Email l.a.kelley@imperial.ac.uk Description O13578 Date Mon Jul 2 19:10:19 BST 2012 Unique Job ID 2287206992d0e851

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template d1vkoa2 Top template information Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Dihydrodipicolinate reductase-like Confidence and coverage Confidence: 17.0% Coverage: 38% 42 residues ( 38% of your sequence) have been modelled with 17.0% 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. 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 1vko chain A domain 2 Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 17.0% Identity: 19% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 1p1j chain A domain 2 Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 13.4% Identity: 24% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 2bgc chain A domain 1 Region: 25 - 87 Aligned: 61 Modelled: 63 Confidence: 10.7% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: CAP C-terminal domain-like Phyre2 PDB 1sis chain A Region: 38 - 50 Aligned: 13 Modelled: 13 Confidence: 9.5% Identity: 46% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 1vjp chain A domain 2 Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 9.0% Identity: 14% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 3cin chain A Region: 25 - 65 Aligned: 41 Modelled: 41 Confidence: 8.1% Identity: 15% PDB header:isomerase Chain: A: PDB Molecule:myo-inositol-1-phosphate synthase-related protein; PDBTitle: crystal structure of a myo-inositol-1-phosphate synthase-related2 protein (tm_1419) from thermotoga maritima msb8 at 1.70 a resolution Phyre2 PDB 1u1i chain A domain 2 Region: 25 - 66 Aligned: 42 Modelled: 42 Confidence: 7.8% Identity: 31% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Dihydrodipicolinate reductase-like Phyre2 PDB 2pmz chain N Region: 82 - 99 Aligned: 18 Modelled: 18 Confidence: 7.1% Identity: 50% PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 2bgc chain A Region: 36 - 92 Aligned: 56 Modelled: 57 Confidence: 6.8% Identity: 16% PDB header:transcription Chain: A: PDB Molecule:prfa; PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes Phyre2 PDB 1vko chain A Region: 25 - 65 Aligned: 41 Modelled: 41 Confidence: 6.8% Identity: 20% PDB header:isomerase Chain: A: PDB Molecule:inositol-3-phosphate synthase; PDBTitle: crystal structure of inositol-3-phosphate synthase (ce21227) from2 caenorhabditis elegans at 2.30 a resolution Phyre2 PDB 1twf chain J Region: 82 - 99 Aligned: 18 Modelled: 18 Confidence: 6.8% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: RNA polymerase subunit RPB10 Family: RNA polymerase subunit RPB10 Phyre2 PDB 1chl chain A Region: 38 - 50 Aligned: 13 Modelled: 13 Confidence: 6.5% Identity: 38% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 1en2 chain A domain 2 Region: 20 - 39 Aligned: 20 Modelled: 20 Confidence: 6.4% Identity: 40% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant lectins/antimicrobial peptides Family: Hevein-like agglutinin (lectin) domain Phyre2 PDB 1hqz chain 1 Region: 30 - 60 Aligned: 31 Modelled: 31 Confidence: 6.4% Identity: 19% Fold: Gelsolin-like Superfamily: Actin depolymerizing proteins Family: Cofilin-like Phyre2 PDB 1ehd chain A domain 2 Region: 20 - 39 Aligned: 20 Modelled: 20 Confidence: 6.3% Identity: 40% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant lectins/antimicrobial peptides Family: Hevein-like agglutinin (lectin) domain Phyre2 PDB 3a1y chain F Region: 83 - 92 Aligned: 10 Modelled: 10 Confidence: 6.2% Identity: 50% PDB header:ribosomal protein Chain: F: PDB Molecule:50s ribosomal protein p1 (l12p); PDBTitle: the structure of protein complex Phyre2 PDB 2hip chain A Region: 25 - 43 Aligned: 19 Modelled: 19 Confidence: 5.8% Identity: 32% Fold: HIPIP (high potential iron protein) Superfamily: HIPIP (high potential iron protein) Family: HIPIP (high potential iron protein) Phyre2 PDB 2a1i chain A domain 1 Region: 63 - 92 Aligned: 30 Modelled: 30 Confidence: 5.8% Identity: 30% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: XPF/Rad1/Mus81 nuclease Phyre2 PDB 1hpi chain A Region: 25 - 38 Aligned: 14 Modelled: 14 Confidence: 5.3% Identity: 29% Fold: HIPIP (high potential iron protein) Superfamily: HIPIP (high potential iron protein) Family: HIPIP (high potential iron protein) Phyre2 1 d1vkoa2 2 d1p1ja2 3 d2bgca1 4 d1sisa_ 5 d1vjpa2 6 c3cinA_ 7 d1u1ia2 8 c2pmzN_ 9 c2bgcA_ 10 c1vkoA_ 11 d1twfj_ 12 d1chla_ 13 d1en2a2 14 d1hqz1_ 15 d1ehda2 16 c3a1yF_ 17 d2hipa_ 18 d2a1ia1 19 d1hpia_

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