Secondary structure and disorder prediction

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Sequence		M	N	H	D	I	P	L	K	Y	F	D	I	A	D	E	Y	A	T	E	C	A	E	P	V	A	E	A	E	R	T	P	L	A	H	Y	F	Q	L	L	L	T	R	L	M	N	N	E	E	I	S	E	E	A	Q	H	E	M	A	A	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?																						?																		?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.
Sequence		A	G	I	N	P	V	R	I	D	E	I	A	E	F	L	N	Q	W	G	N	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 2fug chain 2 domain 1 Region: 49 - 74 Aligned: 26 Modelled: 26 Confidence: 63.7% Identity: 31% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: NQO2-like Phyre2 PDB 1oxj chain A Region: 3 - 50 Aligned: 47 Modelled: 48 Confidence: 61.4% Identity: 21% PDB header:rna binding protein Chain: A: PDB Molecule:rna-binding protein smaug; PDBTitle: crystal structure of the smaug rna binding domain Phyre2 PDB 3fdq chain B Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 51.8% Identity: 26% PDB header:dna binding protein/dna Chain: B: PDB Molecule:motility gene repressor mogr; PDBTitle: recognition of at-rich dna binding sites by the mogr2 repressor Phyre2 PDB 2dt5 chain A domain 1 Region: 26 - 79 Aligned: 52 Modelled: 54 Confidence: 47.3% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcriptional repressor Rex, N-terminal domain Phyre2 PDB 2dt5 chain A Region: 24 - 79 Aligned: 54 Modelled: 56 Confidence: 43.8% Identity: 17% PDB header:dna binding protein Chain: A: PDB Molecule:at-rich dna-binding protein; PDBTitle: crystal structure of ttha1657 (at-rich dna-binding protein) from2 thermus thermophilus hb8 Phyre2 PDB 2vt2 chain A Region: 30 - 79 Aligned: 48 Modelled: 50 Confidence: 35.2% Identity: 15% PDB header:transcription Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: structure and functional properties of the bacillus2 subtilis transcriptional repressor rex Phyre2 PDB 3ol4 chain B Region: 39 - 81 Aligned: 43 Modelled: 43 Confidence: 30.5% Identity: 28% PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c Phyre2 PDB 2k89 chain A Region: 44 - 77 Aligned: 34 Modelled: 34 Confidence: 24.3% Identity: 18% PDB header:protein binding Chain: A: PDB Molecule:phospholipase a-2-activating protein; PDBTitle: solution structure of a novel ubiquitin-binding domain from2 human plaa (pfuc, gly76-pro77 cis isomer) Phyre2 PDB 3n2l chain A Region: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 24.2% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:orotate phosphoribosyltransferase; PDBTitle: 2.1 angstrom resolution crystal structure of an orotate2 phosphoribosyltransferase (pyre) from vibrio cholerae o1 biovar eltor3 str. n16961 Phyre2 PDB 3ket chain A Region: 24 - 79 Aligned: 54 Modelled: 56 Confidence: 19.5% Identity: 17% PDB header:transcription/dna Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: crystal structure of a rex-family transcriptional regulatory protein2 from streptococcus agalactiae bound to a palindromic operator Phyre2 PDB 1xg7 chain A Region: 39 - 71 Aligned: 32 Modelled: 33 Confidence: 19.2% Identity: 22% Fold: DNA-glycosylase Superfamily: DNA-glycosylase Family: AgoG-like Phyre2 PDB 2dce chain A Region: 68 - 79 Aligned: 12 Modelled: 12 Confidence: 17.5% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:kiaa1915 protein; PDBTitle: solution structure of the swirm domain of human kiaa19152 protein Phyre2 PDB 2fq3 chain A domain 1 Region: 68 - 79 Aligned: 12 Modelled: 12 Confidence: 16.8% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: SWIRM domain Phyre2 PDB 2dw4 chain A domain 1 Region: 68 - 79 Aligned: 12 Modelled: 12 Confidence: 16.6% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: SWIRM domain Phyre2 PDB 2qgs chain A domain 1 Region: 20 - 81 Aligned: 51 Modelled: 59 Confidence: 16.1% Identity: 24% Fold: HD-domain/PDEase-like Superfamily: HD-domain/PDEase-like Family: HD domain Phyre2 PDB 3p8c chain E Region: 68 - 79 Aligned: 12 Modelled: 12 Confidence: 16.1% Identity: 50% PDB header:protein binding Chain: E: PDB Molecule:probable protein brick1; PDBTitle: structure and control of the actin regulatory wave complex Phyre2 PDB 2a4h chain A domain 1 Region: 69 - 78 Aligned: 10 Modelled: 10 Confidence: 15.9% Identity: 30% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Selenoprotein W-related Phyre2 PDB 2kfd chain A Region: 34 - 43 Aligned: 10 Modelled: 10 Confidence: 14.6% Identity: 70% PDB header:nuclear protein Chain: A: PDB Molecule:pre-mrna-processing protein prp40; PDBTitle: prp40 ff4 domain Phyre2 PDB 3pp5 chain A Region: 68 - 78 Aligned: 11 Modelled: 11 Confidence: 14.1% Identity: 55% PDB header:structural protein Chain: A: PDB Molecule:brk1; PDBTitle: high-resolution structure of the trimeric scar/wave complex precursor2 brk1 Phyre2 PDB 1m47 chain A Region: 71 - 78 Aligned: 8 Modelled: 8 Confidence: 12.4% Identity: 75% Fold: 4-helical cytokines Superfamily: 4-helical cytokines Family: Short-chain cytokines Phyre2 1 d2fug21 2 c1oxjA_ 3 c3fdqB_ 4 d2dt5a1 5 c2dt5A_ 6 c2vt2A_ 7 c3ol4B_ 8 c2k89A_ 9 c3n2lA_ 10 c3ketA_ 11 d1xg7a_ 12 c2dceA_ 13 d2fq3a1 14 d2dw4a1 15 d2qgsa1 16 c3p8cE_ 17 d2a4ha1 18 c2kfdA_ 19 c3pp5A_ 20 d1m47a_ 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 d2fug21 63.7 31 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:NQO2-like 2 c1oxjA_ 61.4 21 PDB header:rna binding protein Chain: A: PDB Molecule:rna-binding protein smaug; PDBTitle: crystal structure of the smaug rna binding domain 3 c3fdqB_ 51.8 26 PDB header:dna binding protein/dna Chain: B: PDB Molecule:motility gene repressor mogr; PDBTitle: recognition of at-rich dna binding sites by the mogr2 repressor 4 d2dt5a1 47.3 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional repressor Rex, N-terminal domain 5 c2dt5A_ 43.8 17 PDB header:dna binding protein Chain: A: PDB Molecule:at-rich dna-binding protein; PDBTitle: crystal structure of ttha1657 (at-rich dna-binding protein) from2 thermus thermophilus hb8 6 c2vt2A_ 35.2 15 PDB header:transcription Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: structure and functional properties of the bacillus2 subtilis transcriptional repressor rex 7 c3ol4B_ 30.5 28 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c 8 c2k89A_ 24.3 18 PDB header:protein binding Chain: A: PDB Molecule:phospholipase a-2-activating protein; PDBTitle: solution structure of a novel ubiquitin-binding domain from2 human plaa (pfuc, gly76-pro77 cis isomer) 9 c3n2lA_ 24.2 17 PDB header:transferase Chain: A: PDB Molecule:orotate phosphoribosyltransferase; PDBTitle: 2.1 angstrom resolution crystal structure of an orotate2 phosphoribosyltransferase (pyre) from vibrio cholerae o1 biovar eltor3 str. n16961 10 c3ketA_ 19.5 17 PDB header:transcription/dna Chain: A: PDB Molecule:redox-sensing transcriptional repressor rex; PDBTitle: crystal structure of a rex-family transcriptional regulatory protein2 from streptococcus agalactiae bound to a palindromic operator 11 d1xg7a_ 19.2 22 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:AgoG-like 12 c2dceA_ 17.5 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:kiaa1915 protein; PDBTitle: solution structure of the swirm domain of human kiaa19152 protein 13 d2fq3a1 16.8 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:SWIRM domain 14 d2dw4a1 16.6 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:SWIRM domain 15 d2qgsa1 16.1 24 Fold:HD-domain/PDEase-like Superfamily:HD-domain/PDEase-like Family:HD domain 16 c3p8cE_ 16.1 50 PDB header:protein binding Chain: E: PDB Molecule:probable protein brick1; PDBTitle: structure and control of the actin regulatory wave complex 17 d2a4ha1 15.9 30 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Selenoprotein W-related 18 c2kfdA_ 14.6 70 PDB header:nuclear protein Chain: A: PDB Molecule:pre-mrna-processing protein prp40; PDBTitle: prp40 ff4 domain 19 c3pp5A_ 14.1 55 PDB header:structural protein Chain: A: PDB Molecule:brk1; PDBTitle: high-resolution structure of the trimeric scar/wave complex precursor2 brk1 20 d1m47a_ 12.4 75 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 21 d1jsxa_ not modelled 11.7 10 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:Glucose-inhibited division protein B (GidB) 22 c3godA_ not modelled 11.2 27 PDB header:immune system Chain: A: PDB Molecule:cas1; PDBTitle: structural basis for dnase activity of a conserved protein2 implicated in crispr-mediated antiviral defense 23 c1xfzA_ not modelled 10.8 52 PDB header:lyase/metal binding protein Chain: A: PDB Molecule:calmodulin-sensitive adenylate cyclase; PDBTitle: crystal structure of anthrax edema factor (ef) in complex2 with calmodulin in the presence of 1 millimolar3 exogenously added calcium chloride 24 c1xfuE_ not modelled 10.8 52 PDB header:lyase/metal binding protein Chain: E: PDB Molecule:calmodulin-sensitive adenylate cyclase; PDBTitle: crystal structure of anthrax edema factor (ef) truncation2 mutant, ef-delta 64 in complex with calmodulin 25 d2hqya1 not modelled 9.6 38 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:FemXAB nonribosomal peptidyltransferases 26 d1regx_ not modelled 9.0 57 Fold:Ferredoxin-like Superfamily:Translational regulator protein regA Family:Translational regulator protein regA 27 c3gr1A_ not modelled 8.6 18 PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) 28 d1khda1 not modelled 8.1 20 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 29 c2zooA_ not modelled 7.7 38 PDB header:oxidoreductase Chain: A: PDB Molecule:probable nitrite reductase; PDBTitle: crystal structure of nitrite reductase from pseudoalteromonas2 haloplanktis tac125 30 c3s83A_ not modelled 7.1 16 PDB header:signaling protein Chain: A: PDB Molecule:ggdef family protein; PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15 31 c2przB_ not modelled 7.0 24 PDB header:transferase Chain: B: PDB Molecule:orotate phosphoribosyltransferase 1; PDBTitle: s. cerevisiae orotate phosphoribosyltransferase complexed2 with omp 32 c3if8B_ not modelled 7.0 18 PDB header:cell cycle Chain: B: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex 33 c3k6zA_ not modelled 6.9 33 PDB header:hydrolase Chain: A: PDB Molecule:possible membrane-associated serine protease; PDBTitle: crystal structure of rv3671c protease, inactive form 34 d1lnsa1 not modelled 6.6 28 Fold:CH domain-like Superfamily:X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain Family:X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain 35 c2hwyB_ not modelled 6.5 30 PDB header:rna binding protein Chain: B: PDB Molecule:protein smg5; PDBTitle: structure of pin domain of human smg5. 36 d1kfta_ not modelled 6.0 22 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain 37 c1kftA_ not modelled 6.0 22 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 38 c3frwF_ not modelled 5.9 22 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 39 d1huua_ not modelled 5.7 10 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 40 d1xqoa_ not modelled 5.6 29 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:AgoG-like 41 d1w53a_ not modelled 5.4 26 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Phosphoserine phosphatase RsbU, N-terminal domain 42 c3nkeA_ not modelled 5.4 23 PDB header:immune system Chain: A: PDB Molecule:protein ygbt; PDBTitle: high resolution structure of the c-terminal domain crisp-associated2 protein cas1 from escherichia coli str. k-12

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