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

M

K

I

I

S

K

M

L

V

G

A

L

A

L

A

V

T

N

V

Y

A

A

E

L

M

T

K

A

E

F

E

K

V

E

S

Q

Y

E

K

I

G

D

I

S

T

S

N

E

M

S

T

A

D

A

K

E

D

L

I

K

Secondary structure

SS confidence

Disorder

?

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?

?

?

?

?

?

?

?

?

?

?

?

?

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?

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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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Sequence

K

A

D

E

K

G

A

D

V

L

V

L

T

S

G

Q

T

D

N

K

I

H

G

T

A

N

I

Y

K

K

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: 1 - 91 Aligned: 91 Modelled: 91 Confidence: 100.0% Identity: 73% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2jna chain A domain 1 Region: 1 - 90 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 25% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 3dfe chain A Region: 54 - 79 Aligned: 26 Modelled: 26 Confidence: 39.0% Identity: 19% 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 Phyre2 PDB 2k4q chain A Region: 36 - 78 Aligned: 43 Modelled: 43 Confidence: 37.8% Identity: 9% 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 3b9n chain B Region: 49 - 73 Aligned: 25 Modelled: 25 Confidence: 29.1% Identity: 16% PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) Phyre2 PDB 3lub chain E Region: 41 - 79 Aligned: 38 Modelled: 39 Confidence: 27.2% Identity: 24% PDB header:hydrolase Chain: E: PDB Molecule:putative creatinine amidohydrolase; PDBTitle: crystal structure of putative creatinine amidohydrolase2 (yp_211512.1) from bacteroides fragilis nctc 9343 at 2.11 a3 resolution Phyre2 PDB 3no4 chain A Region: 41 - 79 Aligned: 38 Modelled: 39 Confidence: 23.1% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:creatinine amidohydrolase; PDBTitle: crystal structure of a creatinine amidohydrolase (npun_f1913) from2 nostoc punctiforme pcc 73102 at 2.00 a resolution Phyre2 PDB 3rof chain A Region: 35 - 76 Aligned: 41 Modelled: 42 Confidence: 18.5% Identity: 10% PDB header:hydrolase Chain: A: PDB Molecule:low molecular weight protein-tyrosine-phosphatase ptpa; PDBTitle: crystal structure of the s. aureus protein tyrosine phosphatase ptpa Phyre2 PDB 1hl8 chain B Region: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 17.7% Identity: 17% PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase Phyre2 PDB 1v7z chain A Region: 41 - 79 Aligned: 38 Modelled: 39 Confidence: 16.9% Identity: 29% Fold: Creatininase Superfamily: Creatininase Family: Creatininase Phyre2 PDB 3sdo chain B Region: 49 - 72 Aligned: 24 Modelled: 24 Confidence: 14.9% Identity: 25% PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei Phyre2 PDB 2y1b chain A Region: 50 - 74 Aligned: 25 Modelled: 25 Confidence: 13.9% Identity: 24% PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf Phyre2 PDB 3etj chain A domain 1 Region: 38 - 69 Aligned: 31 Modelled: 32 Confidence: 12.8% Identity: 13% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: BC C-terminal domain-like Phyre2 PDB 3eyp chain B Region: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 12.1% Identity: 17% 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: 56 - 79 Aligned: 24 Modelled: 24 Confidence: 11.5% Identity: 17% 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 1luc chain A Region: 49 - 73 Aligned: 25 Modelled: 25 Confidence: 11.2% Identity: 12% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 2btv chain B Region: 17 - 88 Aligned: 71 Modelled: 72 Confidence: 10.8% Identity: 11% PDB header:virus Chain: B: PDB Molecule:protein (vp3 core protein); PDBTitle: atomic model for bluetongue virus (btv) core Phyre2 PDB 3qkb chain B Region: 52 - 69 Aligned: 18 Modelled: 18 Confidence: 10.6% Identity: 44% 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 1cdw chain A domain 2 Region: 41 - 60 Aligned: 20 Modelled: 20 Confidence: 10.4% Identity: 15% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1luc chain B Region: 49 - 73 Aligned: 25 Modelled: 25 Confidence: 10.0% Identity: 12% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 1 d2noca1 2 d2jnaa1 3 c3dfeA_ 4 c2k4qA_ 5 c3b9nB_ 6 c3lubE_ 7 c3no4A_ 8 c3rofA_ 9 c1hl8B_ 10 d1v7za_ 11 c3sdoB_ 12 c2y1bA_ 13 d3etja1 14 c3eypB_ 15 c3mo4B_ 16 d1luca_ 17 c2btvB_ 18 c3qkbB_ 19 d1cdwa2 20 d1lucb_ 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

Detailed template information

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

1 d2noca1 100.0 73 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 2 d2jnaa1 100.0 25 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 3 c3dfeA_ 39.0 19 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 4 c2k4qA_ 37.8 9 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 5 c3b9nB_ 29.1 16 PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) 6 c3lubE_ 27.2 24 PDB header:hydrolase Chain: E: PDB Molecule:putative creatinine amidohydrolase; PDBTitle: crystal structure of putative creatinine amidohydrolase2 (yp_211512.1) from bacteroides fragilis nctc 9343 at 2.11 a3 resolution 7 c3no4A_ 23.1 18 PDB header:hydrolase Chain: A: PDB Molecule:creatinine amidohydrolase; PDBTitle: crystal structure of a creatinine amidohydrolase (npun_f1913) from2 nostoc punctiforme pcc 73102 at 2.00 a resolution 8 c3rofA_ 18.5 10 PDB header:hydrolase Chain: A: PDB Molecule:low molecular weight protein-tyrosine-phosphatase ptpa; PDBTitle: crystal structure of the s. aureus protein tyrosine phosphatase ptpa 9 c1hl8B_ 17.7 17 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase 10 d1v7za_ 16.9 29 Fold:Creatininase Superfamily:Creatininase Family:Creatininase 11 c3sdoB_ 14.9 25 PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei 12 c2y1bA_ 13.9 24 PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf 13 d3etja1 12.8 13 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 14 c3eypB_ 12.1 17 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 15 c3mo4B_ 11.5 17 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 16 d1luca_ 11.2 12 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 17 c2btvB_ 10.8 11 PDB header:virus Chain: B: PDB Molecule:protein (vp3 core protein); PDBTitle: atomic model for bluetongue virus (btv) core 18 c3qkbB_ 10.6 44 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 19 d1cdwa2 10.4 15 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 20 d1lucb_ 10.0 12 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 21 d1mp9a2 not modelled 9.0 10 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 22 d1txka2 not modelled 8.9 14 Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:MdoG-like 23 d1hl9a2 not modelled 8.9 17 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Putative alpha-L-fucosidase, catalytic domain 24 c1txkA_ not modelled 8.6 14 PDB header:biosynthetic protein Chain: A: PDB Molecule:glucans biosynthesis protein g; PDBTitle: crystal structure of escherichia coli opgg 25 d1f07a_ not modelled 8.4 10 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:F420 dependent oxidoreductases 26 c3eikB_ not modelled 8.4 15 PDB header:transcription Chain: B: PDB Molecule:tata-box-binding protein; PDBTitle: double stranded dna binding protein 27 d1mp9a1 not modelled 8.1 15 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 28 c2gi4A_ not modelled 7.9 18 PDB header:hydrolase Chain: A: PDB Molecule:possible phosphotyrosine protein phosphatase; PDBTitle: solution structure of the low molecular weight protein2 tyrosine phosphatase from campylobacter jejuni. 29 c2jz7A_ not modelled 7.9 29 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 30 d1nh2a2 not modelled 7.7 9 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 31 c2wvsD_ not modelled 7.4 21 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 32 c1f02T_ not modelled 7.4 23 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 33 c1mp9B_ not modelled 7.1 10 PDB header:dna binding protein Chain: B: PDB Molecule:tata-binding protein; PDBTitle: tbp from a mesothermophilic archaeon, sulfolobus2 acidocaldarius 34 d1tqxa_ not modelled 7.0 21 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:D-ribulose-5-phosphate 3-epimerase 35 d1qnaa2 not modelled 6.9 9 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 36 c1d3uA_ not modelled 6.9 45 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 37 c2z8uQ_ not modelled 6.9 35 PDB header:transcription Chain: Q: PDB Molecule:tata-box-binding protein; PDBTitle: methanococcus jannaschii tbp 38 c2zfdB_ not modelled 6.8 10 PDB header:signaling protein/transferase Chain: B: PDB Molecule:putative uncharacterized protein t20l15_90; PDBTitle: the crystal structure of plant specific calcium binding protein atcbl22 in complex with the regulatory domain of atcipk14 39 c3mp6A_ not modelled 6.6 13 PDB header:histone binding protein Chain: A: PDB Molecule:maltose-binding periplasmic protein, linker, saga- PDBTitle: complex structure of sgf29 and dimethylated h3k4 40 c3cbnA_ not modelled 6.6 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved protein mth639; PDBTitle: crystal structure of a conserved protein (mth639) from2 methanobacterium thermoautotrophicum 41 c3ir9A_ not modelled 6.6 23 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. 42 c1ngmM_ not modelled 6.5 10 PDB header:transcription/dna Chain: M: PDB Molecule:transcription initiation factor tfiid; PDBTitle: crystal structure of a yeast brf1-tbp-dna ternary complex 43 c1rm1A_ not modelled 6.5 10 PDB header:transcription/dna Chain: A: PDB Molecule:tata-box binding protein; PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex 44 d1aisa2 not modelled 6.3 39 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 45 d1nh2a1 not modelled 6.0 26 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 46 c1z69D_ not modelled 5.7 13 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 47 d1aisa1 not modelled 5.6 22 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 48 d1nqka_ not modelled 5.6 22 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 49 d2p1ra1 not modelled 5.6 22 Fold:NAD kinase/diacylglycerol kinase-like Superfamily:NAD kinase/diacylglycerol kinase-like Family:Diacylglycerol kinase-like 50 c3e15D_ not modelled 5.5 18 PDB header:hydrolase Chain: D: PDB Molecule:glucose-6-phosphate 1-dehydrogenase; PDBTitle: 6-phosphogluconolactonase from plasmodium vivax 51 d1zjca1 not modelled 5.2 11 Fold:Thermophilic metalloprotease-like Superfamily:Thermophilic metalloprotease-like Family:Thermophilic metalloprotease (M29) 52 d1fe0a_ not modelled 5.2 20 Fold:Ferredoxin-like Superfamily:HMA, heavy metal-associated domain Family:HMA, heavy metal-associated domain 53 c3ne8A_ not modelled 5.2 17 PDB header:hydrolase Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase; PDBTitle: the crystal structure of a domain from n-acetylmuramoyl-l-alanine2 amidase of bartonella henselae str. houston-1

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