Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	I	A	T	I	K	T	G	L	A	S	L	A	M	L	P	G	L	V	M	A	A	P	A	V	A	D	K	A	D	N	A	F	M	M	I	C	T	A	L	V	L	F	M	T	I	P	G	I	A	L	F	Y	G	G	L	I	R	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	N	V	L	S	M	L	T	Q	V	T	V	T	F	A	L	V	C	I	L	W	V	V	Y	G	Y	S	L	A	F	G	E	G	N	N	F	F	G	N	I	N	W	L	M	L	K	N	I	E	L	T	A	V	M	G	S	I	Y	Q	Y
Secondary structure
SS confidence
Disorder																																																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	H	V	A	F	Q	G	S	F	A	C	I	T	V	G	L	I	V	G	A	L	A	E	R	I	R	F	S	A	V	L	I	F	V	V	V	W	L	T	L	S	Y	I	P	I	A	H	M	V	W	G	G	G	L	L	A	S	H	G	A
Secondary structure
SS confidence
Disorder																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	D	F	A	G	G	T	V	V	H	I	N	A	A	I	A	G	L	V	G	A	Y	L	I	G	K	R	V	G	F	G	K	E	A	F	K	P	H	N	L	P	M	V	F	T	G	T	A	I	L	Y	I	G	W	F	G	F	N	A	G
Secondary structure
SS confidence
Disorder																														?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	A	G	T	A	N	E	I	A	A	L	A	F	V	N	T	V	V	A	T	A	A	A	I	L	G	W	I	F	G	E	W	A	L	R	G	K	P	S	L	L	G	A	C	S	G	A	I	A	G	L	V	G	V	T	P	A	C	G	Y
Secondary structure
SS confidence
Disorder					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		I	G	V	G	G	A	L	I	I	G	V	V	A	G	L	A	G	L	W	G	V	T	M	L	K	R	L	L	R	V	D	D	P	C	D	V	F	G	V	H	G	V	C	G	I	V	G	C	I	M	T	G	I	F	A	A	S	S	L	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		G	V	G	F	A	E	G	V	T	M	G	H	Q	L	L	V	Q	L	E	S	I	A	I	T	I	V	W	S	G	V	V	A	F	I	G	Y	K	L	A	D	L	T	V	G	L	R	V	P	E	E	Q	E	R	E	G	L	D	V	N	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		H	G	E	N	A	Y	N	A
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 2b2h chain A Region: 28 - 427 Aligned: 389 Modelled: 400 Confidence: 100.0% Identity: 39% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 1u7g chain A Region: 25 - 407 Aligned: 383 Modelled: 383 Confidence: 100.0% Identity: 96% Fold: Ammonium transporter Superfamily: Ammonium transporter Family: Ammonium transporter Phyre2 PDB 3c1i chain A Region: 24 - 408 Aligned: 366 Modelled: 385 Confidence: 100.0% Identity: 99% PDB header:transport protein Chain: A: PDB Molecule:ammonia channel; PDBTitle: substrate binding, deprotonation and selectivity at the2 periplasmic entrance of the e. coli ammonia channel amtb Phyre2 PDB 3hd6 chain A Region: 39 - 424 Aligned: 369 Modelled: 386 Confidence: 100.0% Identity: 21% 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 3b9y chain A Region: 42 - 426 Aligned: 343 Modelled: 349 Confidence: 100.0% Identity: 23% 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 3k3g chain A Region: 251 - 330 Aligned: 80 Modelled: 80 Confidence: 30.4% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea Phyre2 PDB 3qnq chain D Region: 378 - 414 Aligned: 37 Modelled: 37 Confidence: 13.1% Identity: 14% 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 1u1h chain A domain 2 Region: 409 - 423 Aligned: 15 Modelled: 15 Confidence: 13.0% Identity: 47% Fold: TIM beta/alpha-barrel Superfamily: UROD/MetE-like Family: Cobalamin-independent methionine synthase Phyre2 PDB 2knc chain A Region: 187 - 218 Aligned: 32 Modelled: 32 Confidence: 12.1% Identity: 25% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2nq5 chain A Region: 409 - 423 Aligned: 15 Modelled: 15 Confidence: 11.8% Identity: 53% PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: crystal structure of methyltransferase from streptococcus2 mutans Phyre2 PDB 1u1h chain A domain 1 Region: 406 - 427 Aligned: 22 Modelled: 22 Confidence: 11.4% Identity: 9% Fold: TIM beta/alpha-barrel Superfamily: UROD/MetE-like Family: Cobalamin-independent methionine synthase Phyre2 PDB 3l7s chain A Region: 409 - 423 Aligned: 15 Modelled: 15 Confidence: 10.8% Identity: 53% PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--homocysteine PDBTitle: crystal structure of mete coordinated with zinc from streptococcus2 mutans Phyre2 PDB 1t7l chain A Region: 409 - 423 Aligned: 15 Modelled: 15 Confidence: 10.7% Identity: 67% PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: crystal structure of cobalamin-independent methionine2 synthase from t. maritima Phyre2 PDB 1u22 chain A Region: 409 - 423 Aligned: 15 Modelled: 15 Confidence: 10.3% Identity: 47% PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: a. thaliana cobalamine independent methionine synthase Phyre2 PDB 3lr4 chain A Region: 318 - 346 Aligned: 28 Modelled: 29 Confidence: 8.7% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: periplasmic domain of the riss sensor protein from burkholderia2 pseudomallei, barium phased at low ph Phyre2 PDB 1z9h chain A domain 1 Region: 299 - 334 Aligned: 36 Modelled: 36 Confidence: 8.6% Identity: 19% Fold: GST C-terminal domain-like Superfamily: GST C-terminal domain-like Family: Glutathione S-transferase (GST), C-terminal domain Phyre2 PDB 1vk5 chain A Region: 393 - 421 Aligned: 29 Modelled: 29 Confidence: 8.5% Identity: 21% Fold: Hypothetical protein At3g22680 Superfamily: Hypothetical protein At3g22680 Family: Hypothetical protein At3g22680 Phyre2 PDB 1vk5 chain A Region: 393 - 421 Aligned: 29 Modelled: 29 Confidence: 8.5% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:expressed protein; PDBTitle: x-ray structure of gene product from arabidopsis thaliana at3g22680 Phyre2 PDB 3da4 chain B Region: 165 - 173 Aligned: 9 Modelled: 9 Confidence: 8.4% Identity: 56% PDB header:antibiotic Chain: B: PDB Molecule:colicin-m; PDBTitle: crystal structure of colicin m, a novel phosphatase2 specifically imported by escherichia coli Phyre2 PDB 2dp3 chain A Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 6.3% Identity: 33% PDB header:isomerase Chain: A: PDB Molecule:triosephosphate isomerase; PDBTitle: crystal structure of a double mutant (c202a/a198v) of triosephosphate2 isomerase from giardia lamblia Phyre2 1 c2b2hA_ 2 d1u7ga_ 3 c3c1iA_ 4 c3hd6A_ 5 c3b9yA_ 6 c3k3gA_ 7 c3qnqD_ 8 d1u1ha2 9 c2kncA_ 10 c2nq5A_ 11 d1u1ha1 12 c3l7sA_ 13 c1t7lA_ 14 c1u22A_ 15 c3lr4A_ 16 d1z9ha1 17 d1vk5a_ 18 c1vk5A_ 19 c3da4B_ 20 c2dp3A_ 21 22 23 24 25 26 27

Detailed template information

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

1 c2b2hA_ 100.0 39 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 2 d1u7ga_ 100.0 96 Fold:Ammonium transporter Superfamily:Ammonium transporter Family:Ammonium transporter 3 c3c1iA_ 100.0 99 PDB header:transport protein Chain: A: PDB Molecule:ammonia channel; PDBTitle: substrate binding, deprotonation and selectivity at the2 periplasmic entrance of the e. coli ammonia channel amtb 4 c3hd6A_ 100.0 21 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 5 c3b9yA_ 100.0 23 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 6 c3k3gA_ 30.4 15 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 7 c3qnqD_ 13.1 14 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 8 d1u1ha2 13.0 47 Fold:TIM beta/alpha-barrel Superfamily:UROD/MetE-like Family:Cobalamin-independent methionine synthase 9 c2kncA_ 12.1 25 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 c2nq5A_ 11.8 53 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: crystal structure of methyltransferase from streptococcus2 mutans 11 d1u1ha1 11.4 9 Fold:TIM beta/alpha-barrel Superfamily:UROD/MetE-like Family:Cobalamin-independent methionine synthase 12 c3l7sA_ 10.8 53 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate--homocysteine PDBTitle: crystal structure of mete coordinated with zinc from streptococcus2 mutans 13 c1t7lA_ 10.7 67 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: crystal structure of cobalamin-independent methionine2 synthase from t. maritima 14 c1u22A_ 10.3 47 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydropteroyltriglutamate-- PDBTitle: a. thaliana cobalamine independent methionine synthase 15 c3lr4A_ 8.7 18 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: periplasmic domain of the riss sensor protein from burkholderia2 pseudomallei, barium phased at low ph 16 d1z9ha1 8.6 19 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain 17 d1vk5a_ 8.5 21 Fold:Hypothetical protein At3g22680 Superfamily:Hypothetical protein At3g22680 Family:Hypothetical protein At3g22680 18 c1vk5A_ 8.5 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:expressed protein; PDBTitle: x-ray structure of gene product from arabidopsis thaliana at3g22680 19 c3da4B_ 8.4 56 PDB header:antibiotic Chain: B: PDB Molecule:colicin-m; PDBTitle: crystal structure of colicin m, a novel phosphatase2 specifically imported by escherichia coli 20 c2dp3A_ 6.3 33 PDB header:isomerase Chain: A: PDB Molecule:triosephosphate isomerase; PDBTitle: crystal structure of a double mutant (c202a/a198v) of triosephosphate2 isomerase from giardia lamblia 21 d1fftb2 not modelled 6.2 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 22 d1ttja_ not modelled 6.0 40 Fold:TIM beta/alpha-barrel Superfamily:Triosephosphate isomerase (TIM) Family:Triosephosphate isomerase (TIM) 23 d1ezfa_ not modelled 6.0 28 Fold:Terpenoid synthases Superfamily:Terpenoid synthases Family:Squalene synthase 24 c1ru7B_ not modelled 5.6 28 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin; PDBTitle: 1934 human h1 hemagglutinin 25 d1kv5a_ not modelled 5.6 40 Fold:TIM beta/alpha-barrel Superfamily:Triosephosphate isomerase (TIM) Family:Triosephosphate isomerase (TIM) 26 c2l9uA_ not modelled 5.2 33 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 27 c1mqlB_ not modelled 5.1 28 PDB header:viral protein Chain: B: PDB Molecule:hemagglutinin ha2 chain; PDBTitle: bha of ukr/63

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