Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	N	F	T	T	S	T	P	H	D	A	L	F	K	T	F	L	T	H	P	D	T	A	R	D	F	M	E	I	H	L	P	K	D	L	R	E	L	C	D	L	D	S	L	K	L	E	S	A	S	F	V	D	E	K	L	R	A	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																									?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		H	S	D	I	L	W	S	V	K	T	R	E	G	D	G	Y	I	Y	V	V	I	E	H	Q	S	R	E	D	I	H	M	A	F	R	L	M	R	Y	S	M	A	V	M	Q	R	H	I	E	H	D	K	R	Q	P	L	P	L	V	I	P
Secondary structure
SS confidence
Disorder																																																?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	L	F	Y	H	G	S	R	S	P	Y	P	W	S	L	C	W	L	D	E	F	A	D	P	T	T	A	R	K	L	Y	N	A	A	F	P	L	V	D	V	T	V	V	P	D	D	E	I	V	Q	H	R	R	V	A	L	L	E	L	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Q	K	H	I	R	Q	R	D	L	M	G	L	I	D	Q	L	V	V	L	L	V	T	E	C	A	N	D	S	Q	I	T	A	L	L	N	Y	I	L	L	T	G	D	E	A	R	F	N	E	F	I	S	E	L	T	R	R	M	P	Q	H
Secondary structure
SS confidence
Disorder					?																																							?		?												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		R	E	R	I	M	T	I	A	E	R	I	H	N	D	G	Y	I	K	G	E	Q	R	I	L	R	L	L	L	Q	N	G	A	D	P	E	W	I	Q	K	I	T	G	L	S	A	E	Q	M	Q	A	L	R	Q	P	L	P	E	R	E	R
Secondary structure
SS confidence
Disorder																															?	?	?	?										?
Disorder confidence
		.	.	.	.	.	.
Sequence		Y	S	W	L	K	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 1a9x chain A domain 1 Region: 196 - 295 Aligned: 100 Modelled: 100 Confidence: 92.8% Identity: 14% Fold: Carbamoyl phosphate synthetase, large subunit connection domain Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain Family: Carbamoyl phosphate synthetase, large subunit connection domain Phyre2 PDB 2x48 chain B Region: 260 - 290 Aligned: 31 Modelled: 31 Confidence: 86.3% Identity: 16% PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 Phyre2 PDB 1p4w chain A Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 80.8% Identity: 13% 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 1trr chain A Region: 259 - 305 Aligned: 47 Modelled: 47 Confidence: 76.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1yio chain A domain 1 Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 76.1% Identity: 13% 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 1x3u chain A Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 76.0% Identity: 13% 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 2krf chain B Region: 259 - 298 Aligned: 40 Modelled: 40 Confidence: 74.2% Identity: 10% 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 1fse chain A Region: 259 - 298 Aligned: 40 Modelled: 40 Confidence: 73.5% Identity: 13% 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 1h0m chain D Region: 259 - 298 Aligned: 40 Modelled: 37 Confidence: 72.7% Identity: 13% 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 2jpc chain A Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 72.5% Identity: 15% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1a04 chain A domain 1 Region: 259 - 298 Aligned: 40 Modelled: 40 Confidence: 71.5% Identity: 10% 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: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 70.0% Identity: 15% 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 2q0o chain A Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 68.2% 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 1zlj chain E Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 67.2% Identity: 21% 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 2rnj chain A Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 65.2% Identity: 10% PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain Phyre2 PDB 1l3l chain A domain 1 Region: 260 - 298 Aligned: 39 Modelled: 36 Confidence: 65.1% Identity: 13% 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 3szt chain B Region: 260 - 298 Aligned: 39 Modelled: 39 Confidence: 63.4% Identity: 8% 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 2gm4 chain B Region: 224 - 294 Aligned: 71 Modelled: 71 Confidence: 63.3% Identity: 15% 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 Phyre2 PDB 1d5y chain A domain 1 Region: 253 - 306 Aligned: 54 Modelled: 54 Confidence: 62.0% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: AraC type transcriptional activator Phyre2 PDB 1vz0 chain A domain 1 Region: 259 - 291 Aligned: 33 Modelled: 33 Confidence: 60.2% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 1 d1a9xa1 2 c2x48B_ 3 d1p4wa_ 4 d1trra_ 5 d1yioa1 6 c1x3uA_ 7 c2krfB_ 8 d1fsea_ 9 c1h0mD_ 10 c2jpcA_ 11 d1a04a1 12 c3cloC_ 13 c2q0oA_ 14 c1zljE_ 15 c2rnjA_ 16 d1l3la1 17 c3sztB_ 18 c2gm4B_ 19 d1d5ya1 20 d1vz0a1 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

Detailed template information

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

1 d1a9xa1 92.8 14 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 2 c2x48B_ 86.3 16 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 3 d1p4wa_ 80.8 13 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) 4 d1trra_ 76.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 5 d1yioa1 76.1 13 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) 6 c1x3uA_ 76.0 13 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 7 c2krfB_ 74.2 10 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 8 d1fsea_ 73.5 13 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 c1h0mD_ 72.7 13 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 10 c2jpcA_ 72.5 15 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 11 d1a04a1 71.5 10 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_ 70.0 15 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 c2q0oA_ 68.2 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 14 c1zljE_ 67.2 21 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 15 c2rnjA_ 65.2 10 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 16 d1l3la1 65.1 13 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) 17 c3sztB_ 63.4 8 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 18 c2gm4B_ 63.3 15 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 19 d1d5ya1 62.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 20 d1vz0a1 60.2 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 21 d1s6la1 not modelled 59.0 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 22 c2avuF_ not modelled 55.9 20 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 23 d2avue1 not modelled 55.7 20 Fold:FlhC-like Superfamily:FlhC-like Family:FlhC-like 24 d1jhga_ not modelled 55.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 25 c1r71B_ not modelled 52.8 18 PDB header:transcription/dna Chain: B: PDB Molecule:transcriptional repressor protein korb; PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna 26 c3c3wB_ not modelled 52.0 21 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 27 d1r71a_ not modelled 51.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 28 d1bl0a1 not modelled 50.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 29 c3qp5C_ not modelled 50.5 10 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 30 c1m6vE_ not modelled 49.5 13 PDB header:ligase Chain: E: PDB Molecule:carbamoyl phosphate synthetase large chain; PDBTitle: crystal structure of the g359f (small subunit) point mutant of2 carbamoyl phosphate synthetase 31 c1u78A_ not modelled 42.9 9 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 32 d2p7vb1 not modelled 41.8 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 33 c1rnlA_ not modelled 41.5 10 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 34 c3fymA_ not modelled 39.7 17 PDB header:dna binding protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus 35 c3d6zA_ not modelled 35.6 22 PDB header:transcription regulator/dna Chain: A: PDB Molecule:multidrug-efflux transporter 1 regulator; PDBTitle: crystal structure of r275e mutant of bmrr bound to dna and rhodamine 36 d1q1ha_ not modelled 35.3 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcription factor E/IIe-alpha, N-terminal domain 37 c1q1hA_ not modelled 35.3 24 PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha 38 d2phcb1 not modelled 34.9 29 Fold:Cyclophilin-like Superfamily:Cyclophilin-like Family:PH0987 C-terminal domain-like 39 c3t76A_ not modelled 34.3 16 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 40 d1ku3a_ not modelled 32.4 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 41 d2cyya1 not modelled 31.9 32 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 42 c3klnC_ not modelled 31.7 15 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 43 c2r0qF_ not modelled 31.2 10 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 44 d1ttya_ not modelled 31.2 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 45 d1ku7a_ not modelled 29.4 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 46 c3t72o_ not modelled 29.0 10 PDB header:transcription/dna Chain: O: PDB Molecule:pho box dna (strand 1); PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex 47 d1smyf2 not modelled 28.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 48 d1ic8a2 not modelled 28.9 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 49 c3mzyA_ not modelled 28.7 10 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 50 c3trbA_ not modelled 28.1 17 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 51 c2z99A_ not modelled 27.8 15 PDB header:cell cycle Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of scpb from mycobacterium tuberculosis 52 c2o8xA_ not modelled 27.0 12 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 53 d1fxza2 not modelled 26.6 24 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 54 d2cg4a1 not modelled 26.3 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 55 d2et1a1 not modelled 26.1 13 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 56 c2zp2B_ not modelled 25.8 38 PDB header:transferase inhibitor Chain: B: PDB Molecule:kinase a inhibitor; PDBTitle: c-terminal domain of kipi from bacillus subtilis 57 c2k9lA_ not modelled 25.1 24 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 58 c2do6A_ not modelled 24.9 17 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of rsgi ruh-065, a uba domain from human2 cdna 59 d2iv2x2 not modelled 24.8 29 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 60 c2cg4B_ not modelled 24.7 21 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 61 c2jnhA_ not modelled 23.5 16 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of the uba domain from cbl-b 62 c2d9sA_ not modelled 23.5 20 PDB header:ligase Chain: A: PDB Molecule:cbl e3 ubiquitin protein ligase; PDBTitle: solution structure of rsgi ruh-049, a uba domain from mouse2 cdna 63 d2cfxa1 not modelled 22.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 64 c2e1cA_ not modelled 22.9 32 PDB header:transcription/dna Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519; PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex 65 c3itcA_ not modelled 22.6 16 PDB header:hydrolase Chain: A: PDB Molecule:renal dipeptidase; PDBTitle: crystal structure of sco3058 with bound citrate and glycerol 66 c2ragB_ not modelled 22.2 21 PDB header:hydrolase Chain: B: PDB Molecule:dipeptidase; PDBTitle: crystal structure of aminohydrolase from caulobacter crescentus 67 d1s7oa_ not modelled 22.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 68 c2ejxA_ not modelled 22.1 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:st0812; PDBTitle: crystal structure of the hypothetical protein st0812 from2 sulfolobus tokodaii 69 c3korD_ not modelled 22.1 15 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 70 c2vbzA_ not modelled 22.0 24 PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan 71 d1rp3a1 not modelled 21.9 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 72 d1z6ra1 not modelled 21.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 73 c2v79B_ not modelled 21.7 15 PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis 74 c2l4aA_ not modelled 21.6 24 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 75 c3b7hA_ not modelled 21.6 16 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 76 d2jioa2 not modelled 20.5 21 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 77 c1h0hA_ not modelled 20.5 19 PDB header:dehydrogenase Chain: A: PDB Molecule:formate dehydrogenase (large subunit); PDBTitle: tungsten containing formate dehydrogenase from2 desulfovibrio gigas 78 c1vz0B_ not modelled 20.3 21 PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus 79 c2phcB_ not modelled 20.2 29 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein ph0987; PDBTitle: crystal structure of conserved uncharacterized protein ph0987 from2 pyrococcus horikoshii 80 c3c1dA_ not modelled 20.0 15 PDB header:recombination, dna binding protein Chain: A: PDB Molecule:regulatory protein recx; PDBTitle: x-ray crystal structure of recx 81 d1l0oc_ not modelled 19.9 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 82 c1l0oC_ not modelled 19.9 15 PDB header:protein binding Chain: C: PDB Molecule:sigma factor; PDBTitle: crystal structure of the bacillus stearothermophilus anti-2 sigma factor spoiiab with the sporulation sigma factor3 sigmaf 83 c2ivfA_ not modelled 19.9 15 PDB header:oxidoreductase Chain: A: PDB Molecule:ethylbenzene dehydrogenase alpha-subunit; PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum 84 d1y9qa1 not modelled 19.5 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 85 d1dpua_ not modelled 19.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 86 c1dpuA_ not modelled 19.5 10 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 87 c2iv2X_ not modelled 19.2 30 PDB header:oxidoreductase Chain: X: PDB Molecule:formate dehydrogenase h; PDBTitle: reinterpretation of reduced form of formate dehydrogenase h2 from e. coli 88 d1xsva_ not modelled 19.2 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 89 d1h0ha2 not modelled 19.2 19 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 90 c2jvlA_ not modelled 18.8 13 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 91 c2vn2B_ not modelled 18.8 15 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 92 c3hugA_ not modelled 18.6 9 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 93 c2cfxD_ not modelled 18.3 14 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 94 c2w7nA_ not modelled 18.1 16 PDB header:transcription/dna Chain: A: PDB Molecule:trfb transcriptional repressor protein; PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation 95 c2dbbA_ not modelled 17.8 11 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 96 d1r69a_ not modelled 17.4 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 97 d2ga1a1 not modelled 17.4 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like 98 c2kw0A_ not modelled 17.2 15 PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli 99 d2a6ca1 not modelled 16.9 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354

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