Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	P	A	L	I	L	I	C	L	L	L	Q	A	C	S	A	T	T	K	E	L	G	N	S	L	W	D	S	L	F	G	T	P	G	V	Q	L	T	D	D	D	I	Q	N	M	P	Y	A	S	Q	Y	M	Q	L	N	G	G	P
Secondary structure
SS confidence
Disorder		?	?	?																?																?	?	?								?		?				?					?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	L	F	V	V	L	A	F	A	E	D	G	Q	Q	K	W	V	T	Q	D	Q	A	T	L	V	T	Q	H	G	R	L	V	K	T	L	L	G	G	D	N	L	I	E	V	N	N	L	A	A	D	P	L	I	K	P	A	Q	I	V	D
Secondary structure
SS confidence
Disorder																														?												?			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	A	S	W	T	R	T	M	G	W	T	E	Y	Q	Q	V	R	Y	A	T	A	R	S	V	F	K	W	D	G	T	D	T	V	K	V	G	S	D	E	T	P	V	R	V	L	D	E	E	V	S	T	D	Q	A	R	W	H	N	R	Y
Secondary structure
SS confidence
Disorder		?																										?	?	?	?																						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.
Sequence		W	I	D	S	E	G	Q	I	R	Q	S	E	Q	Y	L	G	A	D	Y	F	P	V	K	T	T	L	I	K	A	A	K	Q
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 2in5 chain A domain 1 Region: 18 - 211 Aligned: 191 Modelled: 194 Confidence: 100.0% Identity: 41% Fold: YmcC-like Superfamily: YmcC-like Family: YmcC-like Phyre2 PDB 2byo chain A domain 1 Region: 145 - 208 Aligned: 60 Modelled: 64 Confidence: 49.7% Identity: 17% Fold: LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily: Prokaryotic lipoproteins and lipoprotein localization factors Family: LppX-like Phyre2 PDB 3fzx chain A Region: 55 - 208 Aligned: 154 Modelled: 143 Confidence: 31.8% Identity: 16% PDB header:lipid binding protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of a putative exported protein with ymcc-like fold2 (bf2203) from bacteroides fragilis nctc 9343 at 2.22 a resolution Phyre2 PDB 3jsl chain A Region: 80 - 98 Aligned: 19 Modelled: 19 Confidence: 21.7% Identity: 26% PDB header:ligase Chain: A: PDB Molecule:dna ligase; PDBTitle: crystal structure of the adenylation domain of nad+-2 dependent dna ligase from staphylococcus aureus Phyre2 PDB 2x6v chain B Region: 80 - 125 Aligned: 46 Modelled: 46 Confidence: 17.6% Identity: 15% PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form Phyre2 PDB 3iz5 chain P Region: 172 - 187 Aligned: 16 Modelled: 16 Confidence: 17.2% Identity: 25% PDB header:ribosome Chain: P: PDB Molecule:60s ribosomal protein l15 (l15e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 1ffk chain I Region: 172 - 187 Aligned: 16 Modelled: 16 Confidence: 12.9% Identity: 25% Fold: Ribosomal proteins S24e, L23 and L15e Superfamily: Ribosomal proteins S24e, L23 and L15e Family: L15e Phyre2 PDB 1bml chain C domain 3 Region: 176 - 205 Aligned: 30 Modelled: 30 Confidence: 12.5% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 1v9p chain A domain 3 Region: 80 - 98 Aligned: 19 Modelled: 19 Confidence: 12.3% Identity: 32% Fold: ATP-grasp Superfamily: DNA ligase/mRNA capping enzyme, catalytic domain Family: Adenylation domain of NAD+-dependent DNA ligase Phyre2 PDB 1vqo chain M domain 1 Region: 172 - 187 Aligned: 16 Modelled: 16 Confidence: 10.7% Identity: 25% Fold: Ribosomal proteins S24e, L23 and L15e Superfamily: Ribosomal proteins S24e, L23 and L15e Family: L15e Phyre2 PDB 4a1c chain L Region: 172 - 187 Aligned: 16 Modelled: 16 Confidence: 10.2% Identity: 31% PDB header:ribosome Chain: L: PDB Molecule:ribosomal protein l15; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4. Phyre2 PDB 2we7 chain A Region: 82 - 98 Aligned: 17 Modelled: 15 Confidence: 10.2% Identity: 24% PDB header:oxidoreductase Chain: A: PDB Molecule:xanthine dehydrogenase; PDBTitle: crystal structure of mycobacterium tuberculosis rv0376c2 homologue from mycobacterium smegmatis Phyre2 PDB 1a0i chain A domain 1 Region: 84 - 103 Aligned: 20 Modelled: 20 Confidence: 9.8% Identity: 25% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: DNA ligase/mRNA capping enzyme postcatalytic domain Phyre2 PDB 2k6t chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 29% PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: solution structure of the relaxin-like factor Phyre2 PDB 2h8b chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 29% PDB header:hormone/growth factor Chain: A: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 Phyre2 PDB 1jj2 chain L Region: 172 - 187 Aligned: 16 Modelled: 16 Confidence: 9.5% Identity: 25% Fold: Ribosomal proteins S24e, L23 and L15e Superfamily: Ribosomal proteins S24e, L23 and L15e Family: L15e Phyre2 PDB 2k6u chain A Region: 13 - 19 Aligned: 7 Modelled: 7 Confidence: 9.3% Identity: 29% PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: the solution structure of a conformationally restricted2 fully active derivative of the human relaxin-like factor3 (rlf) Phyre2 PDB 1c9l chain A Region: 75 - 90 Aligned: 16 Modelled: 16 Confidence: 9.2% Identity: 31% PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin Phyre2 PDB 3bqo chain A domain 1 Region: 1 - 61 Aligned: 59 Modelled: 61 Confidence: 9.1% Identity: 14% Fold: Telomeric repeat binding factor (TRF) dimerisation domain Superfamily: Telomeric repeat binding factor (TRF) dimerisation domain Family: Telomeric repeat binding factor (TRF) dimerisation domain Phyre2 PDB 1utc chain A domain 2 Region: 75 - 90 Aligned: 16 Modelled: 16 Confidence: 7.9% Identity: 31% Fold: 7-bladed beta-propeller Superfamily: Clathrin heavy-chain terminal domain Family: Clathrin heavy-chain terminal domain Phyre2 1 d2in5a1 2 d2byoa1 3 c3fzxA_ 4 c3jslA_ 5 c2x6vB_ 6 c3iz5P_ 7 d1ffki_ 8 d1bmlc3 9 d1v9pa3 10 d1vqom1 11 c4a1cL_ 12 c2we7A_ 13 d1a0ia1 14 c2k6tA_ 15 c2h8bA_ 16 d1jj2l_ 17 c2k6uA_ 18 c1c9lA_ 19 d3bqoa1 20 d1utca2 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39

Detailed template information

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

1 d2in5a1 100.0 41 Fold:YmcC-like Superfamily:YmcC-like Family:YmcC-like 2 d2byoa1 49.7 17 Fold:LolA-like prokaryotic lipoproteins and lipoprotein localization factors Superfamily:Prokaryotic lipoproteins and lipoprotein localization factors Family:LppX-like 3 c3fzxA_ 31.8 16 PDB header:lipid binding protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of a putative exported protein with ymcc-like fold2 (bf2203) from bacteroides fragilis nctc 9343 at 2.22 a resolution 4 c3jslA_ 21.7 26 PDB header:ligase Chain: A: PDB Molecule:dna ligase; PDBTitle: crystal structure of the adenylation domain of nad+-2 dependent dna ligase from staphylococcus aureus 5 c2x6vB_ 17.6 15 PDB header:transcription/dna Chain: B: PDB Molecule:t-box transcription factor tbx5; PDBTitle: crystal structure of human tbx5 in the dna-bound and dna-2 free form 6 c3iz5P_ 17.2 25 PDB header:ribosome Chain: P: PDB Molecule:60s ribosomal protein l15 (l15e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 7 d1ffki_ 12.9 25 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 8 d1bmlc3 12.5 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 9 d1v9pa3 12.3 32 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 10 d1vqom1 10.7 25 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 11 c4a1cL_ 10.2 31 PDB header:ribosome Chain: L: PDB Molecule:ribosomal protein l15; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4. 12 c2we7A_ 10.2 24 PDB header:oxidoreductase Chain: A: PDB Molecule:xanthine dehydrogenase; PDBTitle: crystal structure of mycobacterium tuberculosis rv0376c2 homologue from mycobacterium smegmatis 13 d1a0ia1 9.8 25 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain 14 c2k6tA_ 9.7 29 PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: solution structure of the relaxin-like factor 15 c2h8bA_ 9.7 29 PDB header:hormone/growth factor Chain: A: PDB Molecule:insulin-like 3; PDBTitle: solution structure of insl3 16 d1jj2l_ 9.5 25 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 17 c2k6uA_ 9.3 29 PDB header:hormone Chain: A: PDB Molecule:insulin-like 3 a chain; PDBTitle: the solution structure of a conformationally restricted2 fully active derivative of the human relaxin-like factor3 (rlf) 18 c1c9lA_ 9.2 31 PDB header:endocytosis/exocytosis Chain: A: PDB Molecule:clathrin; PDBTitle: peptide-in-groove interactions link target proteins to the2 b-propeller of clathrin 19 d3bqoa1 9.1 14 Fold:Telomeric repeat binding factor (TRF) dimerisation domain Superfamily:Telomeric repeat binding factor (TRF) dimerisation domain Family:Telomeric repeat binding factor (TRF) dimerisation domain 20 d1utca2 7.9 31 Fold:7-bladed beta-propeller Superfamily:Clathrin heavy-chain terminal domain Family:Clathrin heavy-chain terminal domain 21 d2blna1 not modelled 7.9 3 Fold:FMT C-terminal domain-like Superfamily:FMT C-terminal domain-like Family:Post formyltransferase domain 22 d1dgsa3 not modelled 7.5 21 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 23 d1p5dx2 not modelled 7.0 29 Fold:Phosphoglucomutase, first 3 domains Superfamily:Phosphoglucomutase, first 3 domains Family:Phosphoglucomutase, first 3 domains 24 c3bu8B_ not modelled 6.8 5 PDB header:dna binding protein Chain: B: PDB Molecule:telomeric repeat-binding factor 2; PDBTitle: crystal structure of trf2 trfh domain and tin2 peptide2 complex 25 d1ogmx1 not modelled 6.7 11 Fold:Dextranase, N-terminal domain Superfamily:Dextranase, N-terminal domain Family:Dextranase, N-terminal domain 26 d1h6fa_ not modelled 6.5 27 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:p53-like transcription factors Family:T-box 27 d2cupa3 not modelled 6.5 40 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 28 c3o44G_ not modelled 6.4 12 PDB header:toxin Chain: G: PDB Molecule:hemolysin; PDBTitle: crystal structure of the vibrio cholerae cytolysin (hlya) heptameric2 pore 29 c3nhaA_ not modelled 6.2 23 PDB header:transport protein Chain: A: PDB Molecule:atp-binding cassette sub-family b member 6, mitochondrial; PDBTitle: nucleotide binding domain of human abcb6 (adp mg bound structure) 30 c3mlqE_ not modelled 6.2 19 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 31 c3f6zB_ not modelled 6.0 20 PDB header:hydrolase Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of pseudomonas aeruginosa mlic in complex2 with hen egg white lysozyme 32 c2jkbA_ not modelled 6.0 18 PDB header:lyase Chain: A: PDB Molecule:sialidase b; PDBTitle: crystal structure of streptococcus pneumoniae nanb in2 complex with 2,7-anhydro-neu5ac 33 c1eb0A_ not modelled 5.9 8 PDB header:chaperone Chain: A: PDB Molecule:urease accessory protein uree; PDBTitle: crystal structure of bacillus pasteurii uree at 1.85 a,2 phased by siras. type i crystal form. 34 d1b04a_ not modelled 5.8 26 Fold:ATP-grasp Superfamily:DNA ligase/mRNA capping enzyme, catalytic domain Family:Adenylation domain of NAD+-dependent DNA ligase 35 d4tsva_ not modelled 5.8 26 Fold:TNF-like Superfamily:TNF-like Family:TNF-like 36 c1bpoA_ not modelled 5.6 31 PDB header:membrane protein Chain: A: PDB Molecule:protein (clathrin); PDBTitle: clathrin heavy-chain terminal domain and linker 37 d2dlqa1 not modelled 5.6 25 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 38 d1bhia_ not modelled 5.5 14 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 39 d1oh0a_ not modelled 5.4 13 Fold:Cystatin-like Superfamily:NTF2-like Family:Ketosteroid isomerase-like

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