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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R

N

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Y

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F

A

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L

L

L

V

L

M

L

S

A

C

S

A

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Q

G

T

P

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P

A

P

P

V

T

D

H

P

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E

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R

R

D

Q

T

Q

G

L

Q

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I

G

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V

S

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

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100

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Sequence

T

M

V

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G

S

P

D

D

A

L

A

E

I

K

A

K

A

V

A

A

K

A

D

Y

Y

V

V

V

M

V

D

E

T

I

V

T

G

Q

W

Y

S

Q

A

I

L

Y

R

K

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 2noc chain A domain 1 Region: 20 - 109 Aligned: 80 Modelled: 90 Confidence: 99.9% Identity: 24% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2jna chain A domain 1 Region: 39 - 108 Aligned: 68 Modelled: 70 Confidence: 99.9% Identity: 22% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2k4q chain A Region: 36 - 89 Aligned: 54 Modelled: 54 Confidence: 66.1% Identity: 13% PDB header:viral protein Chain: A: PDB Molecule:major tail protein v; PDBTitle: the solution structure of gpv, the major tail protein from2 bacteriophage lambda Phyre2 PDB 3qkb chain B Region: 68 - 106 Aligned: 39 Modelled: 39 Confidence: 38.0% Identity: 26% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution Phyre2 PDB 3b9n chain B Region: 65 - 89 Aligned: 25 Modelled: 25 Confidence: 30.6% Identity: 24% PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) Phyre2 PDB 1hl8 chain B Region: 72 - 95 Aligned: 24 Modelled: 24 Confidence: 27.8% Identity: 17% PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase Phyre2 PDB 2pxg chain A Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 20.9% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein; PDBTitle: nmr solution structure of omla Phyre2 PDB 3eyp chain B Region: 72 - 95 Aligned: 24 Modelled: 24 Confidence: 20.8% Identity: 8% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron Phyre2 PDB 3mo4 chain B Region: 72 - 95 Aligned: 24 Modelled: 24 Confidence: 19.9% Identity: 8% PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 Phyre2 PDB 3ls1 chain A Region: 29 - 49 Aligned: 21 Modelled: 21 Confidence: 17.7% Identity: 33% PDB header:photosynthesis Chain: A: PDB Molecule:sll1638 protein; PDBTitle: crystal structure of cyanobacterial psbq from synechocystis2 sp. pcc 6803 complexed with zn2+ Phyre2 PDB 3sdo chain B Region: 65 - 88 Aligned: 24 Modelled: 24 Confidence: 17.5% Identity: 21% PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei Phyre2 PDB 1y2i chain C Region: 68 - 109 Aligned: 42 Modelled: 42 Confidence: 16.6% Identity: 26% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein s0862; PDBTitle: crystal structure of mcsg target apc27401 from shigella2 flexneri Phyre2 PDB 1y2i chain A Region: 68 - 109 Aligned: 42 Modelled: 42 Confidence: 16.6% Identity: 26% Fold: Dodecin subunit-like Superfamily: YbjQ-like Family: YbjQ-like Phyre2 PDB 2jpw chain A Region: 24 - 38 Aligned: 15 Modelled: 15 Confidence: 16.1% Identity: 47% PDB header:contractile protein Chain: A: PDB Molecule:troponin i, cardiac muscle; PDBTitle: solution structure of the bisphosphorylated cardiac2 specific n-extension of cardiac troponin i Phyre2 PDB 1hl9 chain A domain 2 Region: 72 - 95 Aligned: 24 Modelled: 24 Confidence: 14.7% Identity: 17% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Putative alpha-L-fucosidase, catalytic domain Phyre2 PDB 1luc chain A Region: 65 - 88 Aligned: 24 Modelled: 24 Confidence: 14.0% Identity: 25% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 2wvs chain D Region: 72 - 95 Aligned: 24 Modelled: 24 Confidence: 13.4% Identity: 8% PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant Phyre2 PDB 1luc chain B Region: 65 - 88 Aligned: 24 Modelled: 24 Confidence: 13.2% Identity: 8% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 1nh2 chain A domain 2 Region: 57 - 76 Aligned: 20 Modelled: 20 Confidence: 11.4% Identity: 10% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1cdw chain A domain 2 Region: 57 - 76 Aligned: 20 Modelled: 20 Confidence: 10.9% Identity: 10% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 1 d2noca1 2 d2jnaa1 3 c2k4qA_ 4 c3qkbB_ 5 c3b9nB_ 6 c1hl8B_ 7 c2pxgA_ 8 c3eypB_ 9 c3mo4B_ 10 c3ls1A_ 11 c3sdoB_ 12 c1y2iC_ 13 d1y2ia_ 14 c2jpwA_ 15 d1hl9a2 16 d1luca_ 17 c2wvsD_ 18 d1lucb_ 19 d1nh2a2 20 d1cdwa2 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

Detailed template information

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

1 d2noca1 99.9 24 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 2 d2jnaa1 99.9 22 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 3 c2k4qA_ 66.1 13 PDB header:viral protein Chain: A: PDB Molecule:major tail protein v; PDBTitle: the solution structure of gpv, the major tail protein from2 bacteriophage lambda 4 c3qkbB_ 38.0 26 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution 5 c3b9nB_ 30.6 24 PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) 6 c1hl8B_ 27.8 17 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase 7 c2pxgA_ 20.9 16 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein; PDBTitle: nmr solution structure of omla 8 c3eypB_ 20.8 8 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron 9 c3mo4B_ 19.9 8 PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 10 c3ls1A_ 17.7 33 PDB header:photosynthesis Chain: A: PDB Molecule:sll1638 protein; PDBTitle: crystal structure of cyanobacterial psbq from synechocystis2 sp. pcc 6803 complexed with zn2+ 11 c3sdoB_ 17.5 21 PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei 12 c1y2iC_ 16.6 26 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:hypothetical protein s0862; PDBTitle: crystal structure of mcsg target apc27401 from shigella2 flexneri 13 d1y2ia_ 16.6 26 Fold:Dodecin subunit-like Superfamily:YbjQ-like Family:YbjQ-like 14 c2jpwA_ 16.1 47 PDB header:contractile protein Chain: A: PDB Molecule:troponin i, cardiac muscle; PDBTitle: solution structure of the bisphosphorylated cardiac2 specific n-extension of cardiac troponin i 15 d1hl9a2 14.7 17 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Putative alpha-L-fucosidase, catalytic domain 16 d1luca_ 14.0 25 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 17 c2wvsD_ 13.4 8 PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant 18 d1lucb_ 13.2 8 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 19 d1nh2a2 11.4 10 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 20 d1cdwa2 10.9 10 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 21 d2g39a1 not modelled 10.7 13 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:CoA transferase alpha subunit-like 22 c1z69D_ not modelled 9.9 30 PDB header:oxidoreductase Chain: D: PDB Molecule:coenzyme f420-dependent n(5),n(10)- PDBTitle: crystal structure of methylenetetrahydromethanopterin2 reductase (mer) in complex with coenzyme f420 23 d1qnaa2 not modelled 9.2 10 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 24 c3eikB_ not modelled 9.1 15 PDB header:transcription Chain: B: PDB Molecule:tata-box-binding protein; PDBTitle: double stranded dna binding protein 25 d1mp9a1 not modelled 8.9 20 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 26 c3gzaB_ not modelled 8.6 25 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase (np_812709.1) from2 bacteroides thetaiotaomicron vpi-5482 at 1.60 a resolution 27 d1mp9a2 not modelled 8.5 15 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 28 d1aisa2 not modelled 8.5 20 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 29 d1f07a_ not modelled 8.4 28 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:F420 dependent oxidoreductases 30 c3ir9A_ not modelled 8.3 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:peptide chain release factor subunit 1; PDBTitle: c-terminal domain of peptide chain release factor from2 methanosarcina mazei. 31 d2bsqe1 not modelled 8.2 30 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Trafficking protein A-like 32 c1d3uA_ not modelled 8.0 20 PDB header:gene regulation/dna Chain: A: PDB Molecule:tata-binding protein; PDBTitle: tata-binding protein/transcription factor (ii)b/bre+tata-2 box complex from pyrococcus woesei 33 c2jz7A_ not modelled 7.9 19 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 34 c1kqfB_ not modelled 7.9 21 PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli 35 c1mp9B_ not modelled 7.7 15 PDB header:dna binding protein Chain: B: PDB Molecule:tata-binding protein; PDBTitle: tbp from a mesothermophilic archaeon, sulfolobus2 acidocaldarius 36 d2hqsa2 not modelled 7.4 19 Fold:Anticodon-binding domain-like Superfamily:TolB, N-terminal domain Family:TolB, N-terminal domain 37 c1rm1A_ not modelled 7.0 10 PDB header:transcription/dna Chain: A: PDB Molecule:tata-box binding protein; PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex 38 c1ngmM_ not modelled 7.0 10 PDB header:transcription/dna Chain: M: PDB Molecule:transcription initiation factor tfiid; PDBTitle: crystal structure of a yeast brf1-tbp-dna ternary complex 39 d3etja1 not modelled 7.0 13 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 40 c2amlB_ not modelled 7.0 11 PDB header:transferase Chain: B: PDB Molecule:sis domain protein; PDBTitle: crystal structure of lmo0035 protein (46906266) from listeria2 monocytogenes 4b f2365 at 1.50 a resolution 41 c2z8uQ_ not modelled 6.9 30 PDB header:transcription Chain: Q: PDB Molecule:tata-box-binding protein; PDBTitle: methanococcus jannaschii tbp 42 c2i7gA_ not modelled 6.9 21 PDB header:oxidoreductase Chain: A: PDB Molecule:monooxygenase; PDBTitle: crystal structure of monooxygenase from agrobacterium tumefaciens 43 c3dnfB_ not modelled 6.8 18 PDB header:oxidoreductase Chain: B: PDB Molecule:4-hydroxy-3-methylbut-2-enyl diphosphate reductase; PDBTitle: structure of (e)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase,2 the terminal enzyme of the non-mevalonate pathway 44 d1vjpa1 not modelled 6.5 15 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 45 d2qrra1 not modelled 6.4 22 Fold:Ferredoxin-like Superfamily:ACT-like Family:NIL domain-like 46 c1tvlA_ not modelled 6.4 29 PDB header:oxidoreductase Chain: A: PDB Molecule:protein ytnj; PDBTitle: structure of ytnj from bacillus subtilis 47 d1tvla_ not modelled 6.4 29 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 48 c1f02T_ not modelled 6.2 33 PDB header:cell adhesion Chain: T: PDB Molecule:translocated intimin receptor; PDBTitle: crystal structure of c-terminal 282-residue fragment of2 intimin in complex with translocated intimin receptor3 (tir) intimin-binding domain 49 c3hajA_ not modelled 6.1 8 PDB header:endocytosis Chain: A: PDB Molecule:human pacsin2 f-bar; PDBTitle: crystal structure of human pacsin2 f-bar domain (p2121212 lattice) 50 d1ycga1 not modelled 6.1 11 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Flavodoxin-related 51 d1zjca1 not modelled 6.1 19 Fold:Thermophilic metalloprotease-like Superfamily:Thermophilic metalloprotease-like Family:Thermophilic metalloprotease (M29) 52 c2k38A_ not modelled 6.0 19 PDB header:antimicrobial protein Chain: A: PDB Molecule:cupiennin-1a; PDBTitle: cupiennin 1a, nmr, minimized average structure 53 c1k4uP_ not modelled 6.0 40 PDB header:hormone/growth factor Chain: P: PDB Molecule:phagocyte nadph oxidase subunit p47phox; PDBTitle: solution structure of the c-terminal sh3 domain of p67phox2 complexed with the c-terminal tail region of p47phox 54 c3euaD_ not modelled 5.9 11 PDB header:isomerase Chain: D: PDB Molecule:putative fructose-aminoacid-6-phosphate deglycase; PDBTitle: crystal structure of a putative phosphosugar isomerase (bsu32610) from2 bacillus subtilis at 1.90 a resolution 55 d1nqka_ not modelled 5.8 30 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 56 d2bbaa1 not modelled 5.7 16 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Ephrin receptor ligand binding domain 57 d1wu7a1 not modelled 5.5 28 Fold:Anticodon-binding domain-like Superfamily:Class II aaRS ABD-related Family:Anticodon-binding domain of Class II aaRS 58 c3fkjA_ not modelled 5.4 14 PDB header:isomerase Chain: A: PDB Molecule:putative phosphosugar isomerases; PDBTitle: crystal structure of a putative phosphosugar isomerase (stm_0572) from2 salmonella typhimurium lt2 at 2.12 a resolution 59 c3mi6A_ not modelled 5.2 19 PDB header:hydrolase Chain: A: PDB Molecule:alpha-galactosidase; PDBTitle: crystal structure of the alpha-galactosidase from lactobacillus2 brevis, northeast structural genomics consortium target lbr11. 60 d1nh2a1 not modelled 5.1 22 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 61 d2ayia1 not modelled 5.1 18 Fold:Thermophilic metalloprotease-like Superfamily:Thermophilic metalloprotease-like Family:Thermophilic metalloprotease (M29) 62 c3dfeA_ not modelled 5.1 28 PDB header:signaling protein Chain: A: PDB Molecule:putative pii-like signaling protein; PDBTitle: crystal structure of a putative pii-like signaling protein2 (yp_323533.1) from anabaena variabilis atcc 29413 at 2.35 a3 resolution

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