Email l.a.kelley@imperial.ac.uk Description A0PJW8 Date Thu Apr 26 09:47:47 BST 2012 Unique Job ID 558d7d777b0370fc

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template d1tvfa1 Top template information Fold:Penicillin-binding protein associated domain Superfamily:Penicillin-binding protein associated domain Family:Pencillin binding protein 4 (PbpD), C-terminal domain Confidence and coverage Confidence: 8.4% Coverage: 10% 11 residues ( 10% of your sequence) have been modelled with 8.4% confidence by the single highest scoring template. You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library. Please note: You must be registered and logged in to use Phyrealarm. Warning: 65% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted. 3D viewing Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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 1tvf chain A domain 1 Region: 12 - 22 Aligned: 11 Modelled: 11 Confidence: 8.4% Identity: 27% Fold: Penicillin-binding protein associated domain Superfamily: Penicillin-binding protein associated domain Family: Pencillin binding protein 4 (PbpD), C-terminal domain Phyre2 PDB 2g4r chain B Region: 61 - 87 Aligned: 27 Modelled: 27 Confidence: 7.9% Identity: 7% PDB header:biosynthetic protein Chain: B: PDB Molecule:molybdopterin biosynthesis mog protein; PDBTitle: anomalous substructure of moga Phyre2 PDB 1uuy chain A Region: 61 - 87 Aligned: 27 Modelled: 27 Confidence: 7.8% Identity: 11% Fold: Molybdenum cofactor biosynthesis proteins Superfamily: Molybdenum cofactor biosynthesis proteins Family: MogA-like Phyre2 PDB 1mkz chain A Region: 61 - 87 Aligned: 27 Modelled: 27 Confidence: 7.0% Identity: 4% Fold: Molybdenum cofactor biosynthesis proteins Superfamily: Molybdenum cofactor biosynthesis proteins Family: MogA-like Phyre2 PDB 3rfq chain C Region: 61 - 87 Aligned: 27 Modelled: 27 Confidence: 6.7% Identity: 4% PDB header:biosynthetic protein Chain: C: PDB Molecule:pterin-4-alpha-carbinolamine dehydratase moab2; PDBTitle: crystal structure of pterin-4-alpha-carbinolamine dehydratase moab22 from mycobacterium marinum Phyre2 PDB 3kog chain A Region: 16 - 25 Aligned: 10 Modelled: 10 Confidence: 6.5% Identity: 50% PDB header:membrane protein Chain: A: PDB Molecule:putative pore-forming toxin; PDBTitle: crystal structure of putative pore-forming toxin (yp_001301288.1) from2 bacteroides vulgatus atcc 8482 at 1.85 a resolution Phyre2 PDB 1jlj chain A Region: 61 - 87 Aligned: 27 Modelled: 27 Confidence: 5.9% Identity: 7% Fold: Molybdenum cofactor biosynthesis proteins Superfamily: Molybdenum cofactor biosynthesis proteins Family: MogA-like Phyre2 PDB 2zjr chain S domain 1 Region: 15 - 25 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 27% Fold: Ribosomal protein L25-like Superfamily: Ribosomal protein L25-like Family: Ribosomal protein L25-like Phyre2 1 d1tvfa1 2 c2g4rB_ 3 d1uuya_ 4 d1mkza_ 5 c3rfqC_ 6 c3kogA_ 7 d1jlja_ 8 d2zjrs1

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