Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Y	P	M	D	R	I	Q	Q	K	H	A	R	Q	I	D	L	L	E	N	L	T	A	V	I	Q	D	Y	P	N	P	A	C	I	R	D	E	T	G	K	F	I	F	C	N	T	L	F	H	E	S	F	L	T	Q	D	Q	S	A	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?																																												?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	W	L	L	S	Q	R	D	F	C	E	L	I	S	V	T	E	M	E	A	Y	R	N	E	H	T	H	L	N	L	V	E	D	V	F	I	Q	N	R	F	W	T	I	S	V	Q	S	F	L	N	G	H	R	N	I	I	L	W	Q	F
Secondary structure
SS confidence
Disorder							?	?	?													?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	D	A	A	H	V	R	H	K	D	S	Y	N	Q	K	T	I	V	S	D	D	I	R	N	I	I	R	R	M	S	D	D	S	S	V	S	S	Y	V	N	D	V	F	Y	L	Y	S	T	G	I	S	H	N	A	I	A	R	I	L	N
Secondary structure
SS confidence
Disorder										?								?	?	?	?	?	?	?	?				?			?	?	?	?	?																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.
Sequence		I	S	I	S	T	S	K	K	H	A	S	L	I	C	D	Y	F	S	V	S	N	K	D	E	L	I	I	L	L	Y	N	K	K	F	I	Y	Y	L	Y	E	K	A	M	C	I	I	N	T	R
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 3clo chain C Region: 13 - 205 Aligned: 189 Modelled: 193 Confidence: 97.9% Identity: 14% 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 1p4w chain A Region: 137 - 215 Aligned: 79 Modelled: 79 Confidence: 97.6% Identity: 19% 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 2jpc chain A Region: 161 - 215 Aligned: 55 Modelled: 55 Confidence: 97.5% Identity: 25% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1x3u chain A Region: 161 - 215 Aligned: 55 Modelled: 55 Confidence: 97.5% Identity: 20% 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 3c3w chain B Region: 160 - 205 Aligned: 46 Modelled: 46 Confidence: 97.5% Identity: 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 Phyre2 PDB 3szt chain B Region: 160 - 215 Aligned: 56 Modelled: 56 Confidence: 97.4% Identity: 23% 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 Phyre2 PDB 1zlj chain E Region: 161 - 217 Aligned: 57 Modelled: 57 Confidence: 97.4% Identity: 16% 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 1yio chain A domain 1 Region: 161 - 206 Aligned: 46 Modelled: 46 Confidence: 97.4% Identity: 28% 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 2q0o chain A Region: 160 - 206 Aligned: 47 Modelled: 47 Confidence: 97.3% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 3kln chain C Region: 161 - 208 Aligned: 48 Modelled: 48 Confidence: 97.3% Identity: 25% PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst Phyre2 PDB 2krf chain B Region: 150 - 215 Aligned: 66 Modelled: 66 Confidence: 97.2% Identity: 12% 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 1h0m chain D Region: 160 - 206 Aligned: 47 Modelled: 47 Confidence: 97.2% Identity: 15% PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna Phyre2 PDB 1fse chain A Region: 161 - 215 Aligned: 55 Modelled: 55 Confidence: 97.2% Identity: 24% 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: 150 - 215 Aligned: 66 Modelled: 66 Confidence: 97.2% Identity: 23% PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain Phyre2 PDB 1rnl chain A Region: 161 - 214 Aligned: 54 Modelled: 54 Confidence: 97.1% Identity: 24% PDB header:signal transduction protein Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl; PDBTitle: the nitrate/nitrite response regulator protein narl from narl Phyre2 PDB 3qp5 chain C Region: 160 - 205 Aligned: 46 Modelled: 46 Confidence: 97.1% Identity: 30% PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) Phyre2 PDB 1l3l chain A domain 1 Region: 151 - 215 Aligned: 65 Modelled: 65 Confidence: 97.1% 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 1a04 chain A domain 1 Region: 150 - 205 Aligned: 56 Modelled: 56 Confidence: 97.0% Identity: 25% 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 1zn2 chain A Region: 161 - 205 Aligned: 45 Modelled: 45 Confidence: 96.8% Identity: 29% PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr Phyre2 PDB 3p7n chain B Region: 21 - 206 Aligned: 171 Modelled: 171 Confidence: 95.5% Identity: 14% PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis Phyre2 1 c3cloC_ 2 d1p4wa_ 3 c2jpcA_ 4 c1x3uA_ 5 c3c3wB_ 6 c3sztB_ 7 c1zljE_ 8 d1yioa1 9 c2q0oA_ 10 c3klnC_ 11 c2krfB_ 12 c1h0mD_ 13 d1fsea_ 14 c2rnjA_ 15 c1rnlA_ 16 c3qp5C_ 17 d1l3la1 18 d1a04a1 19 c1zn2A_ 20 c3p7nB_ 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 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105

Detailed template information

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

1 c3cloC_ 97.9 14 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 2 d1p4wa_ 97.6 19 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 c2jpcA_ 97.5 25 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 4 c1x3uA_ 97.5 20 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 5 c3c3wB_ 97.5 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 6 c3sztB_ 97.4 23 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 7 c1zljE_ 97.4 16 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 8 d1yioa1 97.4 28 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) 9 c2q0oA_ 97.3 13 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 10 c3klnC_ 97.3 25 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 11 c2krfB_ 97.2 12 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 12 c1h0mD_ 97.2 15 PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna 13 d1fsea_ 97.2 24 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) 14 c2rnjA_ 97.2 23 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 15 c1rnlA_ 97.1 24 PDB header:signal transduction protein Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl; PDBTitle: the nitrate/nitrite response regulator protein narl from narl 16 c3qp5C_ 97.1 30 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 17 d1l3la1 97.1 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) 18 d1a04a1 97.0 25 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) 19 c1zn2A_ 96.8 29 PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr 20 c3p7nB_ 95.5 14 PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis 21 c3mqoB_ not modelled 93.8 14 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: the crystal structure of the pas domain in complex with isopropanol of2 a transcriptional regulator in the luxr family from burkholderia3 thailandensis to 1.7a 22 c2qkpD_ not modelled 93.5 10 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of c-terminal domain of smu_1151c from streptococcus2 mutans 23 c2v1bA_ not modelled 93.2 10 PDB header:transferase Chain: A: PDB Molecule:nph1-1; PDBTitle: n- and c-terminal helices of oat lov2 (404-546) are2 involved in light-induced signal transduction (room3 temperature (293k) light structure of lov2 (404-546)) 24 c3mzyA_ not modelled 92.3 21 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 25 c3mxqC_ not modelled 91.2 11 PDB header:transferase Chain: C: PDB Molecule:sensor protein; PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae 26 c2pr6A_ not modelled 90.1 9 PDB header:flavoprotein, signaling protein Chain: A: PDB Molecule:blue-light photoreceptor; PDBTitle: structural basis for light-dependent signaling in the dimeric lov2 photosensor ytva (light structure) 27 d1or7a1 not modelled 90.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 28 c3luqC_ not modelled 89.1 11 PDB header:transferase Chain: C: PDB Molecule:sensor protein; PDBTitle: the crystal structure of a pas domain from a sensory box2 histidine kinase regulator from geobacter sulfurreducens to3 2.5a 29 d1rp3a2 not modelled 88.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 30 c1kgsA_ not modelled 88.9 9 PDB header:dna binding protein Chain: A: PDB Molecule:dna binding response regulator d; PDBTitle: crystal structure at 1.50 a of an ompr/phob homolog from thermotoga2 maritima 31 c3mfxA_ not modelled 88.6 22 PDB header:transcription Chain: A: PDB Molecule:sensory box/ggdef family protein; PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b 32 c2o8xA_ not modelled 87.7 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 33 c3oloB_ not modelled 86.3 8 PDB header:transferase Chain: B: PDB Molecule:two-component sensor histidine kinase; PDBTitle: crystal structure of a pas domain from two-component sensor histidine2 kinase 34 c2gj3A_ not modelled 86.0 8 PDB header:transferase Chain: A: PDB Molecule:nitrogen fixation regulatory protein; PDBTitle: crystal structure of the fad-containing pas domain of the2 protein nifl from azotobacter vinelandii. 35 c1or7A_ not modelled 85.0 16 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 36 d1xsva_ not modelled 84.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 37 c3hugA_ not modelled 84.6 24 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 38 c3b33A_ not modelled 84.5 15 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus 39 c3lyxA_ not modelled 83.9 11 PDB header:transcription Chain: A: PDB Molecule:sensory box/ggdef domain protein; PDBTitle: crystal structure of the pas domain of the protein cps_12912 from colwellia psychrerythraea. northeast structural3 genomics consortium target id csr222b 40 c3k3dA_ not modelled 83.5 10 PDB header:signaling protein Chain: A: PDB Molecule:protein rv1364c/mt1410; PDBTitle: the n-terminal pas domain crystal structure of rv1364c from2 mycobacterium tuberculosis at 2.3 angstrom 41 d1nwza_ not modelled 83.0 9 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 42 c3caxA_ not modelled 82.6 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein pf0695; PDBTitle: crystal structure of uncharacterized protein pf0695 43 d1smyf2 not modelled 82.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 44 c3mjqB_ not modelled 82.3 6 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the pas domain of q24qt8_deshy protein from2 desulfitobacterium hafniense. northeast structural genomics3 consortium target dhr85c. 45 c3bwlA_ not modelled 81.4 11 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of pas domain of htr-like protein from haloarcula2 marismortui 46 c2l4rA_ not modelled 81.3 15 PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily h member 2; PDBTitle: nmr solution structure of the n-terminal pas domain of herg 47 d1ew0a_ not modelled 81.2 12 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 48 c3pxpA_ not modelled 81.2 26 PDB header:transcription regulator Chain: A: PDB Molecule:helix-turn-helix domain protein; PDBTitle: crystal structure of a pas and dna binding domain containing protein2 (caur_2278) from chloroflexus aurantiacus j-10-fl at 2.30 a3 resolution 49 d1ttya_ not modelled 80.6 3 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 50 c3a0rA_ not modelled 80.1 9 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of histidine kinase thka (tm1359) in complex with2 response regulator protein trra (tm1360) 51 c3kx0X_ not modelled 80.1 9 PDB header:signaling protein Chain: X: PDB Molecule:uncharacterized protein rv1364c/mt1410; PDBTitle: crystal structure of the pas domain of rv1364c 52 c2w0nA_ not modelled 79.6 22 PDB header:transferase Chain: A: PDB Molecule:sensor protein dcus; PDBTitle: plasticity of pas domain and potential role for signal2 transduction in the histidine-kinase dcus 53 c2r78D_ not modelled 79.2 10 PDB header:transferase Chain: D: PDB Molecule:sensor protein; PDBTitle: crystal structure of a domain of the sensory box sensor2 histidine kinase/response regulator from geobacter3 sulfurreducens 54 d2p7vb1 not modelled 78.5 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 55 d1s7oa_ not modelled 76.2 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 56 c2r0qF_ not modelled 75.3 19 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 57 c2jheB_ not modelled 73.7 15 PDB header:transcription Chain: B: PDB Molecule:transcription regulator tyrr; PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190) 58 d1mzua_ not modelled 70.8 13 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 59 c3fg8B_ not modelled 69.3 8 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein rha05790; PDBTitle: crystal structure of pas domain of rha05790 60 c1v9yA_ not modelled 68.8 9 PDB header:signaling protein Chain: A: PDB Molecule:heme pas sensor protein; PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form) 61 d1v9ya_ not modelled 68.8 9 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 62 d1otda_ not modelled 68.4 12 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 63 c2q1zA_ not modelled 67.6 16 PDB header:transcription Chain: A: PDB Molecule:rpoe, ecf sige; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 64 c2gm4B_ not modelled 64.8 18 PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna 65 c1rp3G_ not modelled 63.0 14 PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm 66 d1xj3a1 not modelled 62.5 11 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 67 d1ku3a_ not modelled 58.4 3 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 68 c1u78A_ not modelled 50.3 18 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 69 c3fc7B_ not modelled 46.7 7 PDB header:transferase Chain: B: PDB Molecule:htr-like protein; PDBTitle: the crystal structure of a domain of htr-like protein from haloarcula2 marismortui atcc 43049 70 c2krcA_ not modelled 41.5 13 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase subunit delta; PDBTitle: solution structure of the n-terminal domain of bacillus2 subtilis delta subunit of rna polymerase 71 c6paxA_ not modelled 40.6 22 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 72 c2guzO_ not modelled 38.7 24 PDB header:chaperone, protein transport Chain: O: PDB Molecule:mitochondrial import inner membrane translocase PDBTitle: structure of the tim14-tim16 complex of the mitochondrial2 protein import motor 73 d1pdnc_ not modelled 38.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 74 c2vlgD_ not modelled 37.6 9 PDB header:transferase Chain: D: PDB Molecule:sporulation kinase a; PDBTitle: kina pas-a domain, homodimer 75 d1hcra_ not modelled 35.7 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 76 d1y28a_ not modelled 35.6 10 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 77 d1ijwc_ not modelled 35.2 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 78 c3trbA_ not modelled 34.2 24 PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii 79 c3mr0B_ not modelled 31.2 9 PDB header:transcription regulator Chain: B: PDB Molecule:sensory box histidine kinase/response regulator; PDBTitle: crystal structure of sensory box histidine kinase/response regulator2 from burkholderia thailandensis e264 80 d1ku7a_ not modelled 31.0 4 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 81 d2id6a1 not modelled 29.3 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 82 d1jt6a1 not modelled 27.8 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 83 c3a0vA_ not modelled 26.7 13 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m) 84 c3gecA_ not modelled 26.4 8 PDB header:circadian clock protein Chain: A: PDB Molecule:period circadian protein; PDBTitle: crystal structure of a tandem pas domain fragment of2 drosophila period 85 d2gfna1 not modelled 26.4 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 86 c1ui6B_ not modelled 23.9 17 PDB header:antibiotic Chain: B: PDB Molecule:a-factor receptor homolog; PDBTitle: crystal structure of gamma-butyrolactone receptor (arpa-like protein) 87 c3onqB_ not modelled 23.8 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:regulator of polyketide synthase expression; PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis 88 c1wa9A_ not modelled 23.7 8 PDB header:circadian rhythm Chain: A: PDB Molecule:period circadian protein; PDBTitle: crystal structure of the pas repeat region of the2 drosophila clock protein period 89 c2g7sA_ not modelled 23.7 31 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: the crystal structure of transcriptional regulator, tetr family, from2 agrobacterium tumefaciens 90 d1jnua_ not modelled 23.2 21 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Flavin-binding PAS domain 91 c2o7tA_ not modelled 23.0 17 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of a tetr family transcriptional regulator2 (ncgl1578, cgl1640) from corynebacterium glutamicum at 2.10 a3 resolution 92 d1ttea1 not modelled 22.9 21 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 93 c3dnvB_ not modelled 22.9 21 PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein 94 d1uptd_ not modelled 22.2 15 Fold:GRIP domain Superfamily:GRIP domain Family:GRIP domain 95 c1bjzA_ not modelled 22.1 28 PDB header:transcription regulation Chain: A: PDB Molecule:tetracycline repressor; PDBTitle: tetracycline chelated mg2+-ion initiates helix unwinding for tet2 repressor induction 96 c3lisB_ not modelled 22.0 15 PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form) 97 c2gfnA_ not modelled 21.8 24 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator pksa related protein; PDBTitle: crystal structure of hth-type transcriptional regulator pksa related2 protein from rhodococcus sp. rha1 98 d2fbqa1 not modelled 21.6 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 99 c3ni7A_ not modelled 21.3 41 PDB header:transcription regulator Chain: A: PDB Molecule:bacterial regulatory proteins, tetr family; PDBTitle: crystal structure of the tetr transcriptional regulator from2 nitrosomonas europaea atcc 19718 100 c2p6tH_ not modelled 21.2 11 PDB header:transcription Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family; PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis 101 c2oqrA_ not modelled 21.0 5 PDB header:transcription,signaling protein Chain: A: PDB Molecule:sensory transduction protein regx3; PDBTitle: the structure of the response regulator regx3 from mycobacterium2 tuberculosis 102 c3bjbE_ not modelled 21.0 24 PDB header:transcription regulator Chain: E: PDB Molecule:probable transcriptional regulator, tetr family protein; PDBTitle: crystal structure of a tetr transcriptional regulator from rhodococcus2 sp. rha1 103 c3omtA_ not modelled 20.9 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. 104 c2dg8D_ not modelled 20.6 28 PDB header:gene regulation Chain: D: PDB Molecule:putative tetr-family transcriptional regulatory protein; PDBTitle: crystal structure of the putative trasncriptional regulator sco75182 from streptomyces coelicolor a3(2) 105 d1t56a1 not modelled 20.6 31 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