Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	E	S	T	T	S	S	P	H	D	A	V	F	K	T	F	M	F	T	P	E	T	A	R	D	F	L	E	I	H	L	P	E	P	L	R	K	L	C	N	L	Q	T	L	R	L	E	P	T	S	F	I	E	K	S	L	R	A	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																									?	?	?	?			?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	S	D	V	L	W	S	V	E	T	S	D	G	D	G	Y	I	Y	C	V	I	E	H	Q	S	S	A	E	K	N	M	A	F	R	L	M	R	Y	A	T	A	A	M	Q	R	H	Q	D	K	G	Y	D	R	V	P	L	V	V	P	L
Secondary structure
SS confidence
Disorder																																																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	F	Y	H	G	E	T	S	P	Y	P	Y	S	L	N	W	L	D	E	F	D	D	P	Q	L	A	R	Q	L	Y	T	E	A	F	L	L	V	D	I	T	I	V	P	D	D	E	I	M	Q	H	R	R	I	A	L	L	E	L	I	Q
Secondary structure
SS confidence
Disorder								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		K	H	I	R	D	R	D	L	I	G	M	V	D	R	I	T	T	L	L	V	R	G	F	T	N	D	S	Q	L	Q	T	L	F	N	Y	L	L	Q	C	G	D	T	S	R	F	T	R	F	I	E	E	I	A	E	R	S	P	L	Q	K
Secondary structure
SS confidence
Disorder																																								?	?		?	?												?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.
Sequence		E	R	L	M	T	I	A	E	R	L	R	Q	E	G	H	Q	I	G	W	Q	E	G	M	H	E	Q	A	I	K	I	A	L	R	M	L	E	Q	G	F	E	R	E	I	V	L	A	T	T	Q	L	T	D	A	D	I	P	N	C	H
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: 268 - 298 Aligned: 31 Modelled: 31 Confidence: 84.8% Identity: 13% 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: 267 - 295 Aligned: 29 Modelled: 29 Confidence: 82.3% Identity: 7% PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 Phyre2 PDB 2gm4 chain B Region: 227 - 298 Aligned: 72 Modelled: 72 Confidence: 67.0% Identity: 13% 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 1s6l chain A domain 1 Region: 271 - 298 Aligned: 28 Modelled: 28 Confidence: 65.7% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 1p4w chain A Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 64.5% Identity: 16% 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 1vol chain A domain 2 Region: 219 - 299 Aligned: 81 Modelled: 81 Confidence: 60.9% Identity: 12% Fold: Cyclin-like Superfamily: Cyclin-like Family: Transcription factor IIB (TFIIB), core domain Phyre2 PDB 2jpc chain A Region: 267 - 297 Aligned: 31 Modelled: 31 Confidence: 60.7% Identity: 6% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1x3u chain A Region: 267 - 297 Aligned: 31 Modelled: 31 Confidence: 60.1% Identity: 6% 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 1a04 chain A domain 1 Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 55.7% 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 1yio chain A domain 1 Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 54.3% Identity: 6% 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 2phc chain B Region: 278 - 299 Aligned: 22 Modelled: 22 Confidence: 53.1% Identity: 27% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein ph0987; PDBTitle: crystal structure of conserved uncharacterized protein ph0987 from2 pyrococcus horikoshii Phyre2 PDB 2krf chain B Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 53.0% Identity: 19% 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 1zlj chain E Region: 267 - 297 Aligned: 31 Modelled: 31 Confidence: 52.6% 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 1vz0 chain A domain 1 Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 52.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 1fse chain A Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 52.4% Identity: 9% 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: 267 - 297 Aligned: 31 Modelled: 31 Confidence: 52.0% 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 3mml chain D Region: 278 - 299 Aligned: 22 Modelled: 22 Confidence: 47.0% Identity: 27% PDB header:hydrolase Chain: D: PDB Molecule:allophanate hydrolase subunit 1; PDBTitle: allophanate hydrolase complex from mycobacterium smegmatis, msmeg0435-2 msmeg0436 Phyre2 PDB 1h0m chain D Region: 266 - 297 Aligned: 32 Modelled: 32 Confidence: 46.1% 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 1r71 chain B Region: 266 - 298 Aligned: 33 Modelled: 33 Confidence: 43.1% Identity: 15% 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 Phyre2 PDB 1l3l chain A domain 1 Region: 267 - 297 Aligned: 31 Modelled: 31 Confidence: 42.3% 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 1 d1a9xa1 2 c2x48B_ 3 c2gm4B_ 4 d1s6la1 5 d1p4wa_ 6 d1vola2 7 c2jpcA_ 8 c1x3uA_ 9 d1a04a1 10 d1yioa1 11 c2phcB_ 12 c2krfB_ 13 c1zljE_ 14 d1vz0a1 15 d1fsea_ 16 c2rnjA_ 17 c3mmlD_ 18 c1h0mD_ 19 c1r71B_ 20 d1l3la1 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 84.8 13 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_ 82.3 7 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 3 c2gm4B_ 67.0 13 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 4 d1s6la1 65.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 5 d1p4wa_ 64.5 16 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 d1vola2 60.9 12 Fold:Cyclin-like Superfamily:Cyclin-like Family:Transcription factor IIB (TFIIB), core domain 7 c2jpcA_ 60.7 6 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 8 c1x3uA_ 60.1 6 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 9 d1a04a1 55.7 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) 10 d1yioa1 54.3 6 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 c2phcB_ 53.1 27 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein ph0987; PDBTitle: crystal structure of conserved uncharacterized protein ph0987 from2 pyrococcus horikoshii 12 c2krfB_ 53.0 19 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 13 c1zljE_ 52.6 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 14 d1vz0a1 52.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 15 d1fsea_ 52.4 9 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) 16 c2rnjA_ 52.0 10 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 17 c3mmlD_ 47.0 27 PDB header:hydrolase Chain: D: PDB Molecule:allophanate hydrolase subunit 1; PDBTitle: allophanate hydrolase complex from mycobacterium smegmatis, msmeg0435-2 msmeg0436 18 c1h0mD_ 46.1 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 19 c1r71B_ 43.1 15 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 20 d1l3la1 42.3 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) 21 c3oepA_ not modelled 41.2 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein ttha0988; PDBTitle: crystal structure of ttha0988 in space group p43212 22 c3cloC_ not modelled 40.0 19 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 23 c1u78A_ not modelled 39.3 6 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 24 d1r71a_ not modelled 38.5 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 25 c2q0oA_ not modelled 37.4 10 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 26 d1aisb2 not modelled 35.8 15 Fold:Cyclin-like Superfamily:Cyclin-like Family:Transcription factor IIB (TFIIB), core domain 27 c3mzyA_ not modelled 34.5 19 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 28 d2p7vb1 not modelled 33.6 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 29 d1trra_ not modelled 33.1 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 30 d1q08a_ not modelled 32.9 20 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 31 c3sztB_ not modelled 32.6 6 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 32 c3trbA_ not modelled 32.6 3 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 33 c1m6vE_ not modelled 32.4 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 34 c3qp5C_ not modelled 32.3 6 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 35 c2k9lA_ not modelled 31.8 5 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 36 d1ijwc_ not modelled 31.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 37 d1rp3a1 not modelled 31.3 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 38 c3fymA_ not modelled 31.3 8 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 39 d1ku2a1 not modelled 30.9 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 40 d1jhga_ not modelled 30.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 41 c3t72o_ not modelled 30.4 11 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 42 d1hcra_ not modelled 30.4 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 43 d1z6ra1 not modelled 29.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 44 d1bl0a2 not modelled 29.4 4 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 45 d2a6ca1 not modelled 28.0 8 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 46 c2o8xA_ not modelled 27.5 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 47 c3t76A_ not modelled 27.5 3 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 48 d2et1a1 not modelled 27.4 0 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 49 c3korD_ not modelled 27.3 16 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 50 c3c3wB_ not modelled 26.8 16 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 51 d1d5ya1 not modelled 26.1 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 52 c2jvlA_ not modelled 24.8 16 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 53 d1smyf2 not modelled 24.3 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 54 d1fxza2 not modelled 24.0 14 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 55 c1vz0B_ not modelled 23.2 19 PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus 56 d1ic8a2 not modelled 23.2 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 57 d1ku7a_ not modelled 23.1 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 58 d1or7a1 not modelled 22.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 59 c1aisB_ not modelled 22.0 18 PDB header:transcription/dna Chain: B: PDB Molecule:protein (transcription initiation factor iib); PDBTitle: tata-binding protein/transcription factor (ii)b/tata-box2 complex from pyrococcus woesei 60 d2iv2x2 not modelled 21.7 23 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 61 d1vola1 not modelled 21.6 11 Fold:Cyclin-like Superfamily:Cyclin-like Family:Transcription factor IIB (TFIIB), core domain 62 d1r8ea1 not modelled 21.1 9 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 63 d1s7oa_ not modelled 20.9 0 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 64 d1ku3a_ not modelled 20.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 65 d5crxb2 not modelled 20.6 13 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 66 d2ga1a1 not modelled 20.4 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like 67 d1xsva_ not modelled 20.3 3 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 68 c3b7hA_ not modelled 20.1 9 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 69 c1c9bI_ not modelled 19.8 13 PDB header:transcription/dna Chain: I: PDB Molecule:general transcription factor iib; PDBTitle: crystal structure of a human tbp core domain-human tfiib2 core domain complex bound to an extended, modified3 adenoviral major late promoter (admlp) 70 d1od5a1 not modelled 19.7 9 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 71 d1fxza1 not modelled 19.5 18 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 72 d1y9qa1 not modelled 19.4 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 73 c1l0oC_ not modelled 18.8 6 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 74 d1l0oc_ not modelled 18.8 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 75 d1ufma_ not modelled 18.6 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif) 76 c2wusR_ not modelled 18.4 6 PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz 77 d1ttya_ not modelled 18.1 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 78 d2cg4a1 not modelled 18.0 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 79 d1dpua_ not modelled 17.9 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 80 c1dpuA_ not modelled 17.9 9 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) 81 d1k61a_ not modelled 17.8 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 82 d1f44a2 not modelled 17.6 15 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 83 d2r5yb1 not modelled 17.5 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 84 d1x2na1 not modelled 17.4 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 85 d1b0na2 not modelled 17.4 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 86 d2cyya1 not modelled 17.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 87 d3bula1 not modelled 17.2 11 Fold:Methionine synthase domain-like Superfamily:Methionine synthase domain Family:Methionine synthase domain 88 c2kpjA_ not modelled 17.1 0 PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a 89 d1uija1 not modelled 16.9 23 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 90 d1uika2 not modelled 16.6 14 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 91 c2q1zA_ not modelled 16.5 18 PDB header:transcription Chain: A: PDB Molecule:rpoe, ecf sige; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 92 d1h0ha2 not modelled 16.3 9 Fold:Formate dehydrogenase/DMSO reductase, domains 1-3 Superfamily:Formate dehydrogenase/DMSO reductase, domains 1-3 Family:Formate dehydrogenase/DMSO reductase, domains 1-3 93 c1rnlA_ not modelled 16.1 13 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 94 c2elhA_ not modelled 16.1 11 PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa 95 d1bl0a1 not modelled 16.0 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 96 d1od5a2 not modelled 15.9 10 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 97 d1g8ma1 not modelled 15.7 17 Fold:Methylglyoxal synthase-like Superfamily:Methylglyoxal synthase-like Family:Inosicase 98 d1q1ha_ not modelled 15.7 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcription factor E/IIe-alpha, N-terminal domain 99 c1q1hA_ not modelled 15.7 16 PDB header:transcription Chain: A: PDB Molecule:transcription factor e; PDBTitle: an extended winged helix domain in general transcription2 factor e/iie alpha

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