Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	E	H	H	Q	P	F	E	E	I	K	L	I	N	A	N	G	A	E	Q	W	S	A	R	Q	L	G	K	L	L	G	Y	S	E	Y	R	H	F	I	P	V	L	T	R	A	K	E	A	C	E	N	S	G	H	T	I	D	D	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?	?		?		?																																						?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	E	E	I	L	D	M	V	K	I	G	S	N	A	K	R	A	L	K	D	I	V	L	S	R	Y	A	C	Y	L	V	V	Q	N	G	D	P	A	K	P	V	I	A	A	G	Q	T	Y	F	A	I	Q	T	R	R	Q	E	L	A	D
Secondary structure
SS confidence
Disorder								?	?	?	?	?	?	?	?	?	?		?																				?	?														?	?					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	E	A	F	K	Q	L	R	E	D	E	K	R	L	F	L	R	N	E	L	K	E	H	N	K	Q	L	V	E	A	A	Q	Q	A	G	V	A	T	A	T	D	F	A	I	F	Q	N	H	G	Y	Q	G	L	Y	G	G	L	D	Q	K
Secondary structure
SS confidence
Disorder			?	?			?	?	?	?																									?		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	I	H	Q	R	K	G	L	K	K	N	Q	K	I	L	D	H	M	G	S	T	E	L	A	A	N	L	F	R	A	T	Q	T	E	E	K	L	K	R	D	G	V	N	S	K	Q	Q	A	N	T	T	H	F	D	V	G	R	K	V	R
Secondary structure
SS confidence
Disorder									?	?																															?	?	?	?	?	?	?	?	?	?	?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.
Sequence		Q	T	I	Q	E	L	G	G	T	M	P	E	E	L	P	T	P	Q	V	S	I	K	Q	L	E	N	S	V	K	I	T	E	K	K
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 2pmz chain N Region: 50 - 88 Aligned: 39 Modelled: 39 Confidence: 33.6% Identity: 31% PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 1ef4 chain A Region: 50 - 88 Aligned: 39 Modelled: 39 Confidence: 26.8% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: RNA polymerase subunit RPB10 Family: RNA polymerase subunit RPB10 Phyre2 PDB 3f6w chain E Region: 22 - 69 Aligned: 48 Modelled: 48 Confidence: 26.3% Identity: 13% PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000 Phyre2 PDB 2qkw chain A domain 1 Region: 219 - 268 Aligned: 48 Modelled: 50 Confidence: 21.4% Identity: 17% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Avirulence protein AvrPto Family: Avirulence protein AvrPto Phyre2 PDB 2qkw chain A Region: 219 - 268 Aligned: 48 Modelled: 50 Confidence: 21.4% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:avirulence protein; PDBTitle: structural basis for activation of plant immunity by2 bacterial effector protein avrpto Phyre2 PDB 1qi9 chain A Region: 76 - 98 Aligned: 22 Modelled: 23 Confidence: 17.1% Identity: 23% Fold: Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily: Acid phosphatase/Vanadium-dependent haloperoxidase Family: Haloperoxidase (bromoperoxidase) Phyre2 PDB 1gw5 chain B Region: 26 - 103 Aligned: 68 Modelled: 78 Confidence: 17.1% Identity: 16% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: Clathrin adaptor core protein Phyre2 PDB 2zop chain A Region: 112 - 213 Aligned: 93 Modelled: 102 Confidence: 15.8% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein tthb164; PDBTitle: x-ray crystal structure of a crispr-associated cmr5 family2 protein from thermus thermophilus hb8 Phyre2 PDB 1twf chain J Region: 50 - 88 Aligned: 39 Modelled: 39 Confidence: 15.7% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: RNA polymerase subunit RPB10 Family: RNA polymerase subunit RPB10 Phyre2 PDB 2bos chain A Region: 17 - 31 Aligned: 15 Modelled: 15 Confidence: 13.5% Identity: 47% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Bacterial AB5 toxins, B-subunits Phyre2 PDB 1m5i chain A Region: 236 - 272 Aligned: 37 Modelled: 37 Confidence: 13.4% Identity: 24% PDB header:antitumor protein Chain: A: PDB Molecule:apc protein; PDBTitle: crystal structure of the coiled coil region 129-250 of the2 tumor suppressor gene product apc Phyre2 PDB 3ol4 chain B Region: 185 - 271 Aligned: 78 Modelled: 87 Confidence: 13.1% Identity: 21% PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c Phyre2 PDB 3omt chain A Region: 22 - 64 Aligned: 43 Modelled: 43 Confidence: 13.0% Identity: 14% 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. Phyre2 PDB 1qhb chain A Region: 76 - 95 Aligned: 19 Modelled: 20 Confidence: 12.7% Identity: 21% Fold: Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily: Acid phosphatase/Vanadium-dependent haloperoxidase Family: Haloperoxidase (bromoperoxidase) Phyre2 PDB 3k2h chain A Region: 10 - 39 Aligned: 29 Modelled: 30 Confidence: 11.9% Identity: 28% PDB header:transferase Chain: A: PDB Molecule:dihydrofolate reductase/thymidylate synthase; PDBTitle: co-crystal structure of dihydrofolate reductase/thymidylate synthase2 from babesia bovis with dump, pemetrexed and nadp Phyre2 PDB 1utx chain A Region: 22 - 61 Aligned: 40 Modelled: 40 Confidence: 11.7% Identity: 23% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 1up8 chain A Region: 76 - 97 Aligned: 21 Modelled: 22 Confidence: 11.7% Identity: 19% Fold: Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily: Acid phosphatase/Vanadium-dependent haloperoxidase Family: Haloperoxidase (bromoperoxidase) Phyre2 PDB 3fm8 chain A Region: 88 - 97 Aligned: 10 Modelled: 10 Confidence: 11.2% Identity: 60% PDB header:transport protein/hydrolase activator Chain: A: PDB Molecule:kinesin-like protein kif13b; PDBTitle: crystal structure of full length centaurin alpha-1 bound with the fha2 domain of kif13b (capri target) Phyre2 PDB 3jsu chain A Region: 10 - 39 Aligned: 29 Modelled: 30 Confidence: 11.0% Identity: 28% PDB header:oxidoreductase, transferase Chain: A: PDB Molecule:dihydrofolate reductase-thymidylate synthase; PDBTitle: quadruple mutant(n51i+c59r+s108n+i164l) plasmodium falciparum2 dihydrofolate reductase-thymidylate synthase(pfdhfr-ts) complexed3 with qn254, nadph, and dump Phyre2 PDB 2dun chain A Region: 47 - 88 Aligned: 37 Modelled: 42 Confidence: 10.7% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:dna polymerase mu; PDBTitle: solution structure of brct domain of dna polymerase mu Phyre2 1 c2pmzN_ 2 d1ef4a_ 3 c3f6wE_ 4 d2qkwa1 5 c2qkwA_ 6 d1qi9a_ 7 d1gw5b_ 8 c2zopA_ 9 d1twfj_ 10 d2bosa_ 11 c1m5iA_ 12 c3ol4B_ 13 c3omtA_ 14 d1qhba_ 15 c3k2hA_ 16 d1utxa_ 17 d1up8a_ 18 c3fm8A_ 19 c3jsuA_ 20 c2dunA_ 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

Detailed template information

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

1 c2pmzN_ 33.6 31 PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 2 d1ef4a_ 26.8 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10 3 c3f6wE_ 26.3 13 PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000 4 d2qkwa1 21.4 17 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Avirulence protein AvrPto Family:Avirulence protein AvrPto 5 c2qkwA_ 21.4 17 PDB header:transferase Chain: A: PDB Molecule:avirulence protein; PDBTitle: structural basis for activation of plant immunity by2 bacterial effector protein avrpto 6 d1qi9a_ 17.1 23 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 7 d1gw5b_ 17.1 16 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:Clathrin adaptor core protein 8 c2zopA_ 15.8 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative uncharacterized protein tthb164; PDBTitle: x-ray crystal structure of a crispr-associated cmr5 family2 protein from thermus thermophilus hb8 9 d1twfj_ 15.7 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10 10 d2bosa_ 13.5 47 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits 11 c1m5iA_ 13.4 24 PDB header:antitumor protein Chain: A: PDB Molecule:apc protein; PDBTitle: crystal structure of the coiled coil region 129-250 of the2 tumor suppressor gene product apc 12 c3ol4B_ 13.1 21 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c 13 c3omtA_ 13.0 14 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. 14 d1qhba_ 12.7 21 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 15 c3k2hA_ 11.9 28 PDB header:transferase Chain: A: PDB Molecule:dihydrofolate reductase/thymidylate synthase; PDBTitle: co-crystal structure of dihydrofolate reductase/thymidylate synthase2 from babesia bovis with dump, pemetrexed and nadp 16 d1utxa_ 11.7 23 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 17 d1up8a_ 11.7 19 Fold:Acid phosphatase/Vanadium-dependent haloperoxidase Superfamily:Acid phosphatase/Vanadium-dependent haloperoxidase Family:Haloperoxidase (bromoperoxidase) 18 c3fm8A_ 11.2 60 PDB header:transport protein/hydrolase activator Chain: A: PDB Molecule:kinesin-like protein kif13b; PDBTitle: crystal structure of full length centaurin alpha-1 bound with the fha2 domain of kif13b (capri target) 19 c3jsuA_ 11.0 28 PDB header:oxidoreductase, transferase Chain: A: PDB Molecule:dihydrofolate reductase-thymidylate synthase; PDBTitle: quadruple mutant(n51i+c59r+s108n+i164l) plasmodium falciparum2 dihydrofolate reductase-thymidylate synthase(pfdhfr-ts) complexed3 with qn254, nadph, and dump 20 c2dunA_ 10.7 16 PDB header:transferase Chain: A: PDB Molecule:dna polymerase mu; PDBTitle: solution structure of brct domain of dna polymerase mu 21 d2coba1 not modelled 10.0 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 22 d1biaa1 not modelled 9.7 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 23 c2of3A_ not modelled 9.4 10 PDB header:structural protein, cell cycle Chain: A: PDB Molecule:zyg-9; PDBTitle: tog domain structure from c.elegans zyg9 24 d1r4pb_ not modelled 9.2 47 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits 25 c1yn3A_ not modelled 9.1 19 PDB header:toxin, protein binding Chain: A: PDB Molecule:truncated cell surface protein map-w; PDBTitle: crystal structures of eap domains from staphylococcus2 aureus reveal an unexpected homology to bacterial3 superantigens 26 c2kygC_ not modelled 9.0 19 PDB header:protein binding Chain: C: PDB Molecule:protein cbfa2t1; PDBTitle: structure of the aml1-eto nervy domain - pka(riia) complex and its2 contribution to aml1-eto activity 27 d2dk5a1 not modelled 8.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RPO3F domain-like 28 d1mhyd_ not modelled 8.6 14 Fold:Ferritin-like Superfamily:Ferritin-like Family:Ribonucleotide reductase-like 29 d1ktba2 not modelled 8.5 12 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 30 c1yn5B_ not modelled 8.2 28 PDB header:unknown function Chain: B: PDB Molecule:eaph2; PDBTitle: crystal structures of eap domains from staphylococcus2 aureus reveal an unexpected homology to bacterial3 superantigens 31 c2jspA_ not modelled 8.2 5 PDB header:gene regulation Chain: A: PDB Molecule:transcriptional regulatory protein ros; PDBTitle: the prokaryotic cys2his2 zinc finger adopts a novel fold as2 revealed by the nmr structure of a. tumefaciens ros dna3 binding domain 32 c1yn4A_ not modelled 8.2 20 PDB header:unknown function Chain: A: PDB Molecule:eaph1; PDBTitle: crystal structures of eap domains from staphylococcus2 aureus reveal an unexpected homology to bacterial3 superantigens 33 c2yu3A_ not modelled 7.5 15 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase iii 39 kda PDBTitle: solution structure of the domain swapped wingedhelix in dna-2 directed rna polymerase iii 39 kda polypeptide 34 c3clbA_ not modelled 7.3 34 PDB header:oxidoreductase, transferase Chain: A: PDB Molecule:dhfr-ts; PDBTitle: structure of bifunctional tcdhfr-ts in complex with tmq 35 c2ewtA_ not modelled 7.1 16 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd 36 c3e7lD_ not modelled 6.6 20 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 37 c3mklB_ not modelled 6.6 14 PDB header:transcription regulator Chain: B: PDB Molecule:hth-type transcriptional regulator gadx; PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12 38 c2yujA_ not modelled 6.6 19 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 39 c2k1gA_ not modelled 6.6 13 PDB header:lipoprotein Chain: A: PDB Molecule:lipoprotein spr; PDBTitle: solution nmr structure of lipoprotein spr from escherichia coli k12.2 northeast structural genomics target er541-37-162 40 c3q9dB_ not modelled 6.3 32 PDB header:unknown function Chain: B: PDB Molecule:protein cpn_0803/cp_1068/cpj0803/cpb0832; PDBTitle: crystal structure of cpn0803 from c. pneumoniae. 41 d1c4qa_ not modelled 6.1 33 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits 42 d2ixna1 not modelled 5.7 22 Fold:PTPA-like Superfamily:PTPA-like Family:PTPA-like 43 d2huha1 not modelled 5.5 38 Fold:C2 domain-like Superfamily:Smr-associated domain-like Family:Smr-associated domain 44 d2nrac2 not modelled 5.4 35 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 45 d1tkna_ not modelled 5.4 19 Fold:STAT-like Superfamily:CAPPD, an extracellular domain of amyloid beta A4 protein Family:CAPPD, an extracellular domain of amyloid beta A4 protein 46 c2nogA_ not modelled 5.4 12 PDB header:dna binding protein Chain: A: PDB Molecule:iswi protein; PDBTitle: sant domain structure of xenopus remodeling factor iswi 47 c1ktbA_ not modelled 5.2 12 PDB header:hydrolase Chain: A: PDB Molecule:alpha-n-acetylgalactosaminidase; PDBTitle: the structure of alpha-n-acetylgalactosaminidase 48 c1w9zB_ not modelled 5.2 45 PDB header:virus coat protein Chain: B: PDB Molecule:vp9; PDBTitle: structure of bannavirus vp9 49 c2zb9A_ not modelled 5.2 15 PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of tetr family transcription regulator2 sco0332 50 c2qw6A_ not modelled 5.2 26 PDB header:hydrolase Chain: A: PDB Molecule:aaa atpase, central region; PDBTitle: crystal structure of the c-terminal domain of an aaa atpase from2 enterococcus faecium do 51 d2qw6a1 not modelled 5.2 26 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:MgsA/YrvN C-terminal domain-like 52 d1sr9a3 not modelled 5.1 13 Fold:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Superfamily:2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain Family:2-isopropylmalate synthase LeuA, allosteric (dimerisation) 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