Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	I	L	I	S	P	A	K	T	L	D	Y	Q	S	P	L	T	T	T	R	Y	T	L	P	E	L	L	D	N	S	Q	Q	L	I	H	E	A	R	K	L	T	P	P	Q	I	S	T	L	M	R	I	S	D	K	L	A	G	I	N
Secondary structure
SS confidence
Disorder		?	?			?	?	?		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	A	R	F	H	D	W	Q	P	D	F	T	P	A	N	A	R	Q	A	I	L	A	F	K	G	D	V	Y	T	G	L	Q	A	E	T	F	S	E	D	D	F	D	F	A	Q	Q	H	L	R	M	L	S	G	L	Y	G	V	L	R	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	D	L	M	Q	P	Y	R	L	E	M	G	I	R	L	E	N	A	R	G	K	D	L	Y	Q	F	W	G	D	I	I	T	N	K	L	N	E	A	L	A	A	Q	G	D	N	V	V	I	N	L	A	S	D	E	Y	F	K	S	V	K
Secondary structure
SS confidence
Disorder																			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	K	K	L	N	A	E	I	I	K	P	V	F	L	D	E	K	N	G	K	F	K	I	I	S	F	Y	A	K	K	A	R	G	L	M	S	R	F	I	I	E	N	R	L	T	K	P	E	Q	L	T	G	F	N	S	E	G	Y	F	F
Secondary structure
SS confidence
Disorder																			?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.
Sequence		D	E	D	S	S	S	N	G	E	L	V	F	K	R	Y	E	Q	R
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 2aq0 chain A domain 1 Region: 35 - 66 Aligned: 31 Modelled: 32 Confidence: 71.4% Identity: 16% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Hef domain-like Phyre2 PDB 2ovr chain A domain 1 Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 35.2% Identity: 14% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 1kft chain A Region: 35 - 66 Aligned: 32 Modelled: 32 Confidence: 31.6% Identity: 19% PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli Phyre2 PDB 1kft chain A Region: 35 - 66 Aligned: 32 Modelled: 32 Confidence: 31.6% Identity: 19% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Excinuclease UvrC C-terminal domain Phyre2 PDB 1nex chain A domain 1 Region: 25 - 64 Aligned: 40 Modelled: 40 Confidence: 30.5% Identity: 18% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 2p1n chain D Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 28.9% Identity: 17% PDB header:signaling protein Chain: D: PDB Molecule:skp1-like protein 1a; PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase Phyre2 PDB 1bd0 chain A domain 2 Region: 106 - 134 Aligned: 27 Modelled: 29 Confidence: 27.0% Identity: 26% Fold: TIM beta/alpha-barrel Superfamily: PLP-binding barrel Family: Alanine racemase-like, N-terminal domain Phyre2 PDB 2ovq chain A Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 26.9% Identity: 14% PDB header:transcription/cell cycle Chain: A: PDB Molecule:s-phase kinase-associated protein 1a; PDBTitle: structure of the skp1-fbw7-cyclinedegc complex Phyre2 PDB 1fse chain A Region: 23 - 64 Aligned: 42 Modelled: 42 Confidence: 26.0% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1nex chain C Region: 25 - 65 Aligned: 41 Modelled: 41 Confidence: 25.6% Identity: 17% PDB header:ligase, cell cycle Chain: C: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: crystal structure of scskp1-sccdc4-cpd peptide complex Phyre2 PDB 1x2i chain A domain 1 Region: 35 - 66 Aligned: 32 Modelled: 32 Confidence: 22.5% Identity: 9% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Hef domain-like Phyre2 PDB 2rjp chain C Region: 124 - 235 Aligned: 93 Modelled: 112 Confidence: 20.3% Identity: 12% PDB header:hydrolase Chain: C: PDB Molecule:adamts-4; PDBTitle: crystal structure of adamts4 with inhibitor bound Phyre2 PDB 2kc2 chain A Region: 182 - 229 Aligned: 45 Modelled: 48 Confidence: 19.3% Identity: 20% PDB header:structural protein Chain: A: PDB Molecule:talin-1; PDBTitle: nmr structure of the f1 domain (residues 86-202) of the2 talin Phyre2 PDB 3iei chain D Region: 151 - 193 Aligned: 43 Modelled: 43 Confidence: 18.6% Identity: 12% PDB header:transferase Chain: D: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxylmethyltransferase-1 in2 complex with s-adenosyl homocysteine Phyre2 PDB 2bgw chain A domain 1 Region: 35 - 66 Aligned: 32 Modelled: 32 Confidence: 18.0% Identity: 16% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Hef domain-like Phyre2 PDB 3mnt chain A Region: 150 - 193 Aligned: 44 Modelled: 44 Confidence: 17.9% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxyl methyltransferase 1 Phyre2 PDB 1rjd chain A Region: 151 - 193 Aligned: 43 Modelled: 43 Confidence: 17.8% Identity: 16% Fold: S-adenosyl-L-methionine-dependent methyltransferases Superfamily: S-adenosyl-L-methionine-dependent methyltransferases Family: Leucine carboxy methyltransferase Ppm1 Phyre2 PDB 2fm9 chain A domain 1 Region: 46 - 106 Aligned: 56 Modelled: 61 Confidence: 16.3% Identity: 14% Fold: SipA N-terminal domain-like Superfamily: SipA N-terminal domain-like Family: SipA N-terminal domain-like Phyre2 PDB 2yfv chain C Region: 142 - 174 Aligned: 29 Modelled: 33 Confidence: 15.7% Identity: 28% PDB header:cell cycle Chain: C: PDB Molecule:scm3; PDBTitle: the heterotrimeric complex of kluyveromyces lactis scm3, cse4 and h4 Phyre2 PDB 2fm8 chain C domain 1 Region: 46 - 106 Aligned: 56 Modelled: 61 Confidence: 15.7% Identity: 14% Fold: SipA N-terminal domain-like Superfamily: SipA N-terminal domain-like Family: SipA N-terminal domain-like Phyre2 1 d2aq0a1 2 d2ovra1 3 c1kftA_ 4 d1kfta_ 5 d1nexa1 6 c2p1nD_ 7 d1bd0a2 8 c2ovqA_ 9 d1fsea_ 10 c1nexC_ 11 d1x2ia1 12 c2rjpC_ 13 c2kc2A_ 14 c3ieiD_ 15 d2bgwa1 16 c3mntA_ 17 d1rjda_ 18 d2fm9a1 19 c2yfvC_ 20 d2fm8c1 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 53 54 55 56 57 58 59 60 61 62 63 64 65 66

Detailed template information

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

1 d2aq0a1 71.4 16 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 2 d2ovra1 35.2 14 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 3 c1kftA_ 31.6 19 PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli 4 d1kfta_ 31.6 19 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain 5 d1nexa1 30.5 18 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 6 c2p1nD_ 28.9 17 PDB header:signaling protein Chain: D: PDB Molecule:skp1-like protein 1a; PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase 7 d1bd0a2 27.0 26 Fold:TIM beta/alpha-barrel Superfamily:PLP-binding barrel Family:Alanine racemase-like, N-terminal domain 8 c2ovqA_ 26.9 14 PDB header:transcription/cell cycle Chain: A: PDB Molecule:s-phase kinase-associated protein 1a; PDBTitle: structure of the skp1-fbw7-cyclinedegc complex 9 d1fsea_ 26.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 10 c1nexC_ 25.6 17 PDB header:ligase, cell cycle Chain: C: PDB Molecule:centromere dna-binding protein complex cbf3 PDBTitle: crystal structure of scskp1-sccdc4-cpd peptide complex 11 d1x2ia1 22.5 9 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 12 c2rjpC_ 20.3 12 PDB header:hydrolase Chain: C: PDB Molecule:adamts-4; PDBTitle: crystal structure of adamts4 with inhibitor bound 13 c2kc2A_ 19.3 20 PDB header:structural protein Chain: A: PDB Molecule:talin-1; PDBTitle: nmr structure of the f1 domain (residues 86-202) of the2 talin 14 c3ieiD_ 18.6 12 PDB header:transferase Chain: D: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxylmethyltransferase-1 in2 complex with s-adenosyl homocysteine 15 d2bgwa1 18.0 16 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 16 c3mntA_ 17.9 11 PDB header:transferase Chain: A: PDB Molecule:leucine carboxyl methyltransferase 1; PDBTitle: crystal structure of human leucine carboxyl methyltransferase 1 17 d1rjda_ 17.8 16 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Leucine carboxy methyltransferase Ppm1 18 d2fm9a1 16.3 14 Fold:SipA N-terminal domain-like Superfamily:SipA N-terminal domain-like Family:SipA N-terminal domain-like 19 c2yfvC_ 15.7 28 PDB header:cell cycle Chain: C: PDB Molecule:scm3; PDBTitle: the heterotrimeric complex of kluyveromyces lactis scm3, cse4 and h4 20 d2fm8c1 15.7 14 Fold:SipA N-terminal domain-like Superfamily:SipA N-terminal domain-like Family:SipA N-terminal domain-like 21 c1wcnA_ not modelled 15.3 9 PDB header:rna-binding protein Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: nmr structure of the carboxyterminal domains of escherichia2 coli nusa 22 d2a1jb1 not modelled 15.2 6 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 23 d1fs2b1 not modelled 14.0 17 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 24 d1k78a1 not modelled 13.8 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 25 d1rcqa2 not modelled 13.7 24 Fold:TIM beta/alpha-barrel Superfamily:PLP-binding barrel Family:Alanine racemase-like, N-terminal domain 26 c2bhnD_ not modelled 12.3 16 PDB header:hydrolase Chain: D: PDB Molecule:xpf endonuclease; PDBTitle: xpf from aeropyrum pernix 27 d6paxa1 not modelled 12.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 28 c2k9lA_ not modelled 11.6 14 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 29 c2pfcA_ not modelled 10.8 21 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein rv0098/mt0107; PDBTitle: structure of mycobacterium tuberculosis rv0098 30 d2i1qa1 not modelled 10.1 18 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 31 d2cg4a1 not modelled 9.6 3 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 32 c2lfcA_ not modelled 9.4 4 PDB header:oxidoreductase Chain: A: PDB Molecule:fumarate reductase, flavoprotein subunit; PDBTitle: solution nmr structure of fumarate reductase flavoprotein subunit from2 lactobacillus plantarum, northeast structural genomics consortium3 target lpr145j 33 d1pzna1 not modelled 7.8 12 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 34 d1lb2b_ not modelled 7.7 8 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 35 c2o8xA_ not modelled 7.3 13 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 36 c2g9pA_ not modelled 7.2 62 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 37 d1lvaa4 not modelled 6.7 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal fragment of elongation factor SelB 38 d1y0pa3 not modelled 6.5 15 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 39 d1szpb1 not modelled 6.4 11 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 40 d1y0ua_ not modelled 6.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 41 c3ijrF_ not modelled 6.3 20 PDB header:oxidoreductase Chain: F: PDB Molecule:oxidoreductase, short chain dehydrogenase/reductase family; PDBTitle: 2.05 angstrom resolution crystal structure of a short chain2 dehydrogenase from bacillus anthracis str. 'ames ancestor' in complex3 with nad+ 42 c2wp0C_ not modelled 6.3 13 PDB header:dna binding protein Chain: C: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: crystal structure of a hoba-dnaa (domain i-ii) complex from2 helicobacter pylori. 43 c1qqp4_ not modelled 6.3 56 PDB header:virus Chain: 4: PDB Molecule:protein (genome polyprotein); PDBTitle: foot-and-mouth disease virus/ oligosaccharide receptor complex. 44 d1cooa_ not modelled 6.2 8 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 45 d2gwfa1 not modelled 6.1 8 Fold:Rhodanese/Cell cycle control phosphatase Superfamily:Rhodanese/Cell cycle control phosphatase Family:Ubiquitin carboxyl-terminal hydrolase 8, USP8 46 c3k0bA_ not modelled 6.0 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:predicted n6-adenine-specific dna methylase; PDBTitle: crystal structure of a predicted n6-adenine-specific dna methylase2 from listeria monocytogenes str. 4b f2365 47 c3g9kD_ not modelled 6.0 21 PDB header:hydrolase Chain: D: PDB Molecule:capsule biosynthesis protein capd; PDBTitle: crystal structure of bacillus anthracis transpeptidase enzyme capd 48 d1d4ca3 not modelled 6.0 4 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 49 d1bmlc1 not modelled 5.9 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 50 d1szpa1 not modelled 5.8 11 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 51 c1giqA_ not modelled 5.8 11 PDB header:toxin Chain: A: PDB Molecule:iota toxin component ia; PDBTitle: crystal structure of the enzymatic componet of iota-toxin2 from clostridium perfringens with nadh 52 c2nrzB_ not modelled 5.7 10 PDB header:hydrolase Chain: B: PDB Molecule:uvrabc system protein c; PDBTitle: crystal structure of the c-terminal half of uvrc bound to2 its catalytic divalent cation 53 d1l4db_ not modelled 5.7 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 54 d1z3eb1 not modelled 5.6 11 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 55 d1xsva_ not modelled 5.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 56 c3us8A_ not modelled 5.6 10 PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase [nadp]; PDBTitle: crystal structure of an isocitrate dehydrogenase from sinorhizobium2 meliloti 1021 57 c3bqsB_ not modelled 5.5 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 listeria monocytogenes, trigonal form 58 c2vswB_ not modelled 5.5 23 PDB header:hydrolase Chain: B: PDB Molecule:dual specificity protein phosphatase 16; PDBTitle: the structure of the rhodanese domain of the human dual2 specificity phosphatase 16 59 d1wc9a_ not modelled 5.4 16 Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:TRAPP components 60 d1vfsa2 not modelled 5.4 27 Fold:TIM beta/alpha-barrel Superfamily:PLP-binding barrel Family:Alanine racemase-like, N-terminal domain 61 d1l4zb_ not modelled 5.3 25 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 62 d2e9xb2 not modelled 5.2 16 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:PSF2 N-terminal domain-like 63 d1b22a_ not modelled 5.2 14 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 64 c1b22A_ not modelled 5.2 14 PDB header:dna binding protein Chain: A: PDB Molecule:dna repair protein rad51; PDBTitle: rad51 (n-terminal domain) 65 d1doqa_ not modelled 5.2 5 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 66 d1a04a1 not modelled 5.1 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators)

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