Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Y	C	I	N	T	D	C	T	Y	T	K	I	A	I	E	Q	L	L	H	E	K	Y	F	D	D	R	R	Y	C	H	S	I	K	I	Y	D	L	R	F	F	K	I	E	D	V	A	Y	K	L	I	Q	L	F	K	E	R	R	K	E
Secondary structure
SS confidence
Disorder		?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	I	I	F	L	C	S	D	R	F	I	H	S	K	E	K	P	R	N	I	F	F	L	D	T	K	D	S	I	R	N	W	S	R	H	L	K	K	L	R	Y	C	N	S	N	L	L	I	C	F	L	F	L	C	G	L	Y	H	I	S
Secondary structure
SS confidence
Disorder													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	F	T	G	K	K	Q	V	I	I	A	C	I	K	K	G	F	S	F	A	E	I	V	N	F	L	N	I	N	A	R	T	L	V	N	Y	L	G	G	L	T	T	Y	F	I	L	P	Y	S	D	S	L	Y	K	Y	I	I	D	N	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200
Sequence		I	A	S	S	T	E	E	Y	H	I	L	L	T	N	Q	R	R	Y	Y	V
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 1fse chain A Region: 120 - 160 Aligned: 41 Modelled: 41 Confidence: 48.8% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1p4w chain A Region: 122 - 186 Aligned: 65 Modelled: 65 Confidence: 45.9% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2rnj chain A Region: 119 - 157 Aligned: 39 Modelled: 39 Confidence: 44.2% Identity: 26% PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain Phyre2 PDB 1sqw chain A domain 2 Region: 170 - 200 Aligned: 31 Modelled: 31 Confidence: 38.4% Identity: 32% Fold: Cystatin-like Superfamily: Pre-PUA domain Family: Nip7p homolog, N-terminal domain Phyre2 PDB 1zlj chain E Region: 119 - 160 Aligned: 42 Modelled: 42 Confidence: 30.9% Identity: 19% PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain Phyre2 PDB 2krf chain B Region: 120 - 157 Aligned: 38 Modelled: 38 Confidence: 30.8% Identity: 29% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a Phyre2 PDB 1yio chain A domain 1 Region: 122 - 157 Aligned: 36 Modelled: 36 Confidence: 30.3% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1rp3 chain A domain 2 Region: 126 - 157 Aligned: 32 Modelled: 32 Confidence: 28.7% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 2jpc chain A Region: 129 - 157 Aligned: 29 Modelled: 29 Confidence: 26.4% Identity: 21% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1a04 chain A domain 1 Region: 119 - 179 Aligned: 61 Modelled: 61 Confidence: 22.8% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1l3l chain A domain 1 Region: 122 - 157 Aligned: 36 Modelled: 36 Confidence: 21.5% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 3clo chain C Region: 118 - 160 Aligned: 43 Modelled: 43 Confidence: 20.3% Identity: 28% PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution Phyre2 PDB 1x3u chain A Region: 122 - 157 Aligned: 36 Modelled: 36 Confidence: 19.3% Identity: 17% PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot Phyre2 PDB 1nh2 chain B Region: 171 - 188 Aligned: 18 Modelled: 18 Confidence: 15.9% Identity: 17% Fold: Transcription factor IIA (TFIIA), alpha-helical domain Superfamily: Transcription factor IIA (TFIIA), alpha-helical domain Family: Transcription factor IIA (TFIIA), alpha-helical domain Phyre2 PDB 1or7 chain A domain 1 Region: 126 - 157 Aligned: 32 Modelled: 32 Confidence: 15.2% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 2lat chain A Region: 104 - 127 Aligned: 24 Modelled: 24 Confidence: 13.3% Identity: 50% PDB header:membrane protein Chain: A: PDB Molecule:dolichyl-diphosphooligosaccharide--protein PDBTitle: solution structure of a human minimembrane protein ost4 Phyre2 PDB 3hug chain A Region: 126 - 157 Aligned: 32 Modelled: 32 Confidence: 13.1% Identity: 31% PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl Phyre2 PDB 2ixo chain A domain 1 Region: 97 - 168 Aligned: 64 Modelled: 72 Confidence: 13.1% Identity: 23% Fold: PTPA-like Superfamily: PTPA-like Family: PTPA-like Phyre2 PDB 2pco chain A Region: 92 - 100 Aligned: 9 Modelled: 9 Confidence: 12.6% Identity: 78% PDB header:toxin Chain: A: PDB Molecule:latarcin-1; PDBTitle: spatial structure and membrane permeabilization for2 latarcin-1, a spider antimicrobial peptide Phyre2 PDB 1gxl chain A Region: 44 - 115 Aligned: 66 Modelled: 72 Confidence: 12.3% Identity: 21% Fold: Smc hinge domain Superfamily: Smc hinge domain Family: Smc hinge domain Phyre2 1 d1fsea_ 2 d1p4wa_ 3 c2rnjA_ 4 d1sqwa2 5 c1zljE_ 6 c2krfB_ 7 d1yioa1 8 d1rp3a2 9 c2jpcA_ 10 d1a04a1 11 d1l3la1 12 c3cloC_ 13 c1x3uA_ 14 d1nh2b_ 15 d1or7a1 16 c2latA_ 17 c3hugA_ 18 d2ixoa1 19 c2pcoA_ 20 d1gxla_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45

Detailed template information

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

1 d1fsea_ 48.8 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 2 d1p4wa_ 45.9 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 3 c2rnjA_ 44.2 26 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 4 d1sqwa2 38.4 32 Fold:Cystatin-like Superfamily:Pre-PUA domain Family:Nip7p homolog, N-terminal domain 5 c1zljE_ 30.9 19 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 6 c2krfB_ 30.8 29 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 7 d1yioa1 30.3 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 8 d1rp3a2 28.7 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 9 c2jpcA_ 26.4 21 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 10 d1a04a1 22.8 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 11 d1l3la1 21.5 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 12 c3cloC_ 20.3 28 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution 13 c1x3uA_ 19.3 17 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot 14 d1nh2b_ 15.9 17 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 15 d1or7a1 15.2 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 16 c2latA_ 13.3 50 PDB header:membrane protein Chain: A: PDB Molecule:dolichyl-diphosphooligosaccharide--protein PDBTitle: solution structure of a human minimembrane protein ost4 17 c3hugA_ 13.1 31 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 18 d2ixoa1 13.1 23 Fold:PTPA-like Superfamily:PTPA-like Family:PTPA-like 19 c2pcoA_ 12.6 78 PDB header:toxin Chain: A: PDB Molecule:latarcin-1; PDBTitle: spatial structure and membrane permeabilization for2 latarcin-1, a spider antimicrobial peptide 20 d1gxla_ 12.3 21 Fold:Smc hinge domain Superfamily:Smc hinge domain Family:Smc hinge domain 21 d1nvpb_ not modelled 11.6 22 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 22 c1nvpB_ not modelled 11.6 22 PDB header:transcription/dna Chain: B: PDB Molecule:transcription initiation factor iia alpha chain; PDBTitle: human tfiia/tbp/dna complex 23 c3sztB_ not modelled 11.5 22 PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone 24 c3c3wB_ not modelled 7.9 17 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 25 c2x3gA_ not modelled 7.8 80 PDB header:viral protein Chain: A: PDB Molecule:sirv1 hypothetical protein orf119; PDBTitle: crystal structure of the hypothetical protein orf119 from2 sulfolobus islandicus rod-shaped virus 1 26 d1u1ha1 not modelled 7.7 29 Fold:TIM beta/alpha-barrel Superfamily:UROD/MetE-like Family:Cobalamin-independent methionine synthase 27 d1xsva_ not modelled 6.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 28 c2uvpB_ not modelled 6.5 58 PDB header:unknown function Chain: B: PDB Molecule:hoba; PDBTitle: crystal structure of hoba (hp1230)from helicobacter pylori 29 d1b0na2 not modelled 6.5 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 30 d1vp7a_ not modelled 6.4 25 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 31 c3e3vA_ not modelled 6.1 26 PDB header:recombination Chain: A: PDB Molecule:regulatory protein recx; PDBTitle: crystal structure of recx from lactobacillus salivarius 32 d1kxpd3 not modelled 5.9 40 Fold:Serum albumin-like Superfamily:Serum albumin-like Family:Serum albumin-like 33 c3d5lA_ not modelled 5.9 26 PDB header:signaling protein Chain: A: PDB Molecule:regulatory protein recx; PDBTitle: crystal structure of regulatory protein recx 34 c3mzyA_ not modelled 5.9 22 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 35 c2cxaA_ not modelled 5.7 27 PDB header:transferase Chain: A: PDB Molecule:leucyl/phenylalanyl-trna-protein transferase; PDBTitle: crystal structure of leucyl/phenylalanyl-trna protein2 transferase from escherichia coli 36 d2cxaa1 not modelled 5.7 27 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:LFTR-like 37 d2go8a1 not modelled 5.7 31 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:PG130-like 38 c2jmlA_ not modelled 5.6 19 PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor 39 c2o8xA_ not modelled 5.4 13 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 40 c3ltiA_ not modelled 5.3 36 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta; PDBTitle: crystal structure of the escherichia coli rna polymerase beta subunit2 beta2-betai4 domains 41 c1u22A_ not modelled 5.3 29 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: a. thaliana cobalamine independent methionine synthase 42 c3zr8X_ not modelled 5.2 31 PDB header:protein binding Chain: X: PDB Molecule:avr3a11; PDBTitle: crystal structure of rxlr effector avr3a11 from phytophthora capsici 43 c2lc2A_ not modelled 5.1 33 PDB header:protein binding Chain: A: PDB Molecule:avr3a4; PDBTitle: solution structure of the rxlr effector p. capsici avr3a4 44 c2a7uB_ not modelled 5.1 13 PDB header:hydrolase Chain: B: PDB Molecule:atp synthase delta chain; PDBTitle: nmr solution structure of the e.coli f-atpase delta subunit n-terminal2 domain in complex with alpha subunit n-terminal 22 residues 45 d1abva_ not modelled 5.1 13 Fold:ATPD N-terminal domain-like Superfamily:N-terminal domain of the delta subunit of the F1F0-ATP synthase Family:N-terminal domain of the delta subunit of the F1F0-ATP synthase

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