Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	Q	P	G	L	D	F	Q	S	A	K	G	G	L	G	E	L	K	R	R	L	L	F	V	I	G	A	L	I	V	F	R	I	G	S	F	I	P	I	P	G	I	D	A	A	V	L	A	K	L	L	E	Q	Q	R	G	T	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																							?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	E	M	F	N	M	F	S	G	G	A	L	S	R	A	S	I	F	A	L	G	I	M	P	Y	I	S	A	S	I	I	I	Q	L	L	T	V	V	H	P	T	L	A	E	I	K	K	E	G	E	S	G	R	R	K	I	S	Q	Y	T
Secondary structure
SS confidence
Disorder													?					?			?	?	?																	?	?	?				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	Y	G	T	L	V	L	A	I	F	Q	S	I	G	I	A	T	G	L	P	N	M	P	G	M	Q	G	L	V	I	N	P	G	F	A	F	Y	F	T	A	V	V	S	L	V	T	G	T	M	F	L	M	W	L	G	E	Q	I	T	E
Secondary structure
SS confidence
Disorder																					?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	G	I	G	N	G	I	S	I	I	I	F	A	G	I	V	A	G	L	P	P	A	I	A	H	T	I	E	Q	A	R	Q	G	D	L	H	F	L	V	L	L	L	V	A	V	L	V	F	A	V	T	F	F	V	V	F	V	E	R	G
Secondary structure
SS confidence
Disorder																															?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Q	R	R	I	V	V	N	Y	A	K	R	Q	Q	G	R	R	V	Y	A	A	Q	S	T	H	L	P	L	K	V	N	M	A	G	V	I	P	A	I	F	A	S	S	I	I	L	F	P	A	T	I	A	S	W	F	G	G	G	T	G	W
Secondary structure
SS confidence
Disorder										?	?	?	?	?	?	?	?	?	?	?	?	?	?												?	?																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		N	W	L	T	T	I	S	L	Y	L	Q	P	G	Q	P	L	Y	V	L	L	Y	A	S	A	I	I	F	F	C	F	F	Y	T	A	L	V	F	N	P	R	E	T	A	D	N	L	K	K	S	G	A	F	V	P	G	I	R	P	G	E
Secondary structure
SS confidence
Disorder																																																		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		Q	T	A	K	Y	I	D	K	V	M	T	R	L	T	L	V	G	A	L	Y	I	T	F	I	C	L	I	P	E	F	M	R	D	A	M	K	V	P	F	Y	F	G	G	T	S	L	L	I	V	V	V	V	I	M	D	F	M	A	Q	V
Secondary structure
SS confidence
Disorder																																					?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.
Sequence		Q	T	L	M	M	S	S	Q	Y	E	S	A	L	K	K	A	N	L	K	G	Y	G	R
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 3j01 chain A Region: 8 - 442 Aligned: 435 Modelled: 435 Confidence: 100.0% Identity: 100% PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment Phyre2 PDB 3din chain F Region: 16 - 434 Aligned: 393 Modelled: 404 Confidence: 100.0% Identity: 43% PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 3dl8 chain H Region: 14 - 434 Aligned: 402 Modelled: 402 Confidence: 100.0% Identity: 46% PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 2zqp chain Y Region: 11 - 427 Aligned: 407 Modelled: 416 Confidence: 100.0% Identity: 41% PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: crystal structure of secye translocon from thermus2 thermophilus Phyre2 PDB 2aki chain Y Region: 1 - 436 Aligned: 400 Modelled: 400 Confidence: 100.0% Identity: 100% PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 2wwb chain A Region: 5 - 424 Aligned: 385 Modelled: 420 Confidence: 100.0% Identity: 22% PDB header:ribosome Chain: A: PDB Molecule:protein transport protein sec61 subunit alpha isoform 1; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome Phyre2 PDB 1rh5 chain A Region: 5 - 424 Aligned: 372 Modelled: 412 Confidence: 100.0% Identity: 19% Fold: Preprotein translocase SecY subunit Superfamily: Preprotein translocase SecY subunit Family: Preprotein translocase SecY subunit Phyre2 PDB 2wwa chain A Region: 5 - 434 Aligned: 396 Modelled: 430 Confidence: 100.0% Identity: 19% PDB header:ribosome Chain: A: PDB Molecule:sec sixty-one protein homolog; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 3mp7 chain A Region: 19 - 434 Aligned: 356 Modelled: 366 Confidence: 100.0% Identity: 21% PDB header:protein transport Chain: A: PDB Molecule:preprotein translocase subunit secy; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 2nsc chain A Region: 335 - 370 Aligned: 36 Modelled: 36 Confidence: 70.2% Identity: 25% PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima Phyre2 PDB 1p9y chain A Region: 335 - 372 Aligned: 38 Modelled: 38 Confidence: 67.5% Identity: 11% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 1t11 chain A domain 2 Region: 341 - 372 Aligned: 32 Modelled: 32 Confidence: 56.4% Identity: 16% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 1w26 chain A domain 2 Region: 340 - 370 Aligned: 30 Modelled: 31 Confidence: 52.3% Identity: 17% Fold: Ribosome binding domain-like Superfamily: Trigger factor ribosome-binding domain Family: Trigger factor ribosome-binding domain Phyre2 PDB 2d3o chain 1 Region: 340 - 369 Aligned: 29 Modelled: 30 Confidence: 46.0% Identity: 31% PDB header:ribosome Chain: 1: PDB Molecule:trigger factor; PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans Phyre2 PDB 1w26 chain B Region: 340 - 360 Aligned: 20 Modelled: 21 Confidence: 38.5% Identity: 25% PDB header:chaperone Chain: B: PDB Molecule:trigger factor; PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins Phyre2 PDB 3kys chain C Region: 2 - 22 Aligned: 21 Modelled: 21 Confidence: 28.0% Identity: 38% PDB header:transcription/protein binding Chain: C: PDB Molecule:transcriptional enhancer factor tef-1; PDBTitle: crystal structure of human yap and tead complex Phyre2 PDB 1zl8 chain A domain 1 Region: 102 - 123 Aligned: 22 Modelled: 22 Confidence: 27.1% Identity: 18% Fold: L27 domain Superfamily: L27 domain Family: L27 domain Phyre2 PDB 1t11 chain A Region: 340 - 384 Aligned: 43 Modelled: 45 Confidence: 25.8% Identity: 16% PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: trigger factor Phyre2 PDB 3l15 chain A Region: 3 - 22 Aligned: 20 Modelled: 20 Confidence: 25.4% Identity: 45% PDB header:transcription Chain: A: PDB Molecule:transcriptional enhancer factor tef-4; PDBTitle: human tead2 transcriptional factor Phyre2 PDB 1y74 chain A domain 1 Region: 102 - 123 Aligned: 22 Modelled: 22 Confidence: 23.5% Identity: 23% Fold: L27 domain Superfamily: L27 domain Family: L27 domain Phyre2 1 c3j01A_ 2 c3dinF_ 3 c3dl8H_ 4 c2zqpY_ 5 c2akiY_ 6 c2wwbA_ 7 d1rh5a_ 8 c2wwaA_ 9 c3mp7A_ 10 c2nscA_ 11 d1p9ya_ 12 d1t11a2 13 d1w26a2 14 c2d3o1_ 15 c1w26B_ 16 c3kysC_ 17 d1zl8a1 18 c1t11A_ 19 c3l15A_ 20 d1y74a1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

Detailed template information

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

1 c3j01A_ 100.0 100 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 2 c3dinF_ 100.0 43 PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 3 c3dl8H_ 100.0 46 PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 4 c2zqpY_ 100.0 41 PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: crystal structure of secye translocon from thermus2 thermophilus 5 c2akiY_ 100.0 100 PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli 6 c2wwbA_ 100.0 22 PDB header:ribosome Chain: A: PDB Molecule:protein transport protein sec61 subunit alpha isoform 1; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome 7 d1rh5a_ 100.0 19 Fold:Preprotein translocase SecY subunit Superfamily:Preprotein translocase SecY subunit Family:Preprotein translocase SecY subunit 8 c2wwaA_ 100.0 19 PDB header:ribosome Chain: A: PDB Molecule:sec sixty-one protein homolog; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome 9 c3mp7A_ 100.0 21 PDB header:protein transport Chain: A: PDB Molecule:preprotein translocase subunit secy; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes 10 c2nscA_ 70.2 25 PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima 11 d1p9ya_ 67.5 11 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 12 d1t11a2 56.4 16 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 13 d1w26a2 52.3 17 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 14 c2d3o1_ 46.0 31 PDB header:ribosome Chain: 1: PDB Molecule:trigger factor; PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans 15 c1w26B_ 38.5 25 PDB header:chaperone Chain: B: PDB Molecule:trigger factor; PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins 16 c3kysC_ 28.0 38 PDB header:transcription/protein binding Chain: C: PDB Molecule:transcriptional enhancer factor tef-1; PDBTitle: crystal structure of human yap and tead complex 17 d1zl8a1 27.1 18 Fold:L27 domain Superfamily:L27 domain Family:L27 domain 18 c1t11A_ 25.8 16 PDB header:chaperone Chain: A: PDB Molecule:trigger factor; PDBTitle: trigger factor 19 c3l15A_ 25.4 45 PDB header:transcription Chain: A: PDB Molecule:transcriptional enhancer factor tef-4; PDBTitle: human tead2 transcriptional factor 20 d1y74a1 23.5 23 Fold:L27 domain Superfamily:L27 domain Family:L27 domain 21 d1wpga4 not modelled 22.0 10 Fold:Calcium ATPase, transmembrane domain M Superfamily:Calcium ATPase, transmembrane domain M Family:Calcium ATPase, transmembrane domain M 22 d1wmxb_ not modelled 16.6 33 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 30 carbohydrate binding module, CBM30 (PKD repeat) 23 c2bbjB_ not modelled 8.4 15 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 24 d1ebfa2 not modelled 7.9 29 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Homoserine dehydrogenase-like 25 d1zq1c1 not modelled 7.7 21 Fold:GatB/YqeY motif Superfamily:GatB/YqeY motif Family:GatB/GatE C-terminal domain-like 26 c3kpaB_ not modelled 7.5 36 PDB header:ligase Chain: B: PDB Molecule:probable ubiquitin fold modifier conjugating enzyme; PDBTitle: ubiquitin fold modifier conjugating enzyme from leishmania major2 (probable) 27 d1to9a_ not modelled 7.4 25 Fold:Heme oxygenase-like Superfamily:Heme oxygenase-like Family:TENA/THI-4 28 c1to9A_ not modelled 7.4 25 PDB header:biosynthetic protein Chain: A: PDB Molecule:thi-4 protein; PDBTitle: crystal structure of thi-4 protein from bacillus subtilis 29 d1jjcb1 not modelled 7.0 19 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Domains B1 and B5 of PheRS-beta, PheT 30 d2bs2c1 not modelled 7.0 11 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC 31 c3qxlB_ not modelled 6.2 27 PDB header:signaling protein Chain: B: PDB Molecule:ras-specific guanine nucleotide-releasing factor ralgps1; PDBTitle: crystal structure of the cdc25 domain from ral-specific guanine-2 nucleotide exchange factor ralgps1a 32 d1xo1a1 not modelled 6.2 16 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 33 c2voyK_ not modelled 6.0 11 PDB header:hydrolase Chain: K: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 34 d2gycf1 not modelled 5.6 28 Fold:Ribosomal protein L9 C-domain Superfamily:Ribosomal protein L9 C-domain Family:Ribosomal protein L9 C-domain 35 c1mhsA_ not modelled 5.6 13 PDB header:membrane protein, proton transport Chain: A: PDB Molecule:plasma membrane atpase; PDBTitle: model of neurospora crassa proton atpase 36 c1ysmA_ not modelled 5.5 30 PDB header:metal binding protein Chain: A: PDB Molecule:calcyclin-binding protein; PDBTitle: nmr structure of n-terminal domain (residues 1-77) of siah-2 interacting protein. 37 d1ysma1 not modelled 5.5 30 Fold:Long alpha-hairpin Superfamily:Calcyclin-binding protein-like Family:Siah interacting protein N terminal domain-like 38 d1uv7a_ not modelled 5.5 14 Fold:RRF/tRNA synthetase additional domain-like Superfamily:General secretion pathway protein M, EpsM Family:General secretion pathway protein M, EpsM 39 c1uv7A_ not modelled 5.5 14 PDB header:transport Chain: A: PDB Molecule:general secretion pathway protein m; PDBTitle: periplasmic domain of epsm from vibrio cholerae 40 d2huec1 not modelled 5.5 19 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 41 c2k72A_ not modelled 5.4 27 PDB header:hydrolase Chain: A: PDB Molecule:matrix metalloproteinase-23; PDBTitle: solution nmr structure of toxin-like potassium channel2 blocking domain in mmp23 42 d1nexa2 not modelled 5.3 35 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 43 d1qd1a2 not modelled 5.3 16 Fold:Ferredoxin-like Superfamily:Formiminotransferase domain of formiminotransferase-cyclodeaminase. Family:Formiminotransferase domain of formiminotransferase-cyclodeaminase. 44 c8tfvA_ not modelled 5.1 18 PDB header:antimicrobial Chain: A: PDB Molecule:protein (thanatin); PDBTitle: insect defense peptide

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