Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	Q	M	L	T	L	E	E	W	A	A	E	K	Y	R	S	N	P	P	S	V	S	T	L	R	R	Y	A	K	Q	N	L	F	C	P	P	A	M	K	Q	G	R	L	W	R	V	R	E	D	A	E	L	V	G	E	L	V	T	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?						?	?	?	?	?	?	?																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.
Sequence		V	I	K	K	N	D	S	L	L	L	Q	R	I	L	S	N	G	S	Q	T	A
Secondary structure
SS confidence
Disorder					?	?										?	?	?	?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1pm6 chain A Region: 4 - 81 Aligned: 71 Modelled: 78 Confidence: 100.0% Identity: 38% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 1rh6 chain A Region: 4 - 60 Aligned: 54 Modelled: 55 Confidence: 99.9% Identity: 39% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 1z4h chain A Region: 3 - 46 Aligned: 39 Modelled: 44 Confidence: 90.8% Identity: 15% PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:tor inhibition protein; PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase Phyre2 PDB 1r8e chain A domain 1 Region: 3 - 54 Aligned: 48 Modelled: 52 Confidence: 88.6% Identity: 21% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: DNA-binding N-terminal domain of transcription activators Phyre2 PDB 2zhh chain A Region: 4 - 50 Aligned: 43 Modelled: 47 Confidence: 86.2% Identity: 23% PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr Phyre2 PDB 3hh0 chain C Region: 2 - 46 Aligned: 40 Modelled: 41 Confidence: 83.9% Identity: 30% PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus Phyre2 PDB 3d6z chain A Region: 3 - 46 Aligned: 40 Modelled: 40 Confidence: 81.9% Identity: 25% 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 Phyre2 PDB 1q06 chain A Region: 5 - 51 Aligned: 43 Modelled: 47 Confidence: 70.1% Identity: 14% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: DNA-binding N-terminal domain of transcription activators Phyre2 PDB 3gpv chain A Region: 4 - 46 Aligned: 39 Modelled: 43 Confidence: 68.2% Identity: 26% PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis Phyre2 PDB 1y6u chain A Region: 4 - 51 Aligned: 44 Modelled: 48 Confidence: 68.0% Identity: 25% PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases Phyre2 PDB 3qao chain A Region: 2 - 47 Aligned: 41 Modelled: 46 Confidence: 67.5% Identity: 27% PDB header:transcription regulator Chain: A: PDB Molecule:merr-like transcriptional regulator; PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e Phyre2 PDB 2vz4 chain A Region: 5 - 50 Aligned: 42 Modelled: 46 Confidence: 65.0% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna Phyre2 PDB 1r8d chain A Region: 2 - 50 Aligned: 44 Modelled: 45 Confidence: 61.6% Identity: 18% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: DNA-binding N-terminal domain of transcription activators Phyre2 PDB 2jml chain A Region: 3 - 47 Aligned: 41 Modelled: 45 Confidence: 56.9% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor Phyre2 PDB 3gp4 chain B Region: 5 - 51 Aligned: 43 Modelled: 47 Confidence: 50.0% Identity: 19% PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes Phyre2 PDB 2kfs chain A Region: 4 - 47 Aligned: 38 Modelled: 40 Confidence: 41.0% Identity: 13% PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c Phyre2 PDB 1j9i chain A Region: 21 - 53 Aligned: 33 Modelled: 33 Confidence: 35.1% Identity: 15% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Terminase gpNU1 subunit domain Phyre2 PDB 2ezh chain A Region: 7 - 31 Aligned: 24 Modelled: 25 Confidence: 26.0% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 1b4a chain A Region: 7 - 77 Aligned: 59 Modelled: 71 Confidence: 25.3% Identity: 22% PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus Phyre2 PDB 2ezi chain A Region: 7 - 31 Aligned: 24 Modelled: 25 Confidence: 24.1% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 1 d1pm6a_ 2 d1rh6a_ 3 c1z4hA_ 4 d1r8ea1 5 c2zhhA_ 6 c3hh0C_ 7 c3d6zA_ 8 d1q06a_ 9 c3gpvA_ 10 c1y6uA_ 11 c3qaoA_ 12 c2vz4A_ 13 d1r8da_ 14 c2jmlA_ 15 c3gp4B_ 16 c2kfsA_ 17 d1j9ia_ 18 d2ezha_ 19 c1b4aA_ 20 d2ezia_ 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

Detailed template information

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

1 d1pm6a_ 100.0 38 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 2 d1rh6a_ 99.9 39 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 3 c1z4hA_ 90.8 15 PDB header:protein binding, dna binding protein Chain: A: PDB Molecule:tor inhibition protein; PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase 4 d1r8ea1 88.6 21 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 5 c2zhhA_ 86.2 23 PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr 6 c3hh0C_ 83.9 30 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal strucure of a transcriptional regulator, merr family2 from bacillus cereus 7 c3d6zA_ 81.9 25 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 8 d1q06a_ 70.1 14 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 9 c3gpvA_ 68.2 26 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis 10 c1y6uA_ 68.0 25 PDB header:dna binding protein Chain: A: PDB Molecule:excisionase from transposon tn916; PDBTitle: the structure of the excisionase (xis) protein from2 conjugative transposon tn916 provides insights into the3 regulation of heterobivalent tyrosine recombinases 11 c3qaoA_ 67.5 27 PDB header:transcription regulator Chain: A: PDB Molecule:merr-like transcriptional regulator; PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e 12 c2vz4A_ 65.0 19 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna 13 d1r8da_ 61.6 18 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 14 c2jmlA_ 56.9 24 PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor 15 c3gp4B_ 50.0 19 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes 16 c2kfsA_ 41.0 13 PDB header:dna-binding protein Chain: A: PDB Molecule:conserved hypothetical regulatory protein; PDBTitle: nmr structure of rv2175c 17 d1j9ia_ 35.1 15 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Terminase gpNU1 subunit domain 18 d2ezha_ 26.0 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 19 c1b4aA_ 25.3 22 PDB header:repressor Chain: A: PDB Molecule:arginine repressor; PDBTitle: structure of the arginine repressor from bacillus stearothermophilus 20 d2ezia_ 24.1 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 21 d1aoya_ not modelled 23.5 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 22 c3hosA_ not modelled 11.6 25 PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg 23 c3v4gA_ not modelled 10.2 9 PDB header:dna binding protein Chain: A: PDB Molecule:arginine repressor; PDBTitle: 1.60 angstrom resolution crystal structure of an arginine repressor2 from vibrio vulnificus cmcp6 24 d1pqwa_ not modelled 9.9 3 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Alcohol dehydrogenase-like, C-terminal domain 25 d1tvxb_ not modelled 9.9 38 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 26 c3l4hA_ not modelled 9.8 16 PDB header:protein binding Chain: A: PDB Molecule:e3 ubiquitin-protein ligase hecw1; PDBTitle: helical box domain and second ww domain of the human e3 ubiquitin-2 protein ligase hecw1 27 c1t6zB_ not modelled 9.7 18 PDB header:transferase Chain: B: PDB Molecule:riboflavin kinase/fmn adenylyltransferase; PDBTitle: crystal structure of riboflavin bound tm379 28 d1juqa_ not modelled 8.8 10 Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:VHS domain 29 d1r6ra_ not modelled 8.5 22 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 30 c1r6rA_ not modelled 8.5 22 PDB header:viral protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold 31 c2dn4A_ not modelled 7.9 19 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i; PDBTitle: solution structure of rsgi ruh-060, a gtf2i domain in human2 cdna 32 c3hefB_ not modelled 7.8 31 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 33 c3eusB_ not modelled 7.8 9 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi 34 d1sfka_ not modelled 7.7 22 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 35 c2d99A_ not modelled 7.7 19 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-048, a gtf2i domain in human2 cdna 36 d1b4aa1 not modelled 7.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 37 d1q60a_ not modelled 7.4 22 Fold:GTF2I-like repeat Superfamily:GTF2I-like repeat Family:GTF2I-like repeat 38 c2ed2A_ not modelled 7.1 16 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i; PDBTitle: solution structure of rsgi ruh-069, a gtf2i domain in human2 cdna 39 d1tvxa_ not modelled 7.0 38 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 40 c2dn5A_ not modelled 7.0 25 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-057, a gtf2i domain in human2 cdna 41 c2dg6A_ not modelled 7.0 22 PDB header:gene regulation Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2) 42 d1te7a_ not modelled 6.9 4 Fold:PUA domain-like Superfamily:PUA domain-like Family:yqfB-like 43 c2dzqA_ not modelled 6.8 16 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i repeat domain- PDBTitle: solution structure of rsgi ruh-066, a gtf2i domain in human2 cdna 44 c2e3lA_ not modelled 6.7 31 PDB header:transcription Chain: A: PDB Molecule:transcription factor gtf2ird2 beta; PDBTitle: solution structure of rsgi ruh-068, a gtf2i domain in human2 cdna 45 c1iufA_ not modelled 6.6 25 PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein 46 d1f9na1 not modelled 6.4 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Arginine repressor (ArgR), N-terminal DNA-binding domain 47 d1f9pa_ not modelled 6.3 38 Fold:IL8-like Superfamily:Interleukin 8-like chemokines Family:Interleukin 8-like chemokines 48 c2x0kB_ not modelled 6.0 21 PDB header:transferase Chain: B: PDB Molecule:riboflavin biosynthesis protein ribf; PDBTitle: crystal structure of modular fad synthetase from2 corynebacterium ammoniagenes 49 c2ejeA_ not modelled 5.4 16 PDB header:transcription Chain: A: PDB Molecule:general transcription factor ii-i; PDBTitle: solution structure of rsgi ruh-071, a gtf2i domain in human2 cdna 50 c2djyA_ not modelled 5.4 22 PDB header:ligase/signaling protein Chain: A: PDB Molecule:smad ubiquitination regulatory factor 2; PDBTitle: solution structure of smurf2 ww3 domain-smad7 py peptide2 complex 51 c2rn7A_ not modelled 5.1 36 PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125

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