Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	T	I	N	T	E	S	A	L	T	P	R	S	L	R	D	T	R	R	M	N	M	F	V	S	V	A	A	A	V	A	G	L	L	F	G	L	D	I	G	V	I	A	G	A	L	P	F	I	T	D	H	F	V	L	T	S	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	E	W	V	V	S	S	M	M	L	G	A	A	I	G	A	L	F	N	G	W	L	S	F	R	L	G	R	K	Y	S	L	M	A	G	A	I	L	F	V	L	G	S	I	G	S	A	F	A	T	S	V	E	M	L	I	A	A	R	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	L	G	I	A	V	G	I	A	S	Y	T	A	P	L	Y	L	S	E	M	A	S	E	N	V	R	G	K	M	I	S	M	Y	Q	L	M	V	T	L	G	I	V	L	A	F	L	S	D	T	A	F	S	Y	S	G	N	W	R	A	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	G	V	L	A	L	P	A	V	L	L	I	I	L	V	V	F	L	P	N	S	P	R	W	L	A	E	K	G	R	H	I	E	A	E	E	V	L	R	M	L	R	D	T	S	E	K	A	R	E	E	L	N	E	I	R	E	S	L	K
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	K	Q	G	G	W	A	L	F	K	I	N	R	N	V	R	R	A	V	F	L	G	M	L	L	Q	A	M	Q	Q	F	T	G	M	N	I	I	M	Y	Y	A	P	R	I	F	K	M	A	G	F	T	T	T	E	Q	Q	M	I	A	T
Secondary structure
SS confidence
Disorder				?	?		?					?		?	?																																		?	?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	V	V	G	L	T	F	M	F	A	T	F	I	A	V	F	T	V	D	K	A	G	R	K	P	A	L	K	I	G	F	S	V	M	A	L	G	T	L	V	L	G	Y	C	L	M	Q	F	D	N	G	T	A	S	S	G	L	S	W	L
Secondary structure
SS confidence
Disorder																																																			?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		S	V	G	M	T	M	M	C	I	A	G	Y	A	M	S	A	A	P	V	V	W	I	L	C	S	E	I	Q	P	L	K	C	R	D	F	G	I	T	C	S	T	T	T	N	W	V	S	N	M	I	I	G	A	T	F	L	T	L	L	D
Secondary structure
SS confidence
Disorder																												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.
Sequence		S	I	G	A	A	G	T	F	W	L	Y	T	A	L	N	I	A	F	V	G	I	T	F	W	L	I	P	E	T	K	N	V	T	L	E	H	I	E	R	K	L	M	A	G	E	K	L	R	N	I	G	V
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 - 459 Aligned: 422 Modelled: 430 Confidence: 100.0% Identity: 15% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3o7p chain A Region: 20 - 449 Aligned: 407 Modelled: 426 Confidence: 100.0% Identity: 13% 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: 13 - 460 Aligned: 411 Modelled: 429 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2gfp chain A Region: 25 - 439 Aligned: 370 Modelled: 371 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 2xut chain C Region: 24 - 442 Aligned: 416 Modelled: 416 Confidence: 100.0% Identity: 11% 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 3qnq chain D Region: 412 - 469 Aligned: 54 Modelled: 58 Confidence: 30.1% Identity: 17% 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 3b9y chain A Region: 11 - 247 Aligned: 229 Modelled: 237 Confidence: 26.4% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 3ff5 chain B Region: 448 - 463 Aligned: 16 Modelled: 16 Confidence: 25.7% Identity: 25% 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: 450 - 462 Aligned: 13 Modelled: 13 Confidence: 24.8% Identity: 31% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 3c9p chain A Region: 448 - 459 Aligned: 12 Modelled: 12 Confidence: 19.3% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 Phyre2 PDB 2w85 chain A Region: 448 - 470 Aligned: 23 Modelled: 23 Confidence: 18.6% Identity: 17% PDB header:protein transport Chain: A: PDB Molecule:peroxisomal membrane anchor protein pex14; PDBTitle: structure of pex14 in compex with pex19 Phyre2 PDB 2j85 chain A domain 1 Region: 446 - 465 Aligned: 20 Modelled: 20 Confidence: 15.5% Identity: 20% Fold: STIV B116-like Superfamily: STIV B116-like Family: STIV B116-like Phyre2 PDB 2f9j chain P Region: 450 - 467 Aligned: 18 Modelled: 18 Confidence: 15.4% Identity: 28% 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 Phyre2 PDB 1ofc chain X domain 1 Region: 448 - 462 Aligned: 15 Modelled: 15 Confidence: 13.7% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 2g9p chain A Region: 78 - 91 Aligned: 14 Modelled: 14 Confidence: 12.9% Identity: 36% 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 1fs2 chain B domain 1 Region: 450 - 461 Aligned: 12 Modelled: 12 Confidence: 12.8% Identity: 33% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 1egp chain A Region: 446 - 462 Aligned: 17 Modelled: 17 Confidence: 12.7% Identity: 18% PDB header:proteinase inhibitor Chain: A: PDB Molecule:eglin-c; PDBTitle: proteinase inhibitor eglin c with hydrolysed reactive center Phyre2 PDB 2csb chain A domain 1 Region: 453 - 469 Aligned: 17 Modelled: 17 Confidence: 12.2% Identity: 35% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Topoisomerase V repeat domain Phyre2 PDB 3hd6 chain A Region: 332 - 465 Aligned: 133 Modelled: 134 Confidence: 12.0% Identity: 9% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 3oc5 chain A Region: 446 - 464 Aligned: 19 Modelled: 19 Confidence: 11.6% Identity: 42% 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 Phyre2 1 d1pw4a_ 2 c3o7pA_ 3 d1pv7a_ 4 c2gfpA_ 5 c2xutC_ 6 c3qnqD_ 7 c3b9yA_ 8 c3ff5B_ 9 d1fs1b1 10 c3c9pA_ 11 c2w85A_ 12 d2j85a1 13 c2f9jP_ 14 d1ofcx1 15 c2g9pA_ 16 d1fs2b1 17 c1egpA_ 18 d2csba1 19 c3hd6A_ 20 c3oc5A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40

Detailed template information

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

1 d1pw4a_ 100.0 15 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c3o7pA_ 100.0 13 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 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 4 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 5 c2xutC_ 100.0 11 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. 6 c3qnqD_ 30.1 17 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 7 c3b9yA_ 26.4 10 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 8 c3ff5B_ 25.7 25 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 9 d1fs1b1 24.8 31 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 10 c3c9pA_ 19.3 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sp1917; PDBTitle: crystal structure of uncharacterized protein sp1917 11 c2w85A_ 18.6 17 PDB header:protein transport Chain: A: PDB Molecule:peroxisomal membrane anchor protein pex14; PDBTitle: structure of pex14 in compex with pex19 12 d2j85a1 15.5 20 Fold:STIV B116-like Superfamily:STIV B116-like Family:STIV B116-like 13 c2f9jP_ 15.4 28 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 14 d1ofcx1 13.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 15 c2g9pA_ 12.9 36 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 d1fs2b1 12.8 33 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 17 c1egpA_ 12.7 18 PDB header:proteinase inhibitor Chain: A: PDB Molecule:eglin-c; PDBTitle: proteinase inhibitor eglin c with hydrolysed reactive center 18 d2csba1 12.2 35 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 19 c3hd6A_ 12.0 9 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 20 c3oc5A_ 11.6 42 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 21 c3ervA_ not modelled 11.4 15 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 22 c3mmyF_ not modelled 10.0 23 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 23 d1nexa1 not modelled 9.8 25 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 24 d1u7ga_ not modelled 8.8 8 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 25 d2ovra1 not modelled 8.2 33 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 26 d1pyya2 not modelled 7.9 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 27 d2id1a1 not modelled 7.6 15 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Iojap/YbeB-like 28 d2hkja1 not modelled 7.1 18 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain 29 d1jx4a1 not modelled 7.1 41 Fold:Lesion bypass DNA polymerase (Y-family), little finger domain Superfamily:Lesion bypass DNA polymerase (Y-family), little finger domain Family:Lesion bypass DNA polymerase (Y-family), little finger domain 30 d1rp5a2 not modelled 6.6 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 31 d1nh2d1 not modelled 6.5 18 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 32 d1nvpd1 not modelled 6.3 12 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 33 c1bzgA_ not modelled 5.9 17 PDB header:hormone Chain: A: PDB Molecule:parathyroid hormone-related protein; PDBTitle: the solution structure of human parathyroid hormone-related2 protein (1-34) in near-physiological solution, nmr, 303 structures 34 d1ogmx1 not modelled 5.8 26 Fold:Dextranase, N-terminal domain Superfamily:Dextranase, N-terminal domain Family:Dextranase, N-terminal domain 35 d1wmib1 not modelled 5.8 27 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:RelB-like Family:RelB-like 36 d1cwpa_ not modelled 5.8 41 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Bromoviridae-like VP 37 c3hm5A_ not modelled 5.8 13 PDB header:transcription Chain: A: PDB Molecule:dna methyltransferase 1-associated protein 1; PDBTitle: sant domain of human dna methyltransferase 1 associated2 protein 1 38 d1k25a2 not modelled 5.8 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 39 d3cx5c2 not modelled 5.6 13 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 40 c1cwpB_ not modelled 5.4 41 PDB header:virus/rna Chain: B: PDB Molecule:coat protein; PDBTitle: structures of the native and swollen forms of cowpea2 chlorotic mottle virus determined by x-ray crystallography3 and cryo-electron microscopy

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