Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	T	S	E	L	L	K	H	I	Y	D	I	N	L	S	Y	L	L	L	A	Q	R	L	I	V	Q	D	K	A	S	A	M	F	R	L	G	I	N	E	E	M	A	T	T	L	A	A	L	T	L	P	Q	M	V	K	L	A	E	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.
Sequence		N	Q	L	V	C	H	F	R	F	D	S	H	Q	T	I	T	Q	L	T	Q	D	S	R	V	D	D	L	Q	Q	I	H	T	G	I	M	L	S	T	R	L	L	N	D	V	N	Q	P	E	E	A	L	R	K	K	R	A
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 1g8e chain A Region: 1 - 98 Aligned: 98 Modelled: 98 Confidence: 100.0% Identity: 100% Fold: Flagellar transcriptional activator FlhD Superfamily: Flagellar transcriptional activator FlhD Family: Flagellar transcriptional activator FlhD Phyre2 PDB 1g8e chain B Region: 3 - 82 Aligned: 80 Modelled: 80 Confidence: 100.0% Identity: 100% Fold: Flagellar transcriptional activator FlhD Superfamily: Flagellar transcriptional activator FlhD Family: Flagellar transcriptional activator FlhD Phyre2 PDB 1xlm chain A Region: 35 - 71 Aligned: 37 Modelled: 37 Confidence: 18.3% Identity: 19% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 2kq5 chain A Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 16.9% Identity: 36% PDB header:unknown function Chain: A: PDB Molecule:avirulence protein; PDBTitle: solution nmr structure of a section of the repeat domain of the type2 iii effector protein ptha Phyre2 PDB 2fx0 chain A domain 2 Region: 7 - 48 Aligned: 42 Modelled: 42 Confidence: 16.0% Identity: 7% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 1b4u chain A Region: 21 - 67 Aligned: 47 Modelled: 47 Confidence: 11.7% Identity: 6% Fold: LigA subunit of an aromatic-ring-opening dioxygenase LigAB Superfamily: LigA subunit of an aromatic-ring-opening dioxygenase LigAB Family: LigA subunit of an aromatic-ring-opening dioxygenase LigAB Phyre2 PDB 3e46 chain A domain 1 Region: 64 - 89 Aligned: 26 Modelled: 26 Confidence: 10.1% Identity: 23% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 1qt1 chain A Region: 35 - 71 Aligned: 37 Modelled: 37 Confidence: 8.1% Identity: 22% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 3m91 chain B Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 8.0% Identity: 42% PDB header:hydrolase regulator Chain: B: PDB Molecule:prokaryotic ubiquitin-like protein pup; PDBTitle: crystal structure of the prokaryotic ubiquitin-like protein (pup)2 complexed with the amino terminal coiled coil of the mycobacterium3 tuberculosis proteasomal atpase mpa Phyre2 PDB 2glk chain A domain 1 Region: 35 - 71 Aligned: 37 Modelled: 37 Confidence: 7.9% Identity: 22% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 1au7 chain A domain 2 Region: 34 - 67 Aligned: 29 Modelled: 34 Confidence: 7.8% Identity: 24% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: POU-specific domain Phyre2 PDB 3hgf chain A Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 7.6% Identity: 45% PDB header:nucleotide binding protein Chain: A: PDB Molecule:rhoptry protein fragment; PDBTitle: expression, purification, spectroscopical and2 crystallographical studies of segments of the nucleotide3 binding domain of the reticulocyte binding protein py235 of4 plasmodium yoelii Phyre2 PDB 1dd3 chain A domain 1 Region: 1 - 18 Aligned: 18 Modelled: 18 Confidence: 7.3% Identity: 28% 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 1bxc chain A Region: 35 - 71 Aligned: 37 Modelled: 37 Confidence: 6.7% Identity: 30% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 3m9d chain I Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 6.5% Identity: 42% PDB header:chaperone Chain: I: PDB Molecule:prokaryotic ubiquitin-like protein pup; PDBTitle: crystal structure of the prokaryotic ubiquintin-like protein pup2 complexed with the hexameric proteasomal atpase mpa which includes3 the amino terminal coiled coil domain and the inter domain Phyre2 PDB 2fh0 chain A Region: 51 - 78 Aligned: 26 Modelled: 28 Confidence: 5.9% Identity: 23% PDB header:unknown function Chain: A: PDB Molecule:hypothetical 16.0 kda protein in abf2-chl12 PDBTitle: nmr ensemble of the yeast saccharomyces cerevisiae protein2 ymr074cp core region Phyre2 PDB 2i56 chain A Region: 16 - 71 Aligned: 48 Modelled: 56 Confidence: 5.6% Identity: 15% PDB header:isomerase, metal-binding protein Chain: A: PDB Molecule:l-rhamnose isomerase; PDBTitle: crystal structure of l-rhamnose isomerase from pseudomonas2 stutzeri with l-rhamnose Phyre2 PDB 2e8m chain A Region: 37 - 57 Aligned: 21 Modelled: 21 Confidence: 5.6% Identity: 29% PDB header:signaling protein Chain: A: PDB Molecule:epidermal growth factor receptor kinase PDBTitle: solution structure of the c-terminal sam-domain of2 epidermal growth receptor pathway substrate 8 Phyre2 PDB 3eq1 chain A Region: 30 - 92 Aligned: 60 Modelled: 63 Confidence: 5.5% Identity: 10% PDB header:transferase Chain: A: PDB Molecule:porphobilinogen deaminase; PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution Phyre2 PDB 2avu chain F Region: 6 - 97 Aligned: 61 Modelled: 61 Confidence: 5.4% Identity: 31% PDB header:transcription activator Chain: F: PDB Molecule:flagellar transcriptional activator flhc; PDBTitle: structure of the escherichia coli flhdc complex, a2 prokaryotic heteromeric regulator of transcription Phyre2 1 d1g8ea_ 2 d1g8eb_ 3 d1xlma_ 4 c2kq5A_ 5 d2fx0a2 6 d1b4ua_ 7 d3e46a1 8 d1qt1a_ 9 c3m91B_ 10 d2glka1 11 d1au7a2 12 c3hgfA_ 13 d1dd3a1 14 d1bxca_ 15 c3m9dI_ 16 c2fh0A_ 17 c2i56A_ 18 c2e8mA_ 19 c3eq1A_ 20 c2avuF_

Detailed template information

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

1 d1g8ea_ 100.0 100 Fold:Flagellar transcriptional activator FlhD Superfamily:Flagellar transcriptional activator FlhD Family:Flagellar transcriptional activator FlhD 2 d1g8eb_ 100.0 100 Fold:Flagellar transcriptional activator FlhD Superfamily:Flagellar transcriptional activator FlhD Family:Flagellar transcriptional activator FlhD 3 d1xlma_ 18.3 19 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 4 c2kq5A_ 16.9 36 PDB header:unknown function Chain: A: PDB Molecule:avirulence protein; PDBTitle: solution nmr structure of a section of the repeat domain of the type2 iii effector protein ptha 5 d2fx0a2 16.0 7 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 6 d1b4ua_ 11.7 6 Fold:LigA subunit of an aromatic-ring-opening dioxygenase LigAB Superfamily:LigA subunit of an aromatic-ring-opening dioxygenase LigAB Family:LigA subunit of an aromatic-ring-opening dioxygenase LigAB 7 d3e46a1 10.1 23 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 8 d1qt1a_ 8.1 22 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 9 c3m91B_ 8.0 42 PDB header:hydrolase regulator Chain: B: PDB Molecule:prokaryotic ubiquitin-like protein pup; PDBTitle: crystal structure of the prokaryotic ubiquitin-like protein (pup)2 complexed with the amino terminal coiled coil of the mycobacterium3 tuberculosis proteasomal atpase mpa 10 d2glka1 7.9 22 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 11 d1au7a2 7.8 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 12 c3hgfA_ 7.6 45 PDB header:nucleotide binding protein Chain: A: PDB Molecule:rhoptry protein fragment; PDBTitle: expression, purification, spectroscopical and2 crystallographical studies of segments of the nucleotide3 binding domain of the reticulocyte binding protein py235 of4 plasmodium yoelii 13 d1dd3a1 7.3 28 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 14 d1bxca_ 6.7 30 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 15 c3m9dI_ 6.5 42 PDB header:chaperone Chain: I: PDB Molecule:prokaryotic ubiquitin-like protein pup; PDBTitle: crystal structure of the prokaryotic ubiquintin-like protein pup2 complexed with the hexameric proteasomal atpase mpa which includes3 the amino terminal coiled coil domain and the inter domain 16 c2fh0A_ 5.9 23 PDB header:unknown function Chain: A: PDB Molecule:hypothetical 16.0 kda protein in abf2-chl12 PDBTitle: nmr ensemble of the yeast saccharomyces cerevisiae protein2 ymr074cp core region 17 c2i56A_ 5.6 15 PDB header:isomerase, metal-binding protein Chain: A: PDB Molecule:l-rhamnose isomerase; PDBTitle: crystal structure of l-rhamnose isomerase from pseudomonas2 stutzeri with l-rhamnose 18 c2e8mA_ 5.6 29 PDB header:signaling protein Chain: A: PDB Molecule:epidermal growth factor receptor kinase PDBTitle: solution structure of the c-terminal sam-domain of2 epidermal growth receptor pathway substrate 8 19 c3eq1A_ 5.5 10 PDB header:transferase Chain: A: PDB Molecule:porphobilinogen deaminase; PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution 20 c2avuF_ 5.4 31 PDB header:transcription activator Chain: F: PDB Molecule:flagellar transcriptional activator flhc; PDBTitle: structure of the escherichia coli flhdc complex, a2 prokaryotic heteromeric regulator of transcription

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