Secondary structure and disorder prediction

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10

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20

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30

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40

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50

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60

Sequence

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K

N

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A

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S

F

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K

A

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S

E

L

E

Q

I

V

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G

D

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L

E

E

A

L

N

E

F

E

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G

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G

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Q

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Q

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V

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

Sequence

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D

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D

A

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Secondary structure

SS confidence

Disorder

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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 1vp7 chain B Region: 2 - 78 Aligned: 76 Modelled: 77 Confidence: 99.8% Identity: 43% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain A Region: 5 - 70 Aligned: 66 Modelled: 66 Confidence: 99.8% Identity: 47% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain D Region: 8 - 78 Aligned: 64 Modelled: 71 Confidence: 99.7% Identity: 50% PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution Phyre2 PDB 3he4 chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 75.7% Identity: 30% PDB header:de novo protein Chain: A: PDB Molecule:synzip6; PDBTitle: heterospecific coiled-coil pair synzip5:synzip6 Phyre2 PDB 1ic2 chain B Region: 12 - 59 Aligned: 45 Modelled: 48 Confidence: 32.7% Identity: 22% PDB header:contractile protein Chain: B: PDB Molecule:tropomyosin alpha chain, skeletal muscle; PDBTitle: deciphering the design of the tropomyosin molecule Phyre2 PDB 3hxx chain A Region: 10 - 40 Aligned: 31 Modelled: 31 Confidence: 30.1% Identity: 23% PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp Phyre2 PDB 2y0s chain Q Region: 13 - 41 Aligned: 29 Modelled: 29 Confidence: 29.8% Identity: 28% PDB header:transferase Chain: Q: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group Phyre2 PDB 2y0s chain J Region: 13 - 41 Aligned: 29 Modelled: 29 Confidence: 29.8% Identity: 28% PDB header:transferase Chain: J: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group Phyre2 PDB 2o3l chain A domain 1 Region: 1 - 60 Aligned: 60 Modelled: 59 Confidence: 25.8% Identity: 18% Fold: Left-handed superhelix Superfamily: BH3980-like Family: BH3980-like Phyre2 PDB 3hkz chain Y Region: 13 - 41 Aligned: 29 Modelled: 29 Confidence: 23.4% Identity: 34% PDB header:transferase Chain: Y: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea Phyre2 PDB 3u1a chain C Region: 12 - 61 Aligned: 47 Modelled: 47 Confidence: 21.0% Identity: 19% PDB header:contractile protein Chain: C: PDB Molecule:smooth muscle tropomyosin alpha; PDBTitle: n-terminal 81-aa fragment of smooth muscle tropomyosin alpha Phyre2 PDB 2wb1 chain Q Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 19.5% Identity: 32% PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 3k2t chain A Region: 3 - 21 Aligned: 19 Modelled: 19 Confidence: 19.2% Identity: 16% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lmo2511 protein; PDBTitle: crystal structure of lmo2511 protein from listeria2 monocytogenes, northeast structural genomics consortium3 target lkr84a Phyre2 PDB 3hkz chain Z Region: 13 - 41 Aligned: 29 Modelled: 29 Confidence: 19.1% Identity: 34% PDB header:transferase Chain: Z: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea Phyre2 PDB 2wb1 chain J Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 18.8% Identity: 32% 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 Phyre2 PDB 2jzv chain A Region: 2 - 39 Aligned: 38 Modelled: 38 Confidence: 18.0% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:foldase protein prsa; PDBTitle: solution structure of s. aureus prsa-ppiase Phyre2 PDB 1wty chain A Region: 10 - 46 Aligned: 36 Modelled: 37 Confidence: 17.8% Identity: 25% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 3ctw chain B Region: 37 - 59 Aligned: 23 Modelled: 23 Confidence: 17.3% Identity: 35% PDB header:protein binding Chain: B: PDB Molecule:rcda; PDBTitle: crystal structure of rcda from caulobacter crescentus cb15 Phyre2 PDB 1pin chain A domain 2 Region: 3 - 39 Aligned: 37 Modelled: 37 Confidence: 16.8% Identity: 19% Fold: FKBP-like Superfamily: FKBP-like Family: FKBP immunophilin/proline isomerase Phyre2 PDB 2waq chain Q Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 16.6% Identity: 32% PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 1 d1vp7b_ 2 d1vp7a_ 3 c1vp7D_ 4 c3he4A_ 5 c1ic2B_ 6 c3hxxA_ 7 c2y0sQ_ 8 c2y0sJ_ 9 d2o3la1 10 c3hkzY_ 11 c3u1aC_ 12 c2wb1Q_ 13 c3k2tA_ 14 c3hkzZ_ 15 c2wb1J_ 16 c2jzvA_ 17 d1wtya_ 18 c3ctwB_ 19 d1pina2 20 c2waqQ_ 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

Detailed template information

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

1 d1vp7b_ 99.8 43 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 2 d1vp7a_ 99.8 47 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 3 c1vp7D_ 99.7 50 PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution 4 c3he4A_ 75.7 30 PDB header:de novo protein Chain: A: PDB Molecule:synzip6; PDBTitle: heterospecific coiled-coil pair synzip5:synzip6 5 c1ic2B_ 32.7 22 PDB header:contractile protein Chain: B: PDB Molecule:tropomyosin alpha chain, skeletal muscle; PDBTitle: deciphering the design of the tropomyosin molecule 6 c3hxxA_ 30.1 23 PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp 7 c2y0sQ_ 29.8 28 PDB header:transferase Chain: Q: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group 8 c2y0sJ_ 29.8 28 PDB header:transferase Chain: J: PDB Molecule:rna polymerase subunit 13; PDBTitle: crystal structure of sulfolobus shibatae rna polymerase in2 p21 space group 9 d2o3la1 25.8 18 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like 10 c3hkzY_ 23.4 34 PDB header:transferase Chain: Y: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea 11 c3u1aC_ 21.0 19 PDB header:contractile protein Chain: C: PDB Molecule:smooth muscle tropomyosin alpha; PDBTitle: n-terminal 81-aa fragment of smooth muscle tropomyosin alpha 12 c2wb1Q_ 19.5 32 PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 13 c3k2tA_ 19.2 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lmo2511 protein; PDBTitle: crystal structure of lmo2511 protein from listeria2 monocytogenes, northeast structural genomics consortium3 target lkr84a 14 c3hkzZ_ 19.1 34 PDB header:transferase Chain: Z: PDB Molecule:dna-directed rna polymerase subunit 13; PDBTitle: the x-ray crystal structure of rna polymerase from archaea 15 c2wb1J_ 18.8 32 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 16 c2jzvA_ 18.0 13 PDB header:isomerase Chain: A: PDB Molecule:foldase protein prsa; PDBTitle: solution structure of s. aureus prsa-ppiase 17 d1wtya_ 17.8 25 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 18 c3ctwB_ 17.3 35 PDB header:protein binding Chain: B: PDB Molecule:rcda; PDBTitle: crystal structure of rcda from caulobacter crescentus cb15 19 d1pina2 16.8 19 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 20 c2waqQ_ 16.6 32 PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 21 c3iv1F_ not modelled 16.4 22 PDB header:hydrolase Chain: F: PDB Molecule:tumor susceptibility gene 101 protein; PDBTitle: coiled-coil domain of tumor susceptibility gene 101 22 c3pu2G_ not modelled 16.1 29 PDB header:structure genomics, unknown function Chain: G: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the q3j4m4_rhos4 protein from rhodobacter2 sphaeroides. northeast structural genomics consortium target rhr263. 23 c2dl1A_ not modelled 13.1 25 PDB header:protein transport Chain: A: PDB Molecule:spartin; PDBTitle: solution structure of the mit domain from human spartin 24 c2v6xA_ not modelled 12.6 11 PDB header:protein transport Chain: A: PDB Molecule:vacuolar protein sorting-associated protein 4; PDBTitle: stractural insight into the interaction between escrt-iii2 and vps4 25 c2xa6B_ not modelled 12.4 25 PDB header:transcription Chain: B: PDB Molecule:kh domain-containing\,rna-binding\,signal PDBTitle: structural basis for homodimerization of the src-associated2 during mitosis, 68 kd protein (sam68) qua1 domain 26 c2krxA_ not modelled 12.0 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:asl3597 protein; PDBTitle: solution nmr structure of asl3597 from nostoc sp. pcc7120. northeast2 structural genomics consortium target id nsr244. 27 c2ehwD_ not modelled 11.7 33 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein tthb059; PDBTitle: conserved hypothetical proteim (tthb059) from thermo thermophilus hb8 28 d2jq9a1 not modelled 10.7 18 Fold:Spectrin repeat-like Superfamily:MIT domain Family:MIT domain 29 c3l32B_ not modelled 10.7 50 PDB header:viral protein Chain: B: PDB Molecule:phosphoprotein; PDBTitle: structure of the dimerisation domain of the rabies virus2 phosphoprotein 30 c1u2uA_ not modelled 10.3 31 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: nmr solution structure of a designed heterodimeric leucine2 zipper 31 c1eqfA_ not modelled 10.3 10 PDB header:transcription Chain: A: PDB Molecule:rna polymerase ii transcription initiation PDBTitle: crystal structure of the double bromodomain module from2 human tafii250 32 c2r5xA_ not modelled 10.1 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of uncharacterized conserved protein yugn from2 geobacillus kaustophilus hta426 33 d1x79a_ not modelled 9.8 20 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 34 c1yfsB_ not modelled 9.5 6 PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine 35 d1pgya_ not modelled 9.4 41 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 36 c1f8aB_ not modelled 9.2 19 PDB header:isomerase Chain: B: PDB Molecule:peptidyl-prolyl cis-trans isomerase nima- PDBTitle: structural basis for the phosphoserine-proline recognition2 by group iv ww domains 37 d1riqa1 not modelled 9.0 13 Fold:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Superfamily:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) Family:Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 38 c2eqbC_ not modelled 8.1 15 PDB header:endocytosis/exocytosis Chain: C: PDB Molecule:rab guanine nucleotide exchange factor sec2; PDBTitle: crystal structure of the rab gtpase sec4p, the sec2p gef2 domain, and phosphate complex 39 c3cd0B_ not modelled 8.1 33 PDB header:oxidoreductase Chain: B: PDB Molecule:3-hydroxy-3-methylglutaryl-coenzyme a reductase; PDBTitle: thermodynamic and structure guided design of statin hmg-coa2 reductase inhibitors 40 d1dqaa4 not modelled 7.8 33 Fold:Substrate-binding domain of HMG-CoA reductase Superfamily:Substrate-binding domain of HMG-CoA reductase Family:Substrate-binding domain of HMG-CoA reductase 41 c3mstA_ not modelled 7.5 19 PDB header:transport protein Chain: A: PDB Molecule:putative nitrate transport protein; PDBTitle: crystal structure of a putative nitrate transport protein (tvn0104)2 from thermoplasma volcanium at 1.35 a resolution 42 c3o3xA_ not modelled 7.5 22 PDB header:viral protein Chain: A: PDB Molecule:gp41-5; PDBTitle: crystal structure of gp41-5, a single-chain 5-helix-bundle based on2 hiv gp41 43 c3epyA_ not modelled 7.4 10 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 7; PDBTitle: crystal structure of human acyl-coa binding domain 72 complexed with palmitoyl-coa 44 d1wr0a1 not modelled 7.2 21 Fold:Spectrin repeat-like Superfamily:MIT domain Family:MIT domain 45 c1ty4D_ not modelled 7.2 29 PDB header:apoptosis Chain: D: PDB Molecule:egg laying defective egl-1, programmed cell death PDBTitle: crystal structure of a ced-9/egl-1 complex 46 c3iabB_ not modelled 6.8 12 PDB header:hydrolase/rna Chain: B: PDB Molecule:ribonucleases p/mrp protein subunit pop7; PDBTitle: crystal structure of rnase p /rnase mrp proteins pop6, pop72 in a complex with the p3 domain of rnase mrp rna 47 c2xt6B_ not modelled 6.8 29 PDB header:lyase Chain: B: PDB Molecule:2-oxoglutarate decarboxylase; PDBTitle: crystal structure of mycobacterium smegmatis alpha-ketoglutarate2 decarboxylase homodimer (orthorhombic form) 48 d1orja_ not modelled 6.7 13 Fold:Four-helical up-and-down bundle Superfamily:Flagellar export chaperone FliS Family:Flagellar export chaperone FliS 49 d2cpta1 not modelled 6.5 25 Fold:Spectrin repeat-like Superfamily:MIT domain Family:MIT domain 50 d1j3ma_ not modelled 6.4 14 Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like 51 d2ftsa2 not modelled 6.4 15 Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like 52 c3ck4K_ not modelled 6.3 28 PDB header:protein binding Chain: K: PDB Molecule:gcn4 leucine zipper; PDBTitle: a heterospecific leucine zipper tetramer 53 d1m5ya3 not modelled 6.2 33 Fold:FKBP-like Superfamily:FKBP-like Family:FKBP immunophilin/proline isomerase 54 c2cxaA_ not modelled 5.4 35 PDB header:transferase Chain: A: PDB Molecule:leucyl/phenylalanyl-trna-protein transferase; PDBTitle: crystal structure of leucyl/phenylalanyl-trna protein2 transferase from escherichia coli 55 d2cxaa1 not modelled 5.4 35 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:LFTR-like 56 d1uz5a2 not modelled 5.4 25 Fold:MoeA N-terminal region -like Superfamily:MoeA N-terminal region -like Family:MoeA N-terminal region -like 57 d2hh6a1 not modelled 5.4 31 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like 58 c2qr4B_ not modelled 5.3 13 PDB header:hydrolase Chain: B: PDB Molecule:peptidase m3b, oligoendopeptidase f; PDBTitle: crystal structure of oligoendopeptidase-f from enterococcus faecium 59 c2gl2B_ not modelled 5.3 15 PDB header:cell adhesion Chain: B: PDB Molecule:adhesion a; PDBTitle: crystal structure of the tetra muntant (t66g,r67g,f68g,2 y69g) of bacterial adhesin fada 60 c1junB_ not modelled 5.3 23 PDB header:transcription regulation Chain: B: PDB Molecule:c-jun homodimer; PDBTitle: nmr study of c-jun homodimer

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