Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	H	L	F	A	G	L	D	L	H	T	G	L	L	L	L	L	A	L	A	F	V	L	F	Y	E	A	I	N	G	F	H	D	T	A	N	A	V	A	T	V	I	Y	T	R	A	M	R	S	Q	L	A	V	V	M	A	A	V	F
Secondary structure
SS confidence
Disorder		?	?			?	?																																								?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	F	L	G	V	L	L	G	G	L	S	V	A	Y	A	I	V	H	M	L	P	T	D	L	L	L	N	M	G	S	S	H	G	L	A	M	V	F	S	M	L	L	A	A	I	I	W	N	L	G	T	W	Y	F	G	L	P	A	S	S
Secondary structure
SS confidence
Disorder																							?	?	?		?	?	?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	H	T	L	I	G	A	I	I	G	I	G	L	T	N	A	L	M	T	G	T	S	V	V	D	A	L	N	I	P	K	V	L	S	I	F	G	S	L	I	V	S	P	I	V	G	L	V	F	A	G	G	L	I	F	L	L	R	R	Y
Secondary structure
SS confidence
Disorder																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		W	S	G	T	K	K	R	A	R	I	H	L	T	P	A	E	R	E	K	K	D	G	K	K	K	P	P	F	W	T	R	I	A	L	I	L	S	A	I	G	V	A	F	S	H	G	A	N	D	G	Q	K	G	I	G	L	V	M	L	V
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	I	G	V	A	P	A	G	F	V	V	N	M	N	A	T	G	Y	E	I	T	R	T	R	D	A	I	N	N	V	E	A	Y	F	E	Q	H	P	A	L	L	K	Q	A	T	G	A	D	Q	L	V	P	A	P	E	A	G	A	T	Q
Secondary structure
SS confidence
Disorder																	?												?	?				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		P	A	E	F	H	C	H	P	S	N	T	I	N	A	L	N	R	L	K	G	M	L	T	T	D	V	E	S	Y	D	K	L	S	L	D	Q	R	S	Q	M	R	R	I	M	L	C	V	S	D	T	I	D	K	V	V	K	M	P	G	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		S	A	D	D	Q	R	L	L	K	K	L	K	S	D	M	L	S	T	I	E	Y	A	P	V	W	I	I	M	A	V	A	L	A	L	G	I	G	T	M	I	G	W	R	R	V	A	T	T	I	G	E	K	I	G	K	K	G	M	T	Y
Secondary structure
SS confidence
Disorder																?	?	?	?	?																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		A	Q	G	M	S	A	Q	M	T	A	A	V	S	I	G	L	A	S	Y	T	G	M	P	V	S	T	T	H	V	L	S	S	S	V	A	G	T	M	V	V	D	G	G	G	L	Q	R	K	T	V	T	S	I	L	M	A	W	V	F	T
Secondary structure
SS confidence
Disorder																					?					?													?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.
Sequence		L	P	A	A	V	L	L	S	G	G	L	Y	W	L	S	L	Q	F	L
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 2knc chain A Region: 377 - 393 Aligned: 17 Modelled: 17 Confidence: 27.9% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2ia2 chain D Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 20.6% Identity: 15% PDB header:transcription Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: the crystal structure of a putative transcriptional regulator rha061952 from rhodococcus sp. rha1 Phyre2 PDB 2bru chain C Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 17.0% Identity: 42% PDB header:oxidoreductase Chain: C: PDB Molecule:nad(p) transhydrogenase subunit beta; PDBTitle: complex of the domain i and domain iii of escherichia coli2 transhydrogenase Phyre2 PDB 1d4o chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 15.2% Identity: 42% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Transhydrogenase domain III (dIII) Phyre2 PDB 1pt9 chain B Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 15.0% Identity: 42% PDB header:oxidoreductase Chain: B: PDB Molecule:nad(p) transhydrogenase, mitochondrial; PDBTitle: crystal structure analysis of the diii component of transhydrogenase2 with a thio-nicotinamide nucleotide analogue Phyre2 PDB 1pno chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 14.9% Identity: 33% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Transhydrogenase domain III (dIII) Phyre2 PDB 2g7u chain B Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 14.3% Identity: 19% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1 Phyre2 PDB 2k1a chain A Region: 378 - 393 Aligned: 16 Modelled: 16 Confidence: 14.1% Identity: 19% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 3r4k chain D Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 11.6% Identity: 22% PDB header:dna binding protein Chain: D: PDB Molecule:transcriptional regulator, iclr family; PDBTitle: crystal structure of a putative iclr transcriptional regulator2 (tm1040_3717) from silicibacter sp. tm1040 at 2.46 a resolution Phyre2 PDB 1mkm chain A Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 11.1% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:iclr transcriptional regulator; PDBTitle: crystal structure of the thermotoga maritima iclr Phyre2 PDB 1h6i chain A Region: 14 - 177 Aligned: 162 Modelled: 164 Confidence: 9.7% Identity: 13% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 2w2e chain A Region: 3 - 187 Aligned: 175 Modelled: 185 Confidence: 9.7% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 Phyre2 PDB 2xro chain E Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 9.5% Identity: 22% PDB header:dna-binding protein/dna Chain: E: PDB Molecule:hth-type transcriptional regulator ttgv; PDBTitle: crystal structure of ttgv in complex with its dna operator Phyre2 PDB 1vlp chain A domain 2 Region: 434 - 448 Aligned: 15 Modelled: 15 Confidence: 8.5% Identity: 27% Fold: TIM beta/alpha-barrel Superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like Family: Monomeric nicotinate phosphoribosyltransferase C-terminal domain Phyre2 PDB 2o0y chain B Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 8.4% Identity: 22% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp. Phyre2 PDB 1ybe chain A domain 1 Region: 434 - 448 Aligned: 15 Modelled: 15 Confidence: 8.4% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like Family: Monomeric nicotinate phosphoribosyltransferase C-terminal domain Phyre2 PDB 2axt chain J domain 1 Region: 381 - 402 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 27% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 PDB 1s7b chain A Region: 54 - 157 Aligned: 87 Modelled: 91 Confidence: 8.0% Identity: 10% Fold: Multidrug resistance efflux transporter EmrE Superfamily: Multidrug resistance efflux transporter EmrE Family: Multidrug resistance efflux transporter EmrE Phyre2 PDB 1mkm chain A domain 1 Region: 436 - 462 Aligned: 27 Modelled: 27 Confidence: 7.4% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Transcriptional regulator IclR, N-terminal domain Phyre2 PDB 1yir chain A domain 1 Region: 434 - 448 Aligned: 15 Modelled: 15 Confidence: 6.3% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like Family: Monomeric nicotinate phosphoribosyltransferase C-terminal domain Phyre2 1 c2kncA_ 2 c2ia2D_ 3 c2bruC_ 4 d1d4oa_ 5 c1pt9B_ 6 d1pnoa_ 7 c2g7uB_ 8 c2k1aA_ 9 c3r4kD_ 10 c1mkmA_ 11 d1h6ia_ 12 c2w2eA_ 13 c2xroE_ 14 d1vlpa2 15 c2o0yB_ 16 d1ybea1 17 d2axtj1 18 d1s7ba_ 19 d1mkma1 20 d1yira1 21 22 23 24

Detailed template information

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

1 c2kncA_ 27.9 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 c2ia2D_ 20.6 15 PDB header:transcription Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: the crystal structure of a putative transcriptional regulator rha061952 from rhodococcus sp. rha1 3 c2bruC_ 17.0 42 PDB header:oxidoreductase Chain: C: PDB Molecule:nad(p) transhydrogenase subunit beta; PDBTitle: complex of the domain i and domain iii of escherichia coli2 transhydrogenase 4 d1d4oa_ 15.2 42 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Transhydrogenase domain III (dIII) 5 c1pt9B_ 15.0 42 PDB header:oxidoreductase Chain: B: PDB Molecule:nad(p) transhydrogenase, mitochondrial; PDBTitle: crystal structure analysis of the diii component of transhydrogenase2 with a thio-nicotinamide nucleotide analogue 6 d1pnoa_ 14.9 33 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Transhydrogenase domain III (dIII) 7 c2g7uB_ 14.3 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1 8 c2k1aA_ 14.1 19 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 9 c3r4kD_ 11.6 22 PDB header:dna binding protein Chain: D: PDB Molecule:transcriptional regulator, iclr family; PDBTitle: crystal structure of a putative iclr transcriptional regulator2 (tm1040_3717) from silicibacter sp. tm1040 at 2.46 a resolution 10 c1mkmA_ 11.1 19 PDB header:transcription Chain: A: PDB Molecule:iclr transcriptional regulator; PDBTitle: crystal structure of the thermotoga maritima iclr 11 d1h6ia_ 9.7 13 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 12 c2w2eA_ 9.7 14 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 13 c2xroE_ 9.5 22 PDB header:dna-binding protein/dna Chain: E: PDB Molecule:hth-type transcriptional regulator ttgv; PDBTitle: crystal structure of ttgv in complex with its dna operator 14 d1vlpa2 8.5 27 Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:Monomeric nicotinate phosphoribosyltransferase C-terminal domain 15 c2o0yB_ 8.4 22 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp. 16 d1ybea1 8.4 20 Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:Monomeric nicotinate phosphoribosyltransferase C-terminal domain 17 d2axtj1 8.3 27 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 18 d1s7ba_ 8.0 10 Fold:Multidrug resistance efflux transporter EmrE Superfamily:Multidrug resistance efflux transporter EmrE Family:Multidrug resistance efflux transporter EmrE 19 d1mkma1 7.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator IclR, N-terminal domain 20 d1yira1 6.3 20 Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:Monomeric nicotinate phosphoribosyltransferase C-terminal domain 21 d1bw6a_ not modelled 6.1 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 22 d2eiaa2 not modelled 6.0 11 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 23 c1vlpA_ not modelled 5.9 27 PDB header:transferase Chain: A: PDB Molecule:nicotinate phosphoribosyltransferase; PDBTitle: crystal structure of a putative nicotinate phosphoribosyltransferase2 (yor209c, npt1) from saccharomyces cerevisiae at 1.75 a resolution 24 c2xgyA_ not modelled 5.5 20 PDB header:viral protein/isomerase Chain: A: PDB Molecule:relik capsid n-terminal domain; PDBTitle: complex of rabbit endogenous lentivirus (relik)capsid with2 cyclophilin a

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