Secondary structure and disorder prediction

1

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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

Q

T

K

K

N

E

I

W

V

G

I

F

L

L

A

A

L

L

A

A

L

F

V

C

L

K

A

A

N

V

T

S

I

R

T

E

P

T

Y

T

L

Y

A

T

F

D

N

I

G

G

L

K

A

R

S

P

V

S

I

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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110

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120

Sequence

G

G

V

V

V

G

R

V

A

D

I

T

L

D

P

K

T

Y

L

P

R

V

T

L

E

I

E

Q

R

Y

N

H

I

P

D

T

S

S

L

S

I

R

T

S

G

L

L

G

E

Q

Y

L

A

L

N

V

G

F

E

D

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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140

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150

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160

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170

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180

Sequence

P

E

L

G

T

A

I

L

K

D

G

D

T

I

Q

D

T

K

S

A

M

V

L

E

D

L

I

G

Q

F

L

Y

G

S

K

G

D

D

N

K

N

S

G

D

A

P

A

A

A

P

G

N

N

E

T

T

E

P

V

G

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

T

T

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 1v5v chain A domain 1 Region: 41 - 101 Aligned: 61 Modelled: 61 Confidence: 64.8% Identity: 16% Fold: Elongation factor/aminomethyltransferase common domain Superfamily: Aminomethyltransferase beta-barrel domain Family: Aminomethyltransferase beta-barrel domain Phyre2 PDB 2j5u chain B Region: 61 - 93 Aligned: 33 Modelled: 33 Confidence: 63.6% Identity: 9% PDB header:cell shape regulation Chain: B: PDB Molecule:mrec protein; PDBTitle: mrec lysteria monocytogenes Phyre2 PDB 1v5v chain A Region: 38 - 105 Aligned: 66 Modelled: 68 Confidence: 40.2% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of a component of glycine cleavage system: t-protein2 from pyrococcus horikoshii ot3 at 1.5 a resolution Phyre2 PDB 2qf4 chain A Region: 41 - 108 Aligned: 63 Modelled: 68 Confidence: 32.2% Identity: 14% PDB header:structural protein Chain: A: PDB Molecule:cell shape determining protein mrec; PDBTitle: high resolution structure of the major periplasmic domain from the2 cell shape-determining filament mrec (orthorhombic form) Phyre2 PDB 1pj5 chain A domain 1 Region: 42 - 101 Aligned: 59 Modelled: 60 Confidence: 15.2% Identity: 17% Fold: Elongation factor/aminomethyltransferase common domain Superfamily: Aminomethyltransferase beta-barrel domain Family: Aminomethyltransferase beta-barrel domain Phyre2 PDB 1wos chain A domain 1 Region: 41 - 105 Aligned: 63 Modelled: 65 Confidence: 13.9% Identity: 10% Fold: Elongation factor/aminomethyltransferase common domain Superfamily: Aminomethyltransferase beta-barrel domain Family: Aminomethyltransferase beta-barrel domain Phyre2 PDB 1yx2 chain B Region: 36 - 101 Aligned: 66 Modelled: 66 Confidence: 12.9% Identity: 17% PDB header:transferase Chain: B: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of the probable aminomethyltransferase2 from bacillus subtilis Phyre2 PDB 1cz5 chain A Region: 51 - 116 Aligned: 65 Modelled: 66 Confidence: 11.0% Identity: 11% PDB header:hydrolase Chain: A: PDB Molecule:vcp-like atpase; PDBTitle: nmr structure of vat-n: the n-terminal domain of vat (vcp-2 like atpase of thermoplasma) Phyre2 PDB 2k6z chain A Region: 25 - 61 Aligned: 37 Modelled: 37 Confidence: 10.5% Identity: 16% PDB header:metal transport Chain: A: PDB Molecule:putative uncharacterized protein ttha1943; PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14) Phyre2 PDB 1h9r chain A domain 2 Region: 66 - 108 Aligned: 36 Modelled: 43 Confidence: 9.2% Identity: 8% Fold: OB-fold Superfamily: MOP-like Family: BiMOP, duplicated molybdate-binding domain Phyre2 PDB 1x9l chain A Region: 25 - 59 Aligned: 35 Modelled: 35 Confidence: 8.1% Identity: 9% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: DR1885-like metal-binding protein Family: DR1885-like metal-binding protein Phyre2 PDB 3htr chain B Region: 54 - 81 Aligned: 28 Modelled: 28 Confidence: 7.9% Identity: 11% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein; PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris Phyre2 PDB 1t5e chain B Region: 35 - 61 Aligned: 27 Modelled: 27 Confidence: 7.8% Identity: 22% PDB header:transport protein Chain: B: PDB Molecule:multidrug resistance protein mexa; PDBTitle: the structure of mexa Phyre2 PDB 1nnx chain A Region: 48 - 102 Aligned: 55 Modelled: 55 Confidence: 7.5% Identity: 16% Fold: OB-fold Superfamily: Hypothetical protein YgiW Family: Hypothetical protein YgiW Phyre2 PDB 1vf7 chain A Region: 35 - 61 Aligned: 27 Modelled: 27 Confidence: 7.3% Identity: 22% Fold: HlyD-like secretion proteins Superfamily: HlyD-like secretion proteins Family: HlyD-like secretion proteins Phyre2 PDB 2cp6 chain A domain 1 Region: 50 - 90 Aligned: 41 Modelled: 41 Confidence: 6.9% Identity: 20% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 1gtr chain A domain 1 Region: 41 - 89 Aligned: 49 Modelled: 49 Confidence: 6.8% Identity: 8% Fold: Ribosomal protein L25-like Superfamily: Ribosomal protein L25-like Family: Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain Phyre2 PDB 2vv5 chain A domain 1 Region: 52 - 73 Aligned: 21 Modelled: 22 Confidence: 6.5% Identity: 33% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Mechanosensitive channel protein MscS (YggB), middle domain Phyre2 1 d1v5va1 2 c2j5uB_ 3 c1v5vA_ 4 c2qf4A_ 5 d1pj5a1 6 d1wosa1 7 c1yx2B_ 8 c1cz5A_ 9 c2k6zA_ 10 d1h9ra2 11 d1x9la_ 12 c3htrB_ 13 c1t5eB_ 14 d1nnxa_ 15 d1vf7a_ 16 d2cp6a1 17 d1gtra1 18 d2vv5a1

Detailed template information

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

1 d1v5va1 64.8 16 Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain 2 c2j5uB_ 63.6 9 PDB header:cell shape regulation Chain: B: PDB Molecule:mrec protein; PDBTitle: mrec lysteria monocytogenes 3 c1v5vA_ 40.2 15 PDB header:transferase Chain: A: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of a component of glycine cleavage system: t-protein2 from pyrococcus horikoshii ot3 at 1.5 a resolution 4 c2qf4A_ 32.2 14 PDB header:structural protein Chain: A: PDB Molecule:cell shape determining protein mrec; PDBTitle: high resolution structure of the major periplasmic domain from the2 cell shape-determining filament mrec (orthorhombic form) 5 d1pj5a1 15.2 17 Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain 6 d1wosa1 13.9 10 Fold:Elongation factor/aminomethyltransferase common domain Superfamily:Aminomethyltransferase beta-barrel domain Family:Aminomethyltransferase beta-barrel domain 7 c1yx2B_ 12.9 17 PDB header:transferase Chain: B: PDB Molecule:aminomethyltransferase; PDBTitle: crystal structure of the probable aminomethyltransferase2 from bacillus subtilis 8 c1cz5A_ 11.0 11 PDB header:hydrolase Chain: A: PDB Molecule:vcp-like atpase; PDBTitle: nmr structure of vat-n: the n-terminal domain of vat (vcp-2 like atpase of thermoplasma) 9 c2k6zA_ 10.5 16 PDB header:metal transport Chain: A: PDB Molecule:putative uncharacterized protein ttha1943; PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14) 10 d1h9ra2 9.2 8 Fold:OB-fold Superfamily:MOP-like Family:BiMOP, duplicated molybdate-binding domain 11 d1x9la_ 8.1 9 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:DR1885-like metal-binding protein Family:DR1885-like metal-binding protein 12 c3htrB_ 7.9 11 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein; PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris 13 c1t5eB_ 7.8 22 PDB header:transport protein Chain: B: PDB Molecule:multidrug resistance protein mexa; PDBTitle: the structure of mexa 14 d1nnxa_ 7.5 16 Fold:OB-fold Superfamily:Hypothetical protein YgiW Family:Hypothetical protein YgiW 15 d1vf7a_ 7.3 22 Fold:HlyD-like secretion proteins Superfamily:HlyD-like secretion proteins Family:HlyD-like secretion proteins 16 d2cp6a1 6.9 20 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 17 d1gtra1 6.8 8 Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain 18 d2vv5a1 6.5 33 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Mechanosensitive channel protein MscS (YggB), middle domain

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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