Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	F	G	T	R	S	A	T	G	K	M	V	K	L	K	L	P	V	D	V	E	S	L	L	I	E	A	S	N	R	S	G	R	S	R	S	F	E	A	V	I	R	L	K	D	H	L	H	R	Y	P	K	F	N	R	A	G	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?		?																			?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	Y	G	K	S	L	V	K	Y	L	T	M	R	L	D	D	E	T	N	Q	L	L	I	A	A	K	N	R	S	G	W	C	K	T	D	E	A	A	D	R	V	I	D	H	L	I	K	F	P	D	F	Y	N	S	E	I	F	R	E	A
Secondary structure
SS confidence
Disorder		?																											?	?	?	?	?	?																										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.
Sequence		D	K	E	E	D	I	T	F	N	T	L
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 1u9p chain A Region: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 68.0% Identity: 25% PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc Phyre2 PDB 2vl7 chain A Region: 20 - 71 Aligned: 48 Modelled: 52 Confidence: 39.4% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:xpd; PDBTitle: structure of s. tokodaii xpd4 Phyre2 PDB 1mnt chain A Region: 16 - 51 Aligned: 36 Modelled: 36 Confidence: 32.8% Identity: 25% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Arc/Mnt-like phage repressors Phyre2 PDB 2eho chain L Region: 52 - 127 Aligned: 74 Modelled: 76 Confidence: 18.5% Identity: 16% PDB header:replication Chain: L: PDB Molecule:gins complex subunit 3; PDBTitle: crystal structure of human gins complex Phyre2 PDB 1ezy chain A Region: 74 - 119 Aligned: 46 Modelled: 46 Confidence: 17.1% Identity: 20% PDB header:signaling protein inhibitor Chain: A: PDB Molecule:regulator of g-protein signaling 4; PDBTitle: high-resolution solution structure of free rgs4 by nmr Phyre2 PDB 3crw chain 1 Region: 25 - 69 Aligned: 43 Modelled: 45 Confidence: 16.9% Identity: 19% PDB header:hydrolase Chain: 1: PDB Molecule:xpd/rad3 related dna helicase; PDBTitle: "xpd_apo" Phyre2 PDB 2jm5 chain A domain 1 Region: 74 - 119 Aligned: 46 Modelled: 46 Confidence: 15.6% Identity: 22% Fold: Regulator of G-protein signaling, RGS Superfamily: Regulator of G-protein signaling, RGS Family: Regulator of G-protein signaling, RGS Phyre2 PDB 3d85 chain D domain 1 Region: 8 - 19 Aligned: 12 Modelled: 12 Confidence: 15.0% Identity: 42% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 PDB 3pt2 chain A Region: 69 - 117 Aligned: 49 Modelled: 49 Confidence: 14.3% Identity: 4% PDB header:hydrolase/protein binding Chain: A: PDB Molecule:rna polymerase; PDBTitle: structure of a viral otu domain protease bound to ubiquitin Phyre2 PDB 1kxp chain D domain 3 Region: 96 - 129 Aligned: 34 Modelled: 34 Confidence: 12.6% Identity: 26% Fold: Serum albumin-like Superfamily: Serum albumin-like Family: Serum albumin-like Phyre2 PDB 3c0r chain C Region: 57 - 123 Aligned: 67 Modelled: 67 Confidence: 12.2% Identity: 16% PDB header:cell cycle, hydrolase Chain: C: PDB Molecule:ubiquitin thioesterase otu1; PDBTitle: structure of ovarian tumor (otu) domain in complex with ubiquitin Phyre2 PDB 1ufa chain A domain 1 Region: 89 - 131 Aligned: 43 Modelled: 43 Confidence: 10.7% Identity: 21% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Families 57/38 glycoside transferase middle domain Family: AmyC C-terminal domain-like Phyre2 PDB 1ygm chain A Region: 10 - 106 Aligned: 79 Modelled: 97 Confidence: 10.4% Identity: 29% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic Phyre2 PDB 2b5d chain X domain 1 Region: 89 - 131 Aligned: 43 Modelled: 43 Confidence: 10.4% Identity: 21% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Families 57/38 glycoside transferase middle domain Family: AmyC C-terminal domain-like Phyre2 PDB 3dtf chain B Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 10.2% Identity: 19% PDB header:transferase Chain: B: PDB Molecule:branched-chain amino acid aminotransferase; PDBTitle: structural analysis of mycobacterial branched chain aminotransferase-2 implications for inhibitor design Phyre2 PDB 1y6i chain A domain 2 Region: 19 - 61 Aligned: 38 Modelled: 43 Confidence: 10.0% Identity: 16% Fold: GUN4-like Superfamily: GUN4-like Family: GUN4-like Phyre2 PDB 3cxb chain A Region: 47 - 74 Aligned: 28 Modelled: 28 Confidence: 9.8% Identity: 25% PDB header:signaling protein Chain: A: PDB Molecule:protein sifa; PDBTitle: crystal structure of sifa and skip Phyre2 PDB 1914 chain A domain 2 Region: 55 - 89 Aligned: 35 Modelled: 35 Confidence: 9.1% Identity: 17% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 2ik8 chain B domain 1 Region: 74 - 119 Aligned: 46 Modelled: 46 Confidence: 8.3% Identity: 24% Fold: Regulator of G-protein signaling, RGS Superfamily: Regulator of G-protein signaling, RGS Family: Regulator of G-protein signaling, RGS Phyre2 PDB 2jpi chain A Region: 45 - 52 Aligned: 8 Modelled: 8 Confidence: 7.7% Identity: 50% PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa Phyre2 1 c1u9pA_ 2 c2vl7A_ 3 d1mnta_ 4 c2ehoL_ 5 c1ezyA_ 6 c3crw1_ 7 d2jm5a1 8 d3d85d1 9 c3pt2A_ 10 d1kxpd3 11 c3c0rC_ 12 d1ufaa1 13 c1ygmA_ 14 d2b5dx1 15 c3dtfB_ 16 d1y6ia2 17 c3cxbA_ 18 d1914a2 19 d2ik8b1 20 c2jpiA_ 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 c1u9pA_ 68.0 25 PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc 2 c2vl7A_ 39.4 21 PDB header:unknown function Chain: A: PDB Molecule:xpd; PDBTitle: structure of s. tokodaii xpd4 3 d1mnta_ 32.8 25 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 4 c2ehoL_ 18.5 16 PDB header:replication Chain: L: PDB Molecule:gins complex subunit 3; PDBTitle: crystal structure of human gins complex 5 c1ezyA_ 17.1 20 PDB header:signaling protein inhibitor Chain: A: PDB Molecule:regulator of g-protein signaling 4; PDBTitle: high-resolution solution structure of free rgs4 by nmr 6 c3crw1_ 16.9 19 PDB header:hydrolase Chain: 1: PDB Molecule:xpd/rad3 related dna helicase; PDBTitle: "xpd_apo" 7 d2jm5a1 15.6 22 Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS 8 d3d85d1 15.0 42 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 9 c3pt2A_ 14.3 4 PDB header:hydrolase/protein binding Chain: A: PDB Molecule:rna polymerase; PDBTitle: structure of a viral otu domain protease bound to ubiquitin 10 d1kxpd3 12.6 26 Fold:Serum albumin-like Superfamily:Serum albumin-like Family:Serum albumin-like 11 c3c0rC_ 12.2 16 PDB header:cell cycle, hydrolase Chain: C: PDB Molecule:ubiquitin thioesterase otu1; PDBTitle: structure of ovarian tumor (otu) domain in complex with ubiquitin 12 d1ufaa1 10.7 21 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Families 57/38 glycoside transferase middle domain Family:AmyC C-terminal domain-like 13 c1ygmA_ 10.4 29 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic 14 d2b5dx1 10.4 21 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Families 57/38 glycoside transferase middle domain Family:AmyC C-terminal domain-like 15 c3dtfB_ 10.2 19 PDB header:transferase Chain: B: PDB Molecule:branched-chain amino acid aminotransferase; PDBTitle: structural analysis of mycobacterial branched chain aminotransferase-2 implications for inhibitor design 16 d1y6ia2 10.0 16 Fold:GUN4-like Superfamily:GUN4-like Family:GUN4-like 17 c3cxbA_ 9.8 25 PDB header:signaling protein Chain: A: PDB Molecule:protein sifa; PDBTitle: crystal structure of sifa and skip 18 d1914a2 9.1 17 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 19 d2ik8b1 8.3 24 Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS 20 c2jpiA_ 7.7 50 PDB header:structural genomics Chain: A: PDB Molecule:hypothetical protein; PDBTitle: chemical shift assignments of pa4090 from pseudomonas2 aeruginosa 21 c2abjG_ not modelled 7.5 10 PDB header:transferase Chain: G: PDB Molecule:branched-chain-amino-acid aminotransferase, cytosolic; PDBTitle: crystal structure of human branched chain amino acid transaminase in a2 complex with an inhibitor, c16h10n2o4f3scl, and pyridoxal 5'3 phosphate. 22 d2a1ha1 not modelled 7.4 10 Fold:D-aminoacid aminotransferase-like PLP-dependent enzymes Superfamily:D-aminoacid aminotransferase-like PLP-dependent enzymes Family:D-aminoacid aminotransferase-like PLP-dependent enzymes 23 d1ljma_ not modelled 7.4 44 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:RUNT domain 24 d1z3xa2 not modelled 6.9 13 Fold:GUN4-like Superfamily:GUN4-like Family:GUN4-like 25 c3enpA_ not modelled 6.9 13 PDB header:hydrolase Chain: A: PDB Molecule:tp53rk-binding protein; PDBTitle: crystal structure of human cgi121 26 c3qqmD_ not modelled 6.8 25 PDB header:transferase Chain: D: PDB Molecule:mlr3007 protein; PDBTitle: crystal structure of a putative amino-acid aminotransferase2 (np_104211.1) from mesorhizobium loti at 2.30 a resolution 27 c3j0gO_ not modelled 6.3 30 PDB header:virus Chain: O: PDB Molecule:e3 protein; PDBTitle: homology model of e3 protein of venezuelan equine encephalitis virus2 tc-83 strain fitted with a cryo-em map 28 d1eaqa_ not modelled 5.9 50 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:RUNT domain 29 d1y9ba1 not modelled 5.7 26 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like 30 d1c4oa2 not modelled 5.7 29 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain 31 c2konA_ not modelled 5.3 42 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of cv_2116 from chromobacterium2 violaceum. northeast structural genomics consortium target3 cvt4(1-82) 32 c2elxA_ not modelled 5.2 20 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 8th c2h2 zinc finger of mouse2 zinc finger protein 406

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