Secondary structure and disorder prediction

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Sequence		M	N	D	T	Y	Q	P	I	N	C	D	D	Y	D	N	L	E	L	A	C	Q	H	H	L	M	L	T	L	E	L	K	D	G	E	K	L	Q	A	K	A	S	D	L	V	S	R	K	N	V	E	Y	L	V	V	E	A	A	G	E	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.
Sequence		R	E	L	R	L	D	K	I	T	S	F	S	H	P	E	I	G	T	V	V	V	S	E	S
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 1sg5 chain A domain 1 Region: 1 - 84 Aligned: 84 Modelled: 84 Confidence: 100.0% Identity: 100% Fold: Rof/RNase P subunit-like Superfamily: Rof/RNase P subunit-like Family: Rof-like Phyre2 PDB 2e12 chain B Region: 23 - 71 Aligned: 49 Modelled: 49 Confidence: 54.5% Identity: 22% PDB header:translation Chain: B: PDB Molecule:hypothetical protein xcc3642; PDBTitle: the crystal structure of xc5848 from xanthomonas campestris2 adopting a novel variant of sm-like motif Phyre2 PDB 1m5q chain 1 Region: 15 - 84 Aligned: 56 Modelled: 53 Confidence: 51.9% Identity: 16% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 3cw1 chain 5 Region: 16 - 43 Aligned: 28 Modelled: 28 Confidence: 41.4% Identity: 25% PDB header:splicing Chain: 5: PDB Molecule:small nuclear ribonucleoprotein g; PDB Fragment:residues 1-215; PDBTitle: crystal structure of human spliceosomal u1 snrnp Phyre2 PDB 1kq1 chain W Region: 12 - 42 Aligned: 31 Modelled: 31 Confidence: 40.6% Identity: 13% PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq Phyre2 PDB 2cgh chain B Region: 14 - 63 Aligned: 47 Modelled: 50 Confidence: 40.1% Identity: 19% PDB header:ligase Chain: B: PDB Molecule:biotin ligase; PDBTitle: crystal structure of biotin ligase from mycobacterium2 tuberculosis Phyre2 PDB 3swn chain C Region: 16 - 72 Aligned: 53 Modelled: 57 Confidence: 37.7% Identity: 15% PDB header:rna binding protein Chain: C: PDB Molecule:u6 snrna-associated sm-like protein lsm7; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings Phyre2 PDB 1b34 chain A Region: 18 - 43 Aligned: 26 Modelled: 26 Confidence: 30.7% Identity: 27% PDB header:rna binding protein Chain: A: PDB Molecule:protein (small nuclear ribonucleoprotein sm d1); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain Phyre2 PDB 1b34 chain A Region: 18 - 43 Aligned: 26 Modelled: 26 Confidence: 30.7% Identity: 27% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 3swn chain T Region: 18 - 43 Aligned: 26 Modelled: 26 Confidence: 27.6% Identity: 19% PDB header:rna binding protein Chain: T: PDB Molecule:u6 snrna-associated sm-like protein lsm6; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings Phyre2 PDB 3d6w chain A Region: 48 - 83 Aligned: 36 Modelled: 36 Confidence: 26.6% Identity: 8% PDB header:dna binding protein Chain: A: PDB Molecule:methyl-accepting/dna response regulator; PDBTitle: lyttr dna-binding domain of putative methyl-accepting/dna response2 regulator from bacillus cereus. Phyre2 PDB 3cw1 chain D Region: 23 - 43 Aligned: 21 Modelled: 21 Confidence: 25.1% Identity: 24% PDB header:splicing Chain: D: PDB Molecule:small nuclear ribonucleoprotein sm d3; PDBTitle: crystal structure of human spliceosomal u1 snrnp Phyre2 PDB 1d3b chain B Region: 21 - 72 Aligned: 52 Modelled: 52 Confidence: 22.9% Identity: 21% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1b34 chain B Region: 14 - 74 Aligned: 61 Modelled: 61 Confidence: 20.4% Identity: 11% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1b34 chain B Region: 14 - 74 Aligned: 61 Modelled: 61 Confidence: 20.4% Identity: 11% PDB header:rna binding protein Chain: B: PDB Molecule:protein (small nuclear ribonucleoprotein sm d2); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain Phyre2 PDB 3qii chain A Region: 23 - 72 Aligned: 48 Modelled: 50 Confidence: 19.3% Identity: 17% PDB header:transcription regulator Chain: A: PDB Molecule:phd finger protein 20; PDBTitle: crystal structure of tudor domain 2 of human phd finger protein 20 Phyre2 PDB 2xk0 chain A Region: 23 - 73 Aligned: 48 Modelled: 51 Confidence: 18.1% Identity: 13% PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) Phyre2 PDB 3cw1 chain Z Region: 18 - 43 Aligned: 26 Modelled: 26 Confidence: 17.6% Identity: 15% PDB header:splicing Chain: Z: PDB Molecule:small nuclear ribonucleoprotein f; PDBTitle: crystal structure of human spliceosomal u1 snrnp Phyre2 PDB 1hk9 chain A Region: 12 - 42 Aligned: 31 Modelled: 31 Confidence: 17.2% Identity: 19% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 2fwk chain B Region: 23 - 43 Aligned: 21 Modelled: 21 Confidence: 16.9% Identity: 5% PDB header:dna binding protein Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5 Phyre2 1 d1sg5a1 2 c2e12B_ 3 d1m5q1_ 4 c3cw15_ 5 c1kq1W_ 6 c2cghB_ 7 c3swnC_ 8 c1b34A_ 9 d1b34a_ 10 c3swnT_ 11 c3d6wA_ 12 c3cw1D_ 13 d1d3bb_ 14 d1b34b_ 15 c1b34B_ 16 c3qiiA_ 17 c2xk0A_ 18 c3cw1Z_ 19 d1hk9a_ 20 c2fwkB_ 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 50 51 52 53 54 55 56 57 58

Detailed template information

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

1 d1sg5a1 100.0 100 Fold:Rof/RNase P subunit-like Superfamily:Rof/RNase P subunit-like Family:Rof-like 2 c2e12B_ 54.5 22 PDB header:translation Chain: B: PDB Molecule:hypothetical protein xcc3642; PDBTitle: the crystal structure of xc5848 from xanthomonas campestris2 adopting a novel variant of sm-like motif 3 d1m5q1_ 51.9 16 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 4 c3cw15_ 41.4 25 PDB header:splicing Chain: 5: PDB Molecule:small nuclear ribonucleoprotein g; PDB Fragment:residues 1-215; PDBTitle: crystal structure of human spliceosomal u1 snrnp 5 c1kq1W_ 40.6 13 PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq 6 c2cghB_ 40.1 19 PDB header:ligase Chain: B: PDB Molecule:biotin ligase; PDBTitle: crystal structure of biotin ligase from mycobacterium2 tuberculosis 7 c3swnC_ 37.7 15 PDB header:rna binding protein Chain: C: PDB Molecule:u6 snrna-associated sm-like protein lsm7; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 8 c1b34A_ 30.7 27 PDB header:rna binding protein Chain: A: PDB Molecule:protein (small nuclear ribonucleoprotein sm d1); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain 9 d1b34a_ 30.7 27 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 10 c3swnT_ 27.6 19 PDB header:rna binding protein Chain: T: PDB Molecule:u6 snrna-associated sm-like protein lsm6; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 11 c3d6wA_ 26.6 8 PDB header:dna binding protein Chain: A: PDB Molecule:methyl-accepting/dna response regulator; PDBTitle: lyttr dna-binding domain of putative methyl-accepting/dna response2 regulator from bacillus cereus. 12 c3cw1D_ 25.1 24 PDB header:splicing Chain: D: PDB Molecule:small nuclear ribonucleoprotein sm d3; PDBTitle: crystal structure of human spliceosomal u1 snrnp 13 d1d3bb_ 22.9 21 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 14 d1b34b_ 20.4 11 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 15 c1b34B_ 20.4 11 PDB header:rna binding protein Chain: B: PDB Molecule:protein (small nuclear ribonucleoprotein sm d2); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain 16 c3qiiA_ 19.3 17 PDB header:transcription regulator Chain: A: PDB Molecule:phd finger protein 20; PDBTitle: crystal structure of tudor domain 2 of human phd finger protein 20 17 c2xk0A_ 18.1 13 PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) 18 c3cw1Z_ 17.6 15 PDB header:splicing Chain: Z: PDB Molecule:small nuclear ribonucleoprotein f; PDBTitle: crystal structure of human spliceosomal u1 snrnp 19 d1hk9a_ 17.2 19 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 20 c2fwkB_ 16.9 5 PDB header:dna binding protein Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5 21 d1a9xb1 not modelled 16.5 24 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Carbamoyl phosphate synthetase, small subunit N-terminal domain Family:Carbamoyl phosphate synthetase, small subunit N-terminal domain 22 c3qhsD_ not modelled 15.7 19 PDB header:rna binding protein Chain: D: PDB Molecule:protein hfq; PDBTitle: crystal structure of full-length hfq from escherichia coli 23 d1i4k1_ not modelled 15.2 15 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 24 c3bw1A_ not modelled 14.5 11 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm3; PDBTitle: crystal structure of homomeric yeast lsm3 exhibiting novel octameric2 ring organisation 25 d1th7a1 not modelled 14.1 15 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 26 c3cw1A_ not modelled 13.5 16 PDB header:splicing Chain: A: PDB Molecule:small nuclear ribonucleoprotein-associated proteins b and PDBTitle: crystal structure of human spliceosomal u1 snrnp 27 c3swnA_ not modelled 13.3 10 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 28 c3hsbB_ not modelled 13.3 16 PDB header:rna binding protein/rna Chain: B: PDB Molecule:protein hfq; PDBTitle: crystal structure of ymah (hfq) from bacillus subtilis in complex with2 an rna aptamer 29 c2ewnA_ not modelled 12.6 11 PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog 30 d1mgqa_ not modelled 12.0 11 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 31 c2ej9A_ not modelled 11.9 9 PDB header:ligase Chain: A: PDB Molecule:putative biotin ligase; PDBTitle: crystal structure of biotin protein ligase from2 methanococcus jannaschii 32 d1i8fa_ not modelled 11.8 10 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 33 d1jbma_ not modelled 11.2 12 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 34 d1d3ba_ not modelled 11.2 23 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 35 c3p8dB_ not modelled 11.0 17 PDB header:protein binding Chain: B: PDB Molecule:medulloblastoma antigen mu-mb-50.72; PDBTitle: crystal structure of the second tudor domain of human phf20 (homodimer2 form) 36 c3pgwQ_ not modelled 10.3 13 PDB header:splicing/dna/rna Chain: Q: PDB Molecule:sm b; PDBTitle: crystal structure of human u1 snrnp 37 d1xg8a_ not modelled 10.2 23 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:YuzD-like 38 c1ssfA_ not modelled 9.5 11 PDB header:cell cycle Chain: A: PDB Molecule:transformation related protein 53 binding PDBTitle: solution structure of the mouse 53bp1 fragment (residues2 1463-1617) 39 d1etha1 not modelled 9.1 17 Fold:Lipase/lipooxygenase domain (PLAT/LH2 domain) Superfamily:Lipase/lipooxygenase domain (PLAT/LH2 domain) Family:Colipase-binding domain 40 d2zgwa1 not modelled 9.1 27 Fold:SH3-like barrel Superfamily:C-terminal domain of transcriptional repressors Family:Biotin repressor (BirA) 41 c1wwtA_ not modelled 8.9 29 PDB header:ligase Chain: A: PDB Molecule:threonyl-trna synthetase, cytoplasmic; PDBTitle: solution structure of the tgs domain from human threonyl-2 trna synthetase 42 c1keeH_ not modelled 8.8 22 PDB header:ligase Chain: H: PDB Molecule:carbamoyl-phosphate synthetase small chain; PDBTitle: inactivation of the amidotransferase activity of carbamoyl phosphate2 synthetase by the antibiotic acivicin 43 d2fwka1 not modelled 8.8 4 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 44 c1y96C_ not modelled 8.8 7 PDB header:rna binding protein Chain: C: PDB Molecule:gem-associated protein 6; PDBTitle: crystal structure of the gemin6/gemin7 heterodimer from the2 human smn complex 45 d1d3bl_ not modelled 8.7 16 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 46 d1h641_ not modelled 8.5 12 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 47 c3mlqE_ not modelled 8.0 21 PDB header:transferase/transcription Chain: E: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain 48 d1u1sa1 not modelled 7.8 19 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 49 c2pvsB_ not modelled 7.7 11 PDB header:hydrolase Chain: B: PDB Molecule:pancreatic lipase-related protein 2; PDBTitle: structure of human pancreatic lipase related protein 22 mutant n336q 50 d1n9ra_ not modelled 7.3 11 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 51 c2advB_ not modelled 6.7 17 PDB header:hydrolase Chain: B: PDB Molecule:glutaryl 7- aminocephalosporanic acid acylase; PDBTitle: crystal structures of glutaryl 7-aminocephalosporanic acid acylase:2 mutational study of activation mechanism 52 c3mlqH_ not modelled 5.9 21 PDB header:transferase/transcription Chain: H: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain 53 c1n9sH_ not modelled 5.8 9 PDB header:translation Chain: H: PDB Molecule:small nuclear ribonucleoprotein f; PDBTitle: crystal structure of yeast smf in spacegroup p43212 54 d1kn0a_ not modelled 5.8 29 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:The homologous-pairing domain of Rad52 recombinase 55 d1kq1a_ not modelled 5.5 13 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 56 c3pgwB_ not modelled 5.5 13 PDB header:splicing/dna/rna Chain: B: PDB Molecule:sm b; PDBTitle: crystal structure of human u1 snrnp 57 d1n9sc_ not modelled 5.2 11 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 58 d2hqxa1 not modelled 5.0 13 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor 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

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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