Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	D	A	K	K	Q	G	R	S	N	K	A	M	T	F	F	V	C	F	L	A	A	L	A	G	L	L	F	G	L	D	I	G	V	I	A	G	A	L	P	F	I	A	D	E	F	Q	I	T	S	H	T	Q	E	W	V	V	S	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	M	F	G	A	A	V	G	A	V	G	S	G	W	L	S	F	K	L	G	R	K	K	S	L	M	I	G	A	I	L	F	V	A	G	S	L	F	S	A	A	A	P	N	V	E	V	L	I	L	S	R	V	L	L	G	L	A	V	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	A	S	Y	T	A	P	L	Y	L	S	E	I	A	P	E	K	I	R	G	S	M	I	S	M	Y	Q	L	M	I	T	I	G	I	L	G	A	Y	L	S	D	T	A	F	S	Y	T	G	A	W	R	W	M	L	G	V	I	I	I	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	I	L	L	L	I	G	V	F	F	L	P	D	S	P	R	W	F	A	A	K	R	R	F	V	D	A	E	R	V	L	L	R	L	R	D	T	S	A	E	A	K	R	E	L	D	E	I	R	E	S	L	Q	V	K	Q	S	G	W	A
Secondary structure
SS confidence
Disorder																																																											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	F	K	E	N	S	N	F	R	R	A	V	F	L	G	V	L	L	Q	V	M	Q	Q	F	T	G	M	N	V	I	M	Y	Y	A	P	K	I	F	E	L	A	G	Y	T	N	T	T	E	Q	M	W	G	T	V	I	V	G	L	T	N
Secondary structure
SS confidence
Disorder					?		?	?																																		?	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	L	A	T	F	I	A	I	G	L	V	D	R	W	G	R	K	P	T	L	T	L	G	F	L	V	M	A	A	G	M	G	V	L	G	T	M	M	H	I	G	I	H	S	P	S	A	Q	Y	F	A	I	A	M	L	L	M	F	I	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		G	F	A	M	S	A	G	P	L	I	W	V	L	C	S	E	I	Q	P	L	K	G	R	D	F	G	I	T	C	S	T	A	T	N	W	I	A	N	M	I	V	G	A	T	F	L	T	M	L	N	T	L	G	N	A	N	T	F	W	V
Secondary structure
SS confidence
Disorder																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.
Sequence		Y	A	A	L	N	V	L	F	I	L	L	T	L	W	L	V	P	E	T	K	H	V	S	L	E	H	I	E	R	N	L	M	K	G	R	K	L	R	E	I	G	A	H	D
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 1pw4 chain A Region: 3 - 449 Aligned: 416 Modelled: 421 Confidence: 100.0% Identity: 13% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3o7p chain A Region: 13 - 439 Aligned: 407 Modelled: 423 Confidence: 100.0% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 1pv7 chain A Region: 12 - 453 Aligned: 411 Modelled: 423 Confidence: 100.0% Identity: 13% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2xut chain C Region: 17 - 432 Aligned: 413 Modelled: 413 Confidence: 100.0% Identity: 12% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 2gfp chain A Region: 18 - 429 Aligned: 370 Modelled: 377 Confidence: 100.0% Identity: 12% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3ff5 chain B Region: 438 - 453 Aligned: 16 Modelled: 16 Confidence: 35.4% Identity: 19% PDB header:protein transport Chain: B: PDB Molecule:peroxisomal biogenesis factor 14; PDBTitle: crystal structure of the conserved n-terminal domain of the2 peroxisomal matrix-protein-import receptor, pex14p Phyre2 PDB 1fs1 chain B domain 1 Region: 440 - 451 Aligned: 12 Modelled: 12 Confidence: 26.1% Identity: 25% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 3mmy chain F Region: 435 - 456 Aligned: 22 Modelled: 22 Confidence: 25.5% Identity: 27% PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 Phyre2 PDB 2w85 chain A Region: 438 - 453 Aligned: 16 Modelled: 16 Confidence: 25.4% Identity: 19% PDB header:protein transport Chain: A: PDB Molecule:peroxisomal membrane anchor protein pex14; PDBTitle: structure of pex14 in compex with pex19 Phyre2 PDB 3c9p chain A Region: 438 - 450 Aligned: 13 Modelled: 13 Confidence: 21.5% Identity: 23% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 Phyre2 PDB 2wwa chain A Region: 418 - 463 Aligned: 46 Modelled: 46 Confidence: 20.9% Identity: 15% 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 1wmi chain B domain 1 Region: 434 - 459 Aligned: 26 Modelled: 26 Confidence: 16.7% Identity: 27% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: RelB-like Family: RelB-like Phyre2 PDB 1fs2 chain B domain 1 Region: 440 - 451 Aligned: 12 Modelled: 12 Confidence: 16.1% Identity: 25% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 2j85 chain A domain 1 Region: 436 - 455 Aligned: 20 Modelled: 20 Confidence: 15.8% Identity: 25% Fold: STIV B116-like Superfamily: STIV B116-like Family: STIV B116-like Phyre2 PDB 2g9p chain A Region: 71 - 84 Aligned: 14 Modelled: 14 Confidence: 13.7% Identity: 43% PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom Phyre2 PDB 1by0 chain A Region: 441 - 464 Aligned: 24 Modelled: 24 Confidence: 13.7% Identity: 33% PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen Phyre2 PDB 3qnq chain D Region: 402 - 457 Aligned: 53 Modelled: 56 Confidence: 12.5% Identity: 13% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1b78 chain A Region: 434 - 459 Aligned: 26 Modelled: 26 Confidence: 12.4% Identity: 12% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: ITPase (Ham1) Phyre2 PDB 1v7r chain A Region: 434 - 459 Aligned: 26 Modelled: 26 Confidence: 11.9% Identity: 12% Fold: Anticodon-binding domain-like Superfamily: ITPase-like Family: ITPase (Ham1) Phyre2 PDB 1nex chain A domain 1 Region: 440 - 464 Aligned: 25 Modelled: 25 Confidence: 11.9% Identity: 16% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 1 d1pw4a_ 2 c3o7pA_ 3 d1pv7a_ 4 c2xutC_ 5 c2gfpA_ 6 c3ff5B_ 7 d1fs1b1 8 c3mmyF_ 9 c2w85A_ 10 c3c9pA_ 11 c2wwaA_ 12 d1wmib1 13 d1fs2b1 14 d2j85a1 15 c2g9pA_ 16 c1by0A_ 17 c3qnqD_ 18 d1b78a_ 19 d1v7ra_ 20 d1nexa1 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

Detailed template information

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

1 d1pw4a_ 100.0 13 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c3o7pA_ 100.0 15 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 3 d1pv7a_ 100.0 13 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 4 c2xutC_ 100.0 12 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 5 c2gfpA_ 100.0 12 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 6 c3ff5B_ 35.4 19 PDB header:protein transport Chain: B: PDB Molecule:peroxisomal biogenesis factor 14; PDBTitle: crystal structure of the conserved n-terminal domain of the2 peroxisomal matrix-protein-import receptor, pex14p 7 d1fs1b1 26.1 25 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 8 c3mmyF_ 25.5 27 PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 9 c2w85A_ 25.4 19 PDB header:protein transport Chain: A: PDB Molecule:peroxisomal membrane anchor protein pex14; PDBTitle: structure of pex14 in compex with pex19 10 c3c9pA_ 21.5 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 11 c2wwaA_ 20.9 15 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 12 d1wmib1 16.7 27 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:RelB-like Family:RelB-like 13 d1fs2b1 16.1 25 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 14 d2j85a1 15.8 25 Fold:STIV B116-like Superfamily:STIV B116-like Family:STIV B116-like 15 c2g9pA_ 13.7 43 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 16 c1by0A_ 13.7 33 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 17 c3qnqD_ 12.5 13 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 18 d1b78a_ 12.4 12 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 19 d1v7ra_ 11.9 12 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 20 d1nexa1 11.9 16 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 21 c2f9jP_ not modelled 11.6 22 PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 22 d2csba1 not modelled 11.2 47 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 23 d2ovra1 not modelled 10.5 25 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 24 d1ofcx1 not modelled 8.0 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 25 c2kncB_ not modelled 8.0 8 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 26 d2hkja1 not modelled 7.8 21 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain 27 c3f46A_ not modelled 7.7 29 PDB header:oxidoreductase Chain: A: PDB Molecule:5,10-methenyltetrahydromethanopterin hydrogenase; PDBTitle: the crystal structure of c176a mutated [fe]-hydrogenase (hmd)2 holoenzyme from methanocaldococcus jannaschii 28 d1k7ka_ not modelled 7.6 8 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 29 d2g5ca1 not modelled 7.3 15 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:TyrA dimerization domain-like 30 d2cara1 not modelled 7.3 8 Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:ITPase (Ham1) 31 d1xpja_ not modelled 6.3 26 Fold:HAD-like Superfamily:HAD-like Family:Hypothetical protein VC0232 32 c3oc5A_ not modelled 6.2 32 PDB header:cell adhesion Chain: A: PDB Molecule:toxin coregulated pilus biosynthesis protein f; PDBTitle: crystal structure of the vibrio cholerae secreted colonization factor2 tcpf 33 d1e3oc2 not modelled 6.1 35 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 34 c1egpA_ not modelled 6.1 13 PDB header:proteinase inhibitor Chain: A: PDB Molecule:eglin-c; PDBTitle: proteinase inhibitor eglin c with hydrolysed reactive center 35 c2xq2A_ not modelled 6.0 8 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 36 d2a26a1 not modelled 6.0 29 Fold:Long alpha-hairpin Superfamily:Calcyclin-binding protein-like Family:Siah interacting protein N terminal domain-like 37 d2a7wa1 not modelled 6.0 7 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:HisE-like (PRA-PH) 38 c2a7wF_ not modelled 6.0 7 PDB header:hydrolase Chain: F: PDB Molecule:phosphoribosyl-atp pyrophosphatase; PDBTitle: crystal structure of phosphoribosyl-atp pyrophosphatase2 from chromobacterium violaceum (atcc 12472). nesg target3 cvr7 39 c3b9yA_ not modelled 6.0 10 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 40 d1xtda2 not modelled 5.8 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 41 d1ni8a_ not modelled 5.8 36 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 42 d1ov9a_ not modelled 5.7 27 Fold:H-NS histone-like proteins Superfamily:H-NS histone-like proteins Family:H-NS histone-like proteins 43 d1y7oa1 not modelled 5.7 17 Fold:ClpP/crotonase Superfamily:ClpP/crotonase Family:Clp protease, ClpP subunit 44 c3ervA_ not modelled 5.7 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative c39-like peptidase; PDBTitle: crystal structure of an putative c39-like peptidase from2 bacillus anthracis 45 c3hm5A_ not modelled 5.6 20 PDB header:transcription Chain: A: PDB Molecule:dna methyltransferase 1-associated protein 1; PDBTitle: sant domain of human dna methyltransferase 1 associated2 protein 1 46 d1v54i_ not modelled 5.5 11 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIc Family:Mitochondrial cytochrome c oxidase subunit VIc 47 c2p1nD_ not modelled 5.4 25 PDB header:signaling protein Chain: D: PDB Molecule:skp1-like protein 1a; PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase 48 d1pyya2 not modelled 5.3 22 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 49 d2ipqx1 not modelled 5.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:STY4665 C-terminal domain-like 50 c1cirA_ not modelled 5.1 20 PDB header:serine protease inhibitor Chain: A: PDB Molecule:chymotrypsin inhibitor 2; PDBTitle: complex of two fragments of ci2 [(1-40)(dot)(41-64)] 51 d1xjsa_ not modelled 5.1 7 Fold:SufE/NifU Superfamily:SufE/NifU Family:NifU/IscU domain 52 d1xeqa1 not modelled 5.1 60 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:N-terminal, RNA-binding domain of nonstructural protein NS1 53 c2rddB_ not modelled 5.0 10 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix.

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