Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	R	L	L	S	V	A	P	V	L	L	W	L	I	T	P	L	A	F	A	Q	L	P	G	I	T	S	Q	P	L	P	G	G	G	Q	S	W	S	L	P	V	Q	T	L	V	F	I	T	S	L	T	F	I	P	A	I	L	L	M
Secondary structure
SS confidence
Disorder		?	?	?												?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	T	S	F	T	R	I	I	I	V	F	G	L	L	R	N	A	L	G	T	P	S	A	P	P	N	Q	V	L	L	G	L	A	L	F	L	T	F	F	I	M	S	P	V	I	D	K	I	Y	V	D	A	Y	Q	P	F	S	E	E	K
Secondary structure
SS confidence
Disorder																	?			?	?	?	?			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	S	M	Q	E	A	L	E	K	G	A	Q	P	L	R	E	F	M	L	R	Q	T	R	E	A	D	L	G	L	F	A	R	L	A	N	T	G	P	L	Q	G	P	E	A	V	P	M	R	I	L	L	P	A	Y	V	T	S	E	L	K
Secondary structure
SS confidence
Disorder																																				?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		T	A	F	Q	I	G	F	T	I	F	I	P	F	L	I	I	D	L	V	I	A	S	V	L	M	A	L	G	M	M	M	V	P	P	A	T	I	A	L	P	F	K	L	M	L	F	V	L	V	D	G	W	Q	L	L	V	G	S	L	A
Secondary structure
SS confidence
Disorder																													?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		Q	S	F	Y	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 1rhz chain B Region: 127 - 196 Aligned: 58 Modelled: 65 Confidence: 51.6% Identity: 14% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 1r0k chain A domain 1 Region: 101 - 137 Aligned: 37 Modelled: 37 Confidence: 19.4% Identity: 16% Fold: Left-handed superhelix Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Phyre2 PDB 1q0q chain A domain 1 Region: 100 - 137 Aligned: 38 Modelled: 38 Confidence: 19.2% Identity: 8% Fold: Left-handed superhelix Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Phyre2 PDB 2y0s chain Q Region: 109 - 137 Aligned: 29 Modelled: 29 Confidence: 18.6% Identity: 17% PDB header:transferase Chain: Q: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group Phyre2 PDB 2y0s chain J Region: 109 - 137 Aligned: 29 Modelled: 29 Confidence: 18.6% Identity: 17% PDB header:transferase Chain: J: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group Phyre2 PDB 1smy chain A domain 1 Region: 116 - 145 Aligned: 30 Modelled: 30 Confidence: 14.5% Identity: 20% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 2j5p chain A domain 1 Region: 176 - 187 Aligned: 12 Modelled: 12 Confidence: 14.3% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: FtsK C-terminal domain-like Phyre2 PDB 2jcy chain A Region: 101 - 155 Aligned: 55 Modelled: 55 Confidence: 13.0% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis Phyre2 PDB 2ve8 chain A domain 1 Region: 176 - 187 Aligned: 12 Modelled: 12 Confidence: 13.0% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: FtsK C-terminal domain-like Phyre2 PDB 2kxa chain A Region: 228 - 233 Aligned: 6 Modelled: 6 Confidence: 12.9% Identity: 50% PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 Phyre2 PDB 2vay chain B Region: 131 - 141 Aligned: 11 Modelled: 11 Confidence: 12.1% Identity: 45% PDB header:metal transport Chain: B: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: calmodulin complexed with cav1.1 iq peptide Phyre2 PDB 2wb1 chain Q Region: 109 - 126 Aligned: 18 Modelled: 18 Confidence: 11.5% Identity: 28% PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 2k6l chain A Region: 128 - 154 Aligned: 27 Modelled: 27 Confidence: 10.7% Identity: 33% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors Phyre2 PDB 2wb1 chain J Region: 109 - 143 Aligned: 35 Modelled: 35 Confidence: 10.5% Identity: 20% PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 1rh5 chain B Region: 185 - 196 Aligned: 12 Modelled: 12 Confidence: 8.9% Identity: 42% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 2bo9 chain B Region: 140 - 166 Aligned: 27 Modelled: 27 Confidence: 8.2% Identity: 19% PDB header:hydrolase Chain: B: PDB Molecule:human latexin; PDBTitle: human carboxypeptidase a4 in complex with human latexin. Phyre2 PDB 2fml chain B Region: 161 - 185 Aligned: 25 Modelled: 25 Confidence: 8.1% Identity: 16% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:mutt/nudix family protein; PDBTitle: crystal structure of mutt/nudix family protein from enterococcus2 faecalis Phyre2 PDB 1ynj chain A domain 1 Region: 116 - 143 Aligned: 28 Modelled: 28 Confidence: 7.9% Identity: 18% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 3gz6 chain A Region: 162 - 185 Aligned: 24 Modelled: 24 Confidence: 7.7% Identity: 21% PDB header:dna binding protein/dna Chain: A: PDB Molecule:mutt/nudix family protein; PDBTitle: crystal structure of shewanella oneidensis nrtr complexed2 with a 27mer dna Phyre2 PDB 2wwb chain B Region: 125 - 194 Aligned: 58 Modelled: 70 Confidence: 7.5% Identity: 14% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome Phyre2 1 d1rhzb_ 2 d1r0ka1 3 d1q0qa1 4 c2y0sQ_ 5 c2y0sJ_ 6 d1smya1 7 d2j5pa1 8 c2jcyA_ 9 d2ve8a1 10 c2kxaA_ 11 c2vayB_ 12 c2wb1Q_ 13 c2k6lA_ 14 c2wb1J_ 15 d1rh5b_ 16 c2bo9B_ 17 c2fmlB_ 18 d1ynja1 19 c3gz6A_ 20 c2wwbB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1rhzb_ 51.6 14 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 2 d1r0ka1 19.4 16 Fold:Left-handed superhelix Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 3 d1q0qa1 19.2 8 Fold:Left-handed superhelix Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 4 c2y0sQ_ 18.6 17 PDB header:transferase Chain: Q: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group 5 c2y0sJ_ 18.6 17 PDB header:transferase Chain: J: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group 6 d1smya1 14.5 20 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 7 d2j5pa1 14.3 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like 8 c2jcyA_ 13.0 15 PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis 9 d2ve8a1 13.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FtsK C-terminal domain-like 10 c2kxaA_ 12.9 50 PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 11 c2vayB_ 12.1 45 PDB header:metal transport Chain: B: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: calmodulin complexed with cav1.1 iq peptide 12 c2wb1Q_ 11.5 28 PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 13 c2k6lA_ 10.7 33 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors 14 c2wb1J_ 10.5 20 PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 15 d1rh5b_ 8.9 42 Fold:Single transmembrane helix Superfamily:Preprotein translocase SecE subunit Family:Preprotein translocase SecE subunit 16 c2bo9B_ 8.2 19 PDB header:hydrolase Chain: B: PDB Molecule:human latexin; PDBTitle: human carboxypeptidase a4 in complex with human latexin. 17 c2fmlB_ 8.1 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:mutt/nudix family protein; PDBTitle: crystal structure of mutt/nudix family protein from enterococcus2 faecalis 18 d1ynja1 7.9 18 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 19 c3gz6A_ 7.7 21 PDB header:dna binding protein/dna Chain: A: PDB Molecule:mutt/nudix family protein; PDBTitle: crystal structure of shewanella oneidensis nrtr complexed2 with a 27mer dna 20 c2wwbB_ 7.5 14 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome 21 c2zykA_ not modelled 6.7 15 PDB header:sugar binding protein Chain: A: PDB Molecule:solute-binding protein; PDBTitle: crystal structure of cyclo/maltodextrin-binding protein2 complexed with gamma-cyclodextrin 22 d1bdfa1 not modelled 6.6 26 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 23 c2pd0D_ not modelled 6.6 44 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: protein cgd2_2020 from cryptosporidium parvum 24 d2fb1a1 not modelled 6.5 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Nudix-associated domain 25 c1r0lD_ not modelled 6.3 16 PDB header:oxidoreductase Chain: D: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: 1-deoxy-d-xylulose 5-phosphate reductoisomerase from2 zymomonas mobilis in complex with nadph 26 c3uorB_ not modelled 5.8 13 PDB header:sugar binding protein Chain: B: PDB Molecule:abc transporter sugar binding protein; PDBTitle: the structure of the sugar-binding protein male from the phytopathogen2 xanthomonas citri 27 c3hkzZ_ not modelled 5.6 20 PDB header:transferase Chain: Z: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea 28 c2uvgA_ not modelled 5.6 24 PDB header:sugar-binding protein Chain: A: PDB Molecule:abc type periplasmic sugar-binding protein; PDBTitle: structure of a periplasmic oligogalacturonide binding2 protein from yersinia enterocolitica 29 c3kk4B_ not modelled 5.5 32 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i 30 c3a14B_ not modelled 5.5 16 PDB header:oxidoreductase Chain: B: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: crystal structure of dxr from thermotoga maritima, in complex with2 nadph 31 c3au9A_ not modelled 5.4 22 PDB header:isomerase/isomerase inhibitor Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: crystal structure of the quaternary complex-1 of an isomerase 32 c2eghA_ not modelled 5.4 8 PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase2 complexed with a magnesium ion, nadph and fosmidomycin 33 c2fb1A_ not modelled 5.4 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of protein bt0354 from bacteroides thetaiotaomicron 34 d1jb0i_ not modelled 5.3 30 Fold:Single transmembrane helix Superfamily:Subunit VIII of photosystem I reaction centre, PsaI Family:Subunit VIII of photosystem I reaction centre, PsaI

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