 Modelled: 16 Confidence: 13.1% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 2i7p chain A domain 1 Region: 31 - 52 Aligned: 22 Modelled: 22 Confidence: 11.7% Identity: 23% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Fumble-like Phyre2 PDB 1m5w chain A Region: 17 - 43 Aligned: 25 Modelled: 27 Confidence: 11.1% Identity: 28% Fold: TIM beta/alpha-barrel Superfamily: Pyridoxine 5'-phosphate synthase Family: Pyridoxine 5'-phosphate synthase Phyre2 PDB 3gk0 chain H Region: 17 - 43 Aligned: 25 Modelled: 27 Confidence: 10.3% Identity: 24% PDB header:transferase Chain: H: PDB Molecule:pyridoxine 5'-phosphate synthase; PDBTitle: crystal structure of pyridoxal phosphate biosynthetic2 protein from burkholderia pseudomallei Phyre2 PDB 1rh6 chain A Region: 53 - 83 Aligned: 27 Modelled: 31 Confidence: 9.6% Identity: 19% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 2k27 chain A Region: 52 - 78 Aligned: 27 Modelled: 27 Confidence: 9.3% Identity: 19% PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain Phyre2 PDB 2i7p chain A Region: 31 - 52 Aligned: 22 Modelled: 22 Confidence: 8.5% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:pantothenate kinase 3; PDBTitle: crystal structure of human pank3 in complex with accoa Phyre2 PDB 6pax chain A Region: 3 - 78 Aligned: 71 Modelled: 76 Confidence: 8.3% Identity: 17% PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions Phyre2 PDB 2i7n chain A domain 2 Region: 31 - 52 Aligned: 22 Modelled: 22 Confidence: 8.1% Identity: 23% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Fumble-like Phyre2 PDB 3smp chain A Region: 31 - 52 Aligned: 22 Modelled: 22 Confidence: 7.8% Identity: 23% PDB header:transferase Chain: A: PDB Molecule:pantothenate kinase 1; PDBTitle: monoclinic crystal structure of human pantothenate kinase 1 alpha Phyre2 1 c2kvcA_ 2 c3ol4B_ 3 d1pdnc_ 4 d3bpya1 5 c2lkyA_ 6 c1e17A_ 7 c3hefB_ 8 d2fnaa1 9 c3co7C_ 10 d1pm6a_ 11 d2ezia_ 12 d2i7pa1 13 d1m5wa_ 14 c3gk0H_ 15 d1rh6a_ 16 c2k27A_ 17 c2i7pA_ 18 c6paxA_ 19 d2i7na2 20 c3smpA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 c2kvcA_ 48.5 23 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a 2 c3ol4B_ 48.4 25 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c 3 d1pdnc_ 34.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 4 d3bpya1 30.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 5 c2lkyA_ 23.9 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of msmeg_1053, the second duf3349 annotated protein2 in the genome of mycobacterium smegmatis, seattle structural genomics3 center for infectious disease target mysma.17112.b 6 c1e17A_ 21.4 12 PDB header:dna binding domain Chain: A: PDB Molecule:afx; PDBTitle: solution structure of the dna binding domain of the human2 forkhead transcription factor afx (foxo4) 7 c3hefB_ 19.5 25 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 8 d2fnaa1 18.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 9 c3co7C_ 17.7 14 PDB header:transcription/dna Chain: C: PDB Molecule:forkhead box protein o1; PDBTitle: crystal structure of foxo1 dbd bound to dbe2 dna 10 d1pm6a_ 13.1 15 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 11 d2ezia_ 13.1 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 12 d2i7pa1 11.7 23 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Fumble-like 13 d1m5wa_ 11.1 28 Fold:TIM beta/alpha-barrel Superfamily:Pyridoxine 5'-phosphate synthase Family:Pyridoxine 5'-phosphate synthase 14 c3gk0H_ 10.3 24 PDB header:transferase Chain: H: PDB Molecule:pyridoxine 5'-phosphate synthase; PDBTitle: crystal structure of pyridoxal phosphate biosynthetic2 protein from burkholderia pseudomallei 15 d1rh6a_ 9.6 19 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 16 c2k27A_ 9.3 19 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 17 c2i7pA_ 8.5 23 PDB header:transferase Chain: A: PDB Molecule:pantothenate kinase 3; PDBTitle: crystal structure of human pank3 in complex with accoa 18 c6paxA_ 8.3 17 PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions 19 d2i7na2 8.1 23 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Fumble-like 20 c3smpA_ 7.8 23 PDB header:transferase Chain: A: PDB Molecule:pantothenate kinase 1; PDBTitle: monoclinic crystal structure of human pantothenate kinase 1 alpha 21 d2v9va2 not modelled 7.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal fragment of elongation factor SelB 22 c3iacA_ not modelled 7.4 14 PDB header:isomerase Chain: A: PDB Molecule:glucuronate isomerase; PDBTitle: 2.2 angstrom crystal structure of glucuronate isomerase from2 salmonella typhimurium. 23 d6paxa2 not modelled 7.3 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 24 d1k78a2 not modelled 6.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 25 c3u5gK_ not modelled 6.7 20 PDB header:ribosome Chain: K: PDB Molecule:40s ribosomal protein s10-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution 26 c2l1xA_ not modelled 6.6 11 PDB header:hormone Chain: A: PDB Molecule:parathyroid hormone; PDBTitle: the solution structure of human parathyroid hormone-related protein 27 c3g73A_ not modelled 6.5 16 PDB header:transcription/dna Chain: A: PDB Molecule:forkhead box protein m1; PDBTitle: structure of the foxm1 dna binding 28 d2ezha_ not modelled 6.4 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 29 c1hj0A_ not modelled 6.3 22 PDB header:actin binding peptide Chain: A: PDB Molecule:thymosin beta9; PDBTitle: thymosin beta9 30 d1d5va_ not modelled 6.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 31 d2ezla_ not modelled 5.8 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 32 d2hfha_ not modelled 5.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 33 c2k8oA_ not modelled 5.5 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-l; PDBTitle: solution structure of integrin alpha l 34 c1qcrD_ not modelled 5.3 8 PDB header: PDB COMPND: 35 d1ni7a_ not modelled 5.3 5 Fold:SufE/NifU Superfamily:SufE/NifU Family:SufE-like 36 d1evsa_ not modelled 5.3 22 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Long-chain cytokines

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