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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V

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A

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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

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N

F

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A

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A

M

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D

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N

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A

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N

G

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V

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

A

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N

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A

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M

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G

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G

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N

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

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200

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210

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220

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230

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240

Sequence

V

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Y

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Secondary structure

SS confidence

Disorder

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Disorder confidence

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250

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260

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270

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Sequence

F

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D

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Secondary structure

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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 2hqs chain A domain 2 Region: 47 - 193 Aligned: 101 Modelled: 101 Confidence: 98.3% Identity: 21% Fold: Anticodon-binding domain-like Superfamily: TolB, N-terminal domain Family: TolB, N-terminal domain Phyre2 PDB 2iqi chain A domain 1 Region: 56 - 196 Aligned: 94 Modelled: 94 Confidence: 96.4% Identity: 15% Fold: Anticodon-binding domain-like Superfamily: XCC0632-like Family: XCC0632-like Phyre2 PDB 3ly8 chain A Region: 60 - 192 Aligned: 89 Modelled: 93 Confidence: 87.5% Identity: 13% PDB header:signaling protein Chain: A: PDB Molecule:transcriptional activator cadc; PDBTitle: crystal structure of mutant d471e of the periplasmic domain of cadc Phyre2 PDB 1wue chain A domain 2 Region: 230 - 257 Aligned: 28 Modelled: 28 Confidence: 41.0% Identity: 18% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 2w8b chain B Region: 48 - 193 Aligned: 100 Modelled: 100 Confidence: 32.6% Identity: 20% PDB header:protein transport/membrane protein Chain: B: PDB Molecule:protein tolb; PDBTitle: crystal structure of processed tolb in complex with pal Phyre2 PDB 2czr chain A domain 1 Region: 90 - 138 Aligned: 40 Modelled: 49 Confidence: 21.3% Identity: 23% Fold: Restriction endonuclease-like Superfamily: TBP-interacting protein-like Family: TBP-interacting protein-like Phyre2 PDB 2gdq chain A domain 2 Region: 226 - 256 Aligned: 31 Modelled: 31 Confidence: 20.5% Identity: 13% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 2mnr chain A domain 2 Region: 226 - 256 Aligned: 31 Modelled: 31 Confidence: 20.5% Identity: 10% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1sjd chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 19.7% Identity: 15% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 3lo7 chain A Region: 178 - 192 Aligned: 15 Modelled: 15 Confidence: 18.6% Identity: 40% PDB header:transferase Chain: A: PDB Molecule:penicillin-binding protein a; PDBTitle: crystal structure of pbpa from mycobacterium tuberculosis Phyre2 PDB 1wuf chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 17.8% Identity: 19% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1jpm chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 17.8% Identity: 11% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1jpd chain X domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 17.3% Identity: 19% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 3ue3 chain A Region: 178 - 192 Aligned: 15 Modelled: 15 Confidence: 16.9% Identity: 47% PDB header:transferase Chain: A: PDB Molecule:septum formation, penicillin binding protein 3, PDBTitle: crystal structure of acinetobacter baumanni pbp3 Phyre2 PDB 1jdf chain A domain 2 Region: 228 - 256 Aligned: 29 Modelled: 29 Confidence: 16.6% Identity: 14% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1r0m chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 16.5% Identity: 15% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 2gl5 chain A domain 2 Region: 226 - 256 Aligned: 31 Modelled: 31 Confidence: 16.3% Identity: 19% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 2chr chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 16.2% Identity: 15% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1nu5 chain A domain 2 Region: 230 - 256 Aligned: 27 Modelled: 27 Confidence: 15.0% Identity: 19% Fold: Enolase N-terminal domain-like Superfamily: Enolase N-terminal domain-like Family: Enolase N-terminal domain-like Phyre2 PDB 1rp5 chain A domain 4 Region: 178 - 192 Aligned: 15 Modelled: 15 Confidence: 14.5% Identity: 40% Fold: beta-lactamase/transpeptidase-like Superfamily: beta-lactamase/transpeptidase-like Family: beta-Lactamase/D-ala carboxypeptidase Phyre2 1 d2hqsa2 2 d2iqia1 3 c3ly8A_ 4 d1wuea2 5 c2w8bB_ 6 d2czra1 7 d2gdqa2 8 d2mnra2 9 d1sjda2 10 c3lo7A_ 11 d1wufa2 12 d1jpma2 13 d1jpdx2 14 c3ue3A_ 15 d1jdfa2 16 d1r0ma2 17 d2gl5a2 18 d2chra2 19 d1nu5a2 20 d1rp5a4 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

Detailed template information

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

1 d2hqsa2 98.3 21 Fold:Anticodon-binding domain-like Superfamily:TolB, N-terminal domain Family:TolB, N-terminal domain 2 d2iqia1 96.4 15 Fold:Anticodon-binding domain-like Superfamily:XCC0632-like Family:XCC0632-like 3 c3ly8A_ 87.5 13 PDB header:signaling protein Chain: A: PDB Molecule:transcriptional activator cadc; PDBTitle: crystal structure of mutant d471e of the periplasmic domain of cadc 4 d1wuea2 41.0 18 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 5 c2w8bB_ 32.6 20 PDB header:protein transport/membrane protein Chain: B: PDB Molecule:protein tolb; PDBTitle: crystal structure of processed tolb in complex with pal 6 d2czra1 21.3 23 Fold:Restriction endonuclease-like Superfamily:TBP-interacting protein-like Family:TBP-interacting protein-like 7 d2gdqa2 20.5 13 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 8 d2mnra2 20.5 10 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 9 d1sjda2 19.7 15 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 10 c3lo7A_ 18.6 40 PDB header:transferase Chain: A: PDB Molecule:penicillin-binding protein a; PDBTitle: crystal structure of pbpa from mycobacterium tuberculosis 11 d1wufa2 17.8 19 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 12 d1jpma2 17.8 11 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 13 d1jpdx2 17.3 19 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 14 c3ue3A_ 16.9 47 PDB header:transferase Chain: A: PDB Molecule:septum formation, penicillin binding protein 3, PDBTitle: crystal structure of acinetobacter baumanni pbp3 15 d1jdfa2 16.6 14 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 16 d1r0ma2 16.5 15 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 17 d2gl5a2 16.3 19 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 18 d2chra2 16.2 15 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 19 d1nu5a2 15.0 19 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 20 d1rp5a4 14.5 40 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 21 d1vqqa3 not modelled 14.4 40 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 22 d1k25a4 not modelled 14.2 40 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 23 d1muca2 not modelled 12.4 15 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 24 c3equB_ not modelled 11.0 53 PDB header:biosynthetic protein Chain: B: PDB Molecule:penicillin-binding protein 2; PDBTitle: crystal structure of penicillin-binding protein 2 from neisseria2 gonorrhoeae 25 d1bqga2 not modelled 10.2 13 Fold:Enolase N-terminal domain-like Superfamily:Enolase N-terminal domain-like Family:Enolase N-terminal domain-like 26 c3pbqA_ not modelled 9.6 47 PDB header:hydrolase/antibiotic Chain: A: PDB Molecule:penicillin-binding protein 3; PDBTitle: crystal structure of pbp3 complexed with imipenem 27 c3mbrX_ not modelled 9.3 25 PDB header:transferase Chain: X: PDB Molecule:glutamine cyclotransferase; PDBTitle: crystal structure of the glutaminyl cyclase from xanthomonas2 campestris 28 d1pyya4 not modelled 9.2 40 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 29 c1mwuA_ not modelled 9.0 40 PDB header:biosynthetic protein Chain: A: PDB Molecule:penicillin-binding protein 2a; PDBTitle: structure of methicillin acyl-penicillin binding protein 2a2 from methicillin resistant staphylococcus aureus strain3 27r at 2.60 a resolution. 30 d2c5wb1 not modelled 8.7 29 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 31 d1tw3a1 not modelled 8.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain 32 c2xzmE_ not modelled 8.1 17 PDB header:ribosome Chain: E: PDB Molecule:ribosomal protein s5 containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 33 c3nqyA_ not modelled 8.0 42 PDB header:hydrolase Chain: A: PDB Molecule:secreted metalloprotease mcp02; PDBTitle: crystal structure of the autoprocessed complex of vibriolysin mcp-022 with a single point mutation e346a 34 c3oc2A_ not modelled 7.8 47 PDB header:penicillin-binding protein Chain: A: PDB Molecule:penicillin-binding protein 3; PDBTitle: crystal structure of penicillin-binding protein 3 from pseudomonas2 aeruginosa 35 c2wadB_ not modelled 6.6 33 PDB header:peptide binding protein Chain: B: PDB Molecule:penicillin-binding protein 2b; PDBTitle: penicillin-binding protein 2b (pbp-2b) from streptococcus2 pneumoniae (strain 5204) 36 d2bg1a1 not modelled 6.2 36 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 37 d1svda1 not modelled 6.2 20 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 38 c1x37A_ not modelled 6.0 21 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent protease la 1; PDBTitle: structure of bacillus subtilis lon protease ssd domain 39 c2kbxA_ not modelled 5.8 11 PDB header:cell adhesion Chain: A: PDB Molecule:integrin-linked protein kinase; PDBTitle: solution structure of ilk-pinch complex 40 c3cb3B_ not modelled 5.7 12 PDB header:isomerase Chain: B: PDB Molecule:mandelate racemase/muconate lactonizing enzyme; PDBTitle: crystal structure of l-talarate dehydratase from polaromonas sp. js6662 complexed with mg and l-glucarate 41 d1bwva1 not modelled 5.6 17 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 42 c1qmfA_ not modelled 5.5 40 PDB header:peptidoglycan synthesis Chain: A: PDB Molecule:penicillin-binding protein 2x; PDBTitle: penicillin-binding protein 2x (pbp-2x) acyl-enzyme complex 43 d2hc5a1 not modelled 5.5 29 Fold:FlaG-like Superfamily:FlaG-like Family:FlaG-like 44 d1qzza1 not modelled 5.5 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain 45 d2olua2 not modelled 5.3 14 Fold:beta-lactamase/transpeptidase-like Superfamily:beta-lactamase/transpeptidase-like Family:beta-Lactamase/D-ala carboxypeptidase 46 c3onrI_ not modelled 5.2 14 PDB header:metal binding protein Chain: I: PDB Molecule:protein transport protein sece2; PDBTitle: crystal structure of the calcium chelating immunodominant antigen,2 calcium dodecin (rv0379),from mycobacterium tuberculosis with a novel3 calcium-binding site

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

---

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