Secondary structure and disorder prediction

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Sequence		M	K	A	K	E	L	R	E	K	S	V	E	E	L	N	T	E	L	L	N	L	L	R	E	Q	F	N	L	R	M	Q	A	A	S	G	Q	L	Q	Q	S	H	L	L	K	Q	V	R	R	D	V	A	R	V	K	T	L	L	N	E	K
Secondary structure
SS confidence
Disorder		?	?							?																										?	?	?	?	?
Disorder confidence
		.	.	.
Sequence		A	G	A
Secondary structure
SS confidence
Disorder			?	?
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 1r73 chain A Region: 1 - 63 Aligned: 63 Modelled: 63 Confidence: 99.9% Identity: 44% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 2zjr chain V domain 1 Region: 1 - 63 Aligned: 63 Modelled: 63 Confidence: 99.9% Identity: 38% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 2j37 chain 5 Region: 1 - 62 Aligned: 62 Modelled: 62 Confidence: 99.9% Identity: 32% PDB header:ribosome Chain: 5: PDB Molecule:ribosomal protein l35; PDBTitle: model of mammalian srp bound to 80s rncs Phyre2 PDB 2gyc chain W domain 1 Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 99.9% Identity: 100% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 1vqo chain V domain 1 Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 99.9% Identity: 33% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 2zkr chain V Region: 1 - 59 Aligned: 59 Modelled: 59 Confidence: 99.9% Identity: 36% PDB header:ribosomal protein/rna Chain: V: PDB Molecule:rna expansion segment es9 part2; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 3bbo chain Z Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 99.9% Identity: 32% PDB header:ribosome Chain: Z: PDB Molecule:ribosomal protein l29; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2hgq chain 1 domain 1 Region: 1 - 62 Aligned: 62 Modelled: 62 Confidence: 99.9% Identity: 39% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 3jyw chain X Region: 1 - 62 Aligned: 60 Modelled: 62 Confidence: 99.9% Identity: 38% PDB header:ribosome Chain: X: PDB Molecule:60s ribosomal protein l35; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution Phyre2 PDB 1s1i chain X Region: 1 - 59 Aligned: 57 Modelled: 59 Confidence: 99.8% Identity: 40% PDB header:ribosome Chain: X: PDB Molecule:60s ribosomal protein l35; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. Phyre2 PDB 4a1e chain U Region: 1 - 62 Aligned: 62 Modelled: 62 Confidence: 99.7% Identity: 29% PDB header:ribosome Chain: U: PDB Molecule:rpl35; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 Phyre2 PDB 2j01 chain 2 domain 1 Region: 5 - 53 Aligned: 49 Modelled: 49 Confidence: 99.3% Identity: 39% Fold: Long alpha-hairpin Superfamily: Ribosomal protein L29 (L29p) Family: Ribosomal protein L29 (L29p) Phyre2 PDB 2a8v chain A Region: 1 - 21 Aligned: 21 Modelled: 21 Confidence: 26.0% Identity: 38% PDB header:protein/rna Chain: A: PDB Molecule:rna binding domain of rho transcription PDBTitle: rho transcription termination factor/rna complex Phyre2 PDB 2hv8 chain D Region: 3 - 29 Aligned: 27 Modelled: 27 Confidence: 21.0% Identity: 26% PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3 Phyre2 PDB 2o1s chain C Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 18.0% Identity: 26% PDB header:transferase Chain: C: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase; PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 escherichia coli Phyre2 PDB 1gjj chain A domain 2 Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 14.9% Identity: 25% Fold: LEM/SAP HeH motif Superfamily: LEM domain Family: LEM domain Phyre2 PDB 1xwy chain A domain 1 Region: 3 - 30 Aligned: 28 Modelled: 28 Confidence: 13.9% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: Metallo-dependent hydrolases Family: TatD Mg-dependent DNase-like Phyre2 PDB 2o1x chain A Region: 3 - 28 Aligned: 26 Modelled: 26 Confidence: 12.9% Identity: 27% PDB header:transferase Chain: A: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase; PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 deinococcus radiodurans Phyre2 PDB 2xus chain A Region: 12 - 38 Aligned: 27 Modelled: 27 Confidence: 11.7% Identity: 19% PDB header:protein binding Chain: A: PDB Molecule:breast cancer metastasis-suppressor 1; PDBTitle: crystal structure of the brms1 n-terminal region Phyre2 PDB 1sy9 chain B Region: 48 - 59 Aligned: 12 Modelled: 12 Confidence: 11.2% Identity: 42% PDB header:calcium-binding protein Chain: B: PDB Molecule:cyclic-nucleotide-gated olfactory channel; PDBTitle: structure of calmodulin complexed with a fragment of the2 olfactory cng channel Phyre2 1 d1r73a_ 2 d2zjrv1 3 c2j375_ 4 d2gycw1 5 d1vqov1 6 c2zkrv_ 7 c3bboZ_ 8 d2hgq11 9 c3jywX_ 10 c1s1iX_ 11 c4a1eU_ 12 d2j0121 13 c2a8vA_ 14 c2hv8D_ 15 c2o1sC_ 16 d1gjja2 17 d1xwya1 18 c2o1xA_ 19 c2xusA_ 20 c1sy9B_ 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

Detailed template information

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

1 d1r73a_ 99.9 44 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 2 d2zjrv1 99.9 38 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 3 c2j375_ 99.9 32 PDB header:ribosome Chain: 5: PDB Molecule:ribosomal protein l35; PDBTitle: model of mammalian srp bound to 80s rncs 4 d2gycw1 99.9 100 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 5 d1vqov1 99.9 33 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 6 c2zkrv_ 99.9 36 PDB header:ribosomal protein/rna Chain: V: PDB Molecule:rna expansion segment es9 part2; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 7 c3bboZ_ 99.9 32 PDB header:ribosome Chain: Z: PDB Molecule:ribosomal protein l29; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 8 d2hgq11 99.9 39 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 9 c3jywX_ 99.9 38 PDB header:ribosome Chain: X: PDB Molecule:60s ribosomal protein l35; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution 10 c1s1iX_ 99.8 40 PDB header:ribosome Chain: X: PDB Molecule:60s ribosomal protein l35; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 11 c4a1eU_ 99.7 29 PDB header:ribosome Chain: U: PDB Molecule:rpl35; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 12 d2j0121 99.3 39 Fold:Long alpha-hairpin Superfamily:Ribosomal protein L29 (L29p) Family:Ribosomal protein L29 (L29p) 13 c2a8vA_ 26.0 38 PDB header:protein/rna Chain: A: PDB Molecule:rna binding domain of rho transcription PDBTitle: rho transcription termination factor/rna complex 14 c2hv8D_ 21.0 26 PDB header:protein transport Chain: D: PDB Molecule:rab11 family-interacting protein 3; PDBTitle: crystal structure of gtp-bound rab11 in complex with fip3 15 c2o1sC_ 18.0 26 PDB header:transferase Chain: C: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase; PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 escherichia coli 16 d1gjja2 14.9 25 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 17 d1xwya1 13.9 11 Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:TatD Mg-dependent DNase-like 18 c2o1xA_ 12.9 27 PDB header:transferase Chain: A: PDB Molecule:1-deoxy-d-xylulose-5-phosphate synthase; PDBTitle: 1-deoxy-d-xylulose 5-phosphate synthase (dxs) from2 deinococcus radiodurans 19 c2xusA_ 11.7 19 PDB header:protein binding Chain: A: PDB Molecule:breast cancer metastasis-suppressor 1; PDBTitle: crystal structure of the brms1 n-terminal region 20 c1sy9B_ 11.2 42 PDB header:calcium-binding protein Chain: B: PDB Molecule:cyclic-nucleotide-gated olfactory channel; PDBTitle: structure of calmodulin complexed with a fragment of the2 olfactory cng channel 21 c1envA_ not modelled 11.0 26 PDB header:viral protein Chain: A: PDB Molecule:hiv-1 envelope protein chimera consisting of a fragment of PDBTitle: atomic structure of the ectodomain from hiv-1 gp41 22 c1gcmC_ not modelled 10.9 25 PDB header:transcription regulation Chain: C: PDB Molecule:gcn4p-ii; PDBTitle: gcn4 leucine zipper core mutant p-li 23 d2odgc1 not modelled 10.8 31 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 24 c2rg8A_ not modelled 9.4 16 PDB header:apoptosis, translation Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: crystal structure of programmed for cell death 4 middle ma32 domain 25 d1jeia_ not modelled 8.5 36 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 26 c1kd8E_ not modelled 8.3 22 PDB header:de novo protein Chain: E: PDB Molecule:gcn4 acid base heterodimer base-d12la16l; PDBTitle: x-ray structure of the coiled coil gcn4 acid base2 heterodimer acid-d12ia16v base-d12la16l 27 c1j1eB_ not modelled 6.9 17 PDB header:contractile protein Chain: B: PDB Molecule:troponin t; PDBTitle: crystal structure of the 52kda domain of human cardiac2 troponin in the ca2+ saturated form 28 d1r8ja1 not modelled 6.8 15 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 29 c1ce9C_ not modelled 6.6 35 PDB header:helix capping Chain: C: PDB Molecule:protein (gcn4-pmse); PDBTitle: helix capping in the gcn4 leucine zipper 30 c1ce9A_ not modelled 6.6 35 PDB header:helix capping Chain: A: PDB Molecule:protein (gcn4-pmse); PDBTitle: helix capping in the gcn4 leucine zipper 31 c1ce9B_ not modelled 6.6 35 PDB header:helix capping Chain: B: PDB Molecule:protein (gcn4-pmse); PDBTitle: helix capping in the gcn4 leucine zipper 32 c1ce9D_ not modelled 6.6 35 PDB header:helix capping Chain: D: PDB Molecule:protein (gcn4-pmse); PDBTitle: helix capping in the gcn4 leucine zipper 33 d1dd3a1 not modelled 6.2 17 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 34 c2wq2A_ not modelled 6.2 13 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4 leucine zipper mutant with three ixxntxx motifs2 coordinating iodide 35 c3czqA_ not modelled 6.1 19 PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from2 sinorhizobium meliloti 36 d1ov9a_ not modelled 6.1 35 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 37 d1sv1a_ not modelled 6.0 15 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 38 d2a1ja1 not modelled 6.0 23 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 39 c2wq0A_ not modelled 5.9 13 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4 leucine zipper mutant with three ixxntxx motifs2 coordinating chloride 40 d1hf8a1 not modelled 5.8 17 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:Phosphoinositide-binding clathrin adaptor, domain 2 41 d1h1js_ not modelled 5.8 19 Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain 42 d2oa5a1 not modelled 5.7 32 Fold:BLRF2-like Superfamily:BLRF2-like Family:BLRF2-like 43 c2kztA_ not modelled 5.7 16 PDB header:apoptosis Chain: A: PDB Molecule:programmed cell death protein 4; PDBTitle: structure of the tandem ma-3 region of pdcd4 44 d1zrja1 not modelled 5.6 38 Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain 45 d1hx8a1 not modelled 5.3 30 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:Phosphoinositide-binding clathrin adaptor, domain 2 46 c2outA_ not modelled 5.1 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mu-like prophage flumu protein gp35, protein PDBTitle: solution structure of hi1506, a novel two domain protein2 from haemophilus influenzae 47 c1gcmB_ not modelled 5.1 26 PDB header:transcription regulation Chain: B: PDB Molecule:gcn4p-ii; PDBTitle: gcn4 leucine zipper core mutant p-li 48 c3layF_ not modelled 5.1 14 PDB header:metal binding protein Chain: F: PDB Molecule:zinc resistance-associated protein; PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2 49 c2jo8B_ not modelled 5.1 35 PDB header:transferase Chain: B: PDB Molecule:serine/threonine-protein kinase 4; PDBTitle: solution structure of c-terminal domain of human mammalian2 sterile 20-like kinase 1 (mst1)

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