Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	M	T	K	T	Q	I	N	K	L	I	K	M	M	N	D	L	D	Y	P	F	E	A	P	L	K	E	S	F	I	E	S	I	I	Q	I	E	F	N	S	N	S	T	N	C	L	E	K	L	C	N	E	V	S	I	L	F	K	N	Q
Secondary structure
SS confidence
Disorder		?	?	?																																?	?	?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	D	Y	L	T	F	L	R	A	M	D	G	F	E	V	N	G	L	R	L	F	S	L	S	I	P	E	P	S	V	K	N	L	F	A	V	N	E	F	Y	R	N	N	D	D	F	I	N	P	D	L	Q	E	R	L	V	I	G	D	Y
Secondary structure
SS confidence
Disorder																									?	?																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.
Sequence		S	I	S	I	F	T	Y	D	I	K	G	D	A	A	N	L	L	I
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 2pag chain A domain 1 Region: 7 - 131 Aligned: 100 Modelled: 107 Confidence: 66.1% Identity: 19% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 1yfn chain A domain 1 Region: 76 - 138 Aligned: 59 Modelled: 63 Confidence: 60.1% Identity: 19% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1ou9 chain A Region: 76 - 138 Aligned: 59 Modelled: 63 Confidence: 55.2% Identity: 20% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1zsz chain C domain 1 Region: 76 - 138 Aligned: 59 Modelled: 63 Confidence: 45.4% Identity: 20% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1ou8 chain A Region: 76 - 131 Aligned: 52 Modelled: 56 Confidence: 42.3% Identity: 19% Fold: SspB-like Superfamily: SspB-like Family: Stringent starvation protein B, SspB Phyre2 PDB 1pon chain B Region: 51 - 74 Aligned: 24 Modelled: 24 Confidence: 23.7% Identity: 33% PDB header:calcium-binding protein Chain: B: PDB Molecule:troponin c; PDBTitle: site iii-site iv troponin c heterodimer, nmr Phyre2 PDB 1e7l chain A domain 1 Region: 59 - 76 Aligned: 18 Modelled: 18 Confidence: 20.7% Identity: 28% Fold: LEM/SAP HeH motif Superfamily: Recombination endonuclease VII, C-terminal and dimerization domains Family: Recombination endonuclease VII, C-terminal and dimerization domains Phyre2 PDB 2f05 chain A domain 1 Region: 28 - 69 Aligned: 42 Modelled: 42 Confidence: 19.4% Identity: 19% Fold: PAH2 domain Superfamily: PAH2 domain Family: PAH2 domain Phyre2 PDB 2icg chain A domain 1 Region: 7 - 130 Aligned: 102 Modelled: 106 Confidence: 13.7% Identity: 21% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 1jvr chain A Region: 23 - 60 Aligned: 31 Modelled: 38 Confidence: 11.9% Identity: 29% Fold: Retroviral matrix proteins Superfamily: Retroviral matrix proteins Family: HTLV-II matrix protein Phyre2 PDB 2hw2 chain A Region: 108 - 123 Aligned: 16 Modelled: 16 Confidence: 11.9% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:rifampin adp-ribosyl transferase; PDBTitle: crystal structure of rifampin adp-ribosyl transferase in2 complex with rifampin Phyre2 PDB 1zd1 chain B Region: 73 - 107 Aligned: 31 Modelled: 35 Confidence: 11.8% Identity: 29% PDB header:transferase Chain: B: PDB Molecule:sulfotransferase 4a1; PDBTitle: human sulfortransferase sult4a1 Phyre2 PDB 2prv chain A domain 1 Region: 61 - 132 Aligned: 72 Modelled: 72 Confidence: 10.0% Identity: 11% Fold: SMI1/KNR4-like Superfamily: SMI1/KNR4-like Family: SMI1/KNR4-like Phyre2 PDB 2a8v chain A Region: 94 - 114 Aligned: 21 Modelled: 21 Confidence: 9.3% Identity: 19% PDB header:protein/rna Chain: A: PDB Molecule:rna binding domain of rho transcription PDBTitle: rho transcription termination factor/rna complex Phyre2 PDB 2i5h chain A domain 1 Region: 107 - 121 Aligned: 15 Modelled: 15 Confidence: 9.3% Identity: 27% Fold: AF1531-like Superfamily: AF1531-like Family: AF1531-like Phyre2 PDB 2i5h chain A Region: 107 - 121 Aligned: 15 Modelled: 15 Confidence: 9.3% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein af1531; PDBTitle: crystal structure of af1531 from archaeoglobus fulgidus,2 pfam duf655 Phyre2 PDB 3lfm chain A Region: 64 - 122 Aligned: 42 Modelled: 42 Confidence: 9.1% Identity: 14% PDB header:oxidoreductase Chain: A: PDB Molecule:protein fto; PDBTitle: crystal structure of the fat mass and obesity associated (fto) protein2 reveals basis for its substrate specificity Phyre2 PDB 1w63 chain P Region: 7 - 132 Aligned: 77 Modelled: 83 Confidence: 8.9% Identity: 22% PDB header:endocytosis Chain: P: PDB Molecule:adaptor-related protein complex 1, mu 1 subunit; PDBTitle: ap1 clathrin adaptor core Phyre2 PDB 2r1f chain B Region: 1 - 62 Aligned: 56 Modelled: 62 Confidence: 8.7% Identity: 18% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:predicted aminodeoxychorismate lyase; PDBTitle: crystal structure of predicted aminodeoxychorismate lyase from2 escherichia coli Phyre2 PDB 1vaz chain A Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 8.2% Identity: 23% Fold: NSFL1 (p97 ATPase) cofactor p47, SEP domain Superfamily: NSFL1 (p97 ATPase) cofactor p47, SEP domain Family: NSFL1 (p97 ATPase) cofactor p47, SEP domain Phyre2 1 d2paga1 2 d1yfna1 3 d1ou9a_ 4 d1zszc1 5 d1ou8a_ 6 c1ponB_ 7 d1e7la1 8 d2f05a1 9 d2icga1 10 d1jvra_ 11 c2hw2A_ 12 c1zd1B_ 13 d2prva1 14 c2a8vA_ 15 d2i5ha1 16 c2i5hA_ 17 c3lfmA_ 18 c1w63P_ 19 c2r1fB_ 20 d1vaza_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Detailed template information

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

1 d2paga1 66.1 19 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 2 d1yfna1 60.1 19 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 3 d1ou9a_ 55.2 20 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 4 d1zszc1 45.4 20 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 5 d1ou8a_ 42.3 19 Fold:SspB-like Superfamily:SspB-like Family:Stringent starvation protein B, SspB 6 c1ponB_ 23.7 33 PDB header:calcium-binding protein Chain: B: PDB Molecule:troponin c; PDBTitle: site iii-site iv troponin c heterodimer, nmr 7 d1e7la1 20.7 28 Fold:LEM/SAP HeH motif Superfamily:Recombination endonuclease VII, C-terminal and dimerization domains Family:Recombination endonuclease VII, C-terminal and dimerization domains 8 d2f05a1 19.4 19 Fold:PAH2 domain Superfamily:PAH2 domain Family:PAH2 domain 9 d2icga1 13.7 21 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 10 d1jvra_ 11.9 29 Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:HTLV-II matrix protein 11 c2hw2A_ 11.9 19 PDB header:transferase Chain: A: PDB Molecule:rifampin adp-ribosyl transferase; PDBTitle: crystal structure of rifampin adp-ribosyl transferase in2 complex with rifampin 12 c1zd1B_ 11.8 29 PDB header:transferase Chain: B: PDB Molecule:sulfotransferase 4a1; PDBTitle: human sulfortransferase sult4a1 13 d2prva1 10.0 11 Fold:SMI1/KNR4-like Superfamily:SMI1/KNR4-like Family:SMI1/KNR4-like 14 c2a8vA_ 9.3 19 PDB header:protein/rna Chain: A: PDB Molecule:rna binding domain of rho transcription PDBTitle: rho transcription termination factor/rna complex 15 d2i5ha1 9.3 27 Fold:AF1531-like Superfamily:AF1531-like Family:AF1531-like 16 c2i5hA_ 9.3 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein af1531; PDBTitle: crystal structure of af1531 from archaeoglobus fulgidus,2 pfam duf655 17 c3lfmA_ 9.1 14 PDB header:oxidoreductase Chain: A: PDB Molecule:protein fto; PDBTitle: crystal structure of the fat mass and obesity associated (fto) protein2 reveals basis for its substrate specificity 18 c1w63P_ 8.9 22 PDB header:endocytosis Chain: P: PDB Molecule:adaptor-related protein complex 1, mu 1 subunit; PDBTitle: ap1 clathrin adaptor core 19 c2r1fB_ 8.7 18 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:predicted aminodeoxychorismate lyase; PDBTitle: crystal structure of predicted aminodeoxychorismate lyase from2 escherichia coli 20 d1vaza_ 8.2 23 Fold:NSFL1 (p97 ATPase) cofactor p47, SEP domain Superfamily:NSFL1 (p97 ATPase) cofactor p47, SEP domain Family:NSFL1 (p97 ATPase) cofactor p47, SEP domain 21 d1vpza_ not modelled 8.1 24 Fold:CsrA-like Superfamily:CsrA-like Family:CsrA-like 22 c1qmoG_ not modelled 7.8 30 PDB header:lectin Chain: G: PDB Molecule:mannose binding lectin, fril; PDBTitle: structure of fril, a legume lectin that delays2 hematopoietic progenitor maturation 23 d1a62a2 not modelled 7.8 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 24 d1tdja2 not modelled 7.7 22 Fold:Ferredoxin-like Superfamily:ACT-like Family:Allosteric threonine deaminase C-terminal domain 25 c3csqC_ not modelled 7.5 31 PDB header:hydrolase Chain: C: PDB Molecule:morphogenesis protein 1; PDBTitle: crystal and cryoem structural studies of a cell wall2 degrading enzyme in the bacteriophage phi29 tail 26 d1a9xa3 not modelled 7.4 22 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like 27 d1kshb_ not modelled 7.3 31 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 28 d2f2ab1 not modelled 7.1 11 Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like 29 d1qtma1 not modelled 6.9 47 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:DnaQ-like 3'-5' exonuclease 30 d1ss6a_ not modelled 6.6 23 Fold:NSFL1 (p97 ATPase) cofactor p47, SEP domain Superfamily:NSFL1 (p97 ATPase) cofactor p47, SEP domain Family:NSFL1 (p97 ATPase) cofactor p47, SEP domain 31 c2f4qA_ not modelled 6.5 23 PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib 32 c3fbyC_ not modelled 6.3 26 PDB header:cell adhesion Chain: C: PDB Molecule:cartilage oligomeric matrix protein; PDBTitle: the crystal structure of the signature domain of cartilage oligomeric2 matrix protein. 33 d1o66a_ not modelled 6.3 14 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Ketopantoate hydroxymethyltransferase PanB 34 c1vpzB_ not modelled 6.1 24 PDB header:rna binding protein Chain: B: PDB Molecule:carbon storage regulator homolog; PDBTitle: crystal structure of a putative carbon storage regulator protein2 (csra, pa0905) from pseudomonas aeruginosa at 2.05 a resolution 35 c1c8m2_ not modelled 6.1 25 PDB header:virus Chain: 2: PDB Molecule:human rhinovirus 16 coat protein; PDB Fragment:residues 2-78; PDBTitle: refined crystal structure of human rhinovirus 16 complexed2 with vp63843 (pleconaril), an anti-picornaviral drug3 currently in clinical trials 36 d1elka_ not modelled 6.0 16 Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:VHS domain 37 c2b1uA_ not modelled 5.9 10 PDB header:metal binding protein Chain: A: PDB Molecule:calmodulin-like protein 5; PDBTitle: solution structure of calmodulin-like skin protein c2 terminal domain 38 d1d8ua_ not modelled 5.6 6 Fold:Globin-like Superfamily:Globin-like Family:Globins 39 c2jppB_ not modelled 5.4 32 PDB header:translation/rna Chain: B: PDB Molecule:translational repressor; PDBTitle: structural basis of rsma/csra rna recognition: structure of2 rsme bound to the shine-dalgarno sequence of hcna mrna 40 d1hdsa_ not modelled 5.2 13 Fold:Globin-like Superfamily:Globin-like Family:Globins 41 c2amiA_ not modelled 5.2 13 PDB header:cell cycle Chain: A: PDB Molecule:caltractin; PDBTitle: solution structure of the calcium-loaded n-terminal sensor2 domain of centrin 42 d1zgha1 not modelled 5.1 22 Fold:FMT C-terminal domain-like Superfamily:FMT C-terminal domain-like Family:Post formyltransferase 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