Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	H	R	K	S	G	R	Q	L	N	R	N	S	S	H	R	Q	A	M	F	R	N	M	A	G	S	L	V	R	H	E	I	I	K	T	T	L	P	K	A	K	E	L	R	R	V	V	E	P	L	I	T	L	A	K	T	D	S	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	N	R	R	L	A	F	A	R	T	R	D	N	E	I	V	A	K	L	F	N	E	L	G	P	R	F	A	S	R	A	G	G	Y	T	R	I	L	K	C	G	F	R	A	G	D	N	A	P	M	A	Y	I	E	L	V	D	R	S	E
Secondary structure
SS confidence
Disorder																																											?	?	?																?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		K	A	E	A	A	A	E
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 2qam chain N domain 1 Region: 1 - 120 Aligned: 120 Modelled: 120 Confidence: 100.0% Identity: 100% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 3bbo chain P Region: 1 - 116 Aligned: 116 Modelled: 116 Confidence: 100.0% Identity: 45% PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2zjr chain K domain 1 Region: 3 - 115 Aligned: 113 Modelled: 113 Confidence: 100.0% Identity: 52% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 1gd8 chain A Region: 14 - 117 Aligned: 104 Modelled: 104 Confidence: 100.0% Identity: 53% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 2cqm chain A domain 1 Region: 20 - 124 Aligned: 105 Modelled: 105 Confidence: 100.0% Identity: 34% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 3h0d chain B Region: 92 - 103 Aligned: 12 Modelled: 12 Confidence: 19.3% Identity: 50% PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex Phyre2 PDB 1xd7 chain A Region: 51 - 94 Aligned: 44 Modelled: 44 Confidence: 15.4% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcriptional regulator Rrf2 Phyre2 PDB 1o65 chain A Region: 89 - 125 Aligned: 32 Modelled: 37 Confidence: 15.0% Identity: 25% Fold: PK beta-barrel domain-like Superfamily: PK beta-barrel domain-like Family: MOSC (MOCO sulphurase C-terminal) domain Phyre2 PDB 2op8 chain A Region: 11 - 31 Aligned: 21 Modelled: 21 Confidence: 14.1% Identity: 5% PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase ywhb; PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase Phyre2 PDB 2z99 chain A Region: 42 - 95 Aligned: 53 Modelled: 54 Confidence: 13.5% Identity: 26% PDB header:cell cycle Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of scpb from mycobacterium tuberculosis Phyre2 PDB 2ic6 chain B Region: 33 - 84 Aligned: 52 Modelled: 52 Confidence: 13.3% Identity: 23% PDB header:viral protein Chain: B: PDB Molecule:nucleocapsid protein; PDBTitle: the coiled-coil domain (residues 1-75) structure of the sin2 nombre virus nucleocapsid protein Phyre2 PDB 1x4q chain A Region: 43 - 85 Aligned: 43 Modelled: 43 Confidence: 10.9% Identity: 26% PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) Phyre2 PDB 1v66 chain A Region: 10 - 44 Aligned: 35 Modelled: 35 Confidence: 10.8% Identity: 26% Fold: LEM/SAP HeH motif Superfamily: SAP domain Family: SAP domain Phyre2 PDB 1otf chain A Region: 11 - 31 Aligned: 21 Modelled: 21 Confidence: 9.9% Identity: 10% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 PDB 1bjp chain A Region: 11 - 31 Aligned: 21 Modelled: 21 Confidence: 8.9% Identity: 14% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 PDB 3ry0 chain A Region: 11 - 31 Aligned: 21 Modelled: 21 Confidence: 8.7% Identity: 10% PDB header:isomerase Chain: A: PDB Molecule:putative tautomerase; PDBTitle: crystal structure of tomn, a 4-oxalocrotonate tautomerase homologue in2 tomaymycin biosynthetic pathway Phyre2 PDB 2qsg chain X Region: 72 - 89 Aligned: 18 Modelled: 18 Confidence: 7.5% Identity: 22% PDB header:dna binding protein/dna Chain: X: PDB Molecule:uv excision repair protein rad23; PDBTitle: crystal structure of rad4-rad23 bound to a uv-damaged dna Phyre2 PDB 2a7w chain A domain 1 Region: 74 - 95 Aligned: 22 Modelled: 22 Confidence: 7.2% Identity: 14% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: HisE-like (PRA-PH) Phyre2 PDB 2x4k chain B Region: 11 - 30 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 5% PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of sar1376, a putative 4-oxalocrotonate2 tautomerase from the methicillin-resistant staphylococcus3 aureus (mrsa) Phyre2 PDB 2a7w chain F Region: 74 - 95 Aligned: 22 Modelled: 22 Confidence: 6.7% Identity: 14% PDB header:hydrolase Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase; PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7 Phyre2 1 d2qamn1 2 c3bboP_ 3 d2zjrk1 4 d1gd8a_ 5 d2cqma1 6 c3h0dB_ 7 d1xd7a_ 8 d1o65a_ 9 c2op8A_ 10 c2z99A_ 11 c2ic6B_ 12 c1x4qA_ 13 d1v66a_ 14 d1otfa_ 15 d1bjpa_ 16 c3ry0A_ 17 c2qsgX_ 18 d2a7wa1 19 c2x4kB_ 20 c2a7wF_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d2qamn1 100.0 100 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 2 c3bboP_ 100.0 45 PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 3 d2zjrk1 100.0 52 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 4 d1gd8a_ 100.0 53 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 5 d2cqma1 100.0 34 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 6 c3h0dB_ 19.3 50 PDB header:transcription/dna Chain: B: PDB Molecule:ctsr; PDBTitle: crystal structure of ctsr in complex with a 26bp dna duplex 7 d1xd7a_ 15.4 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator Rrf2 8 d1o65a_ 15.0 25 Fold:PK beta-barrel domain-like Superfamily:PK beta-barrel domain-like Family:MOSC (MOCO sulphurase C-terminal) domain 9 c2op8A_ 14.1 5 PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase ywhb; PDBTitle: crystal structure of ywhb- homologue of 4-oxalocrotonate tautomerase 10 c2z99A_ 13.5 26 PDB header:cell cycle Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of scpb from mycobacterium tuberculosis 11 c2ic6B_ 13.3 23 PDB header:viral protein Chain: B: PDB Molecule:nucleocapsid protein; PDBTitle: the coiled-coil domain (residues 1-75) structure of the sin2 nombre virus nucleocapsid protein 12 c1x4qA_ 10.9 26 PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) 13 d1v66a_ 10.8 26 Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain 14 d1otfa_ 9.9 10 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 15 d1bjpa_ 8.9 14 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 16 c3ry0A_ 8.7 10 PDB header:isomerase Chain: A: PDB Molecule:putative tautomerase; PDBTitle: crystal structure of tomn, a 4-oxalocrotonate tautomerase homologue in2 tomaymycin biosynthetic pathway 17 c2qsgX_ 7.5 22 PDB header:dna binding protein/dna Chain: X: PDB Molecule:uv excision repair protein rad23; PDBTitle: crystal structure of rad4-rad23 bound to a uv-damaged dna 18 d2a7wa1 7.2 14 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 19 c2x4kB_ 6.8 5 PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of sar1376, a putative 4-oxalocrotonate2 tautomerase from the methicillin-resistant staphylococcus3 aureus (mrsa) 20 c2a7wF_ 6.7 14 PDB header:hydrolase Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase; PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7 21 d1x3zb1 not modelled 6.5 25 Fold:XPC-binding domain Superfamily:XPC-binding domain Family:XPC-binding domain 22 c2wb1J_ not modelled 6.2 19 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 23 c3mb2G_ not modelled 6.1 10 PDB header:isomerase Chain: G: PDB Molecule:4-oxalocrotonate tautomerase family enzyme - alpha subunit; PDBTitle: kinetic and structural characterization of a heterohexamer 4-2 oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl:3 implications for functional and structural diversity in the4 tautomerase superfamily 24 d2fufa1 not modelled 6.1 41 Fold:Origin of replication-binding domain, RBD-like Superfamily:Origin of replication-binding domain, RBD-like Family:The origin DNA-binding domain of SV40 T-antigen 25 c2p9xB_ not modelled 6.1 50 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 26 c2ormA_ not modelled 5.9 10 PDB header:isomerase Chain: A: PDB Molecule:probable tautomerase hp0924; PDBTitle: crystal structure of the 4-oxalocrotonate tautomerase homologue dmpi2 from helicobacter pylori. 27 c3n4dF_ not modelled 5.7 5 PDB header:hydrolase Chain: F: PDB Molecule:putative tautomerase; PDBTitle: crystal structure of cg10062 inactivated by(r)-oxirane-2-carboxylate 28 d1y6xa1 not modelled 5.7 45 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 29 d1mwwa_ not modelled 5.2 10 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:Hypothetical protein HI1388.1 30 c3abfB_ not modelled 5.2 15 PDB header:isomerase Chain: B: PDB Molecule:4-oxalocrotonate tautomerase; PDBTitle: crystal structure of a 4-oxalocrotonate tautomerase homologue2 (tthb242)

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