Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	A	I	S	L	I	N	S	G	V	A	W	F	V	A	A	A	V	L	A	F	L	F	S	F	Q	K	A	L	S	G	W	I	A	G	I	G	G	A	V	G	S	L	Y	T	A	A	A	G	F	T	V	L	T	G	A	V	G	V
Secondary structure
SS confidence
Disorder		?	?	?	?																				?	?	?	?																												?	?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	G	A	L	S	L	V	S	Y	D	V	Q	I	S	P	L	N	A	I	W	L	I	T	L	G	L	C	G	L	F	V	S	L	Y	N	I	D	W	H	R	H	A	Q	V	K	C	N	G	L	Q	I	N	M	L	M	A	A	A	V	C
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	V	I	A	S	N	L	G	M	F	V	V	M	A	E	I	M	A	L	C	A	V	F	L	T	S	N	S	K	E	G	K	L	W	F	A	L	G	R	L	G	T	L	L	L	A	I	A	C	W	L	L	W	Q	R	Y	G	T	L	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	R	L	L	D	M	R	M	Q	Q	L	P	L	G	S	D	I	W	L	L	G	V	I	G	F	G	L	L	A	G	I	I	P	L	H	G	W	V	P	Q	A	H	A	N	A	S	A	P	A	A	A	L	F	S	T	V	V	M	K	I
Secondary structure
SS confidence
Disorder							?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	L	L	G	I	L	T	L	S	L	L	G	G	N	A	P	L	W	W	G	I	A	L	L	V	L	G	M	I	T	A	F	V	G	G	L	Y	A	L	V	E	H	N	I	Q	R	L	L	A	Y	H	T	L	E	N	I	G	I	I	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		L	G	L	G	A	G	V	T	G	I	A	L	E	Q	P	A	L	I	A	L	G	L	V	G	G	L	Y	H	L	L	N	H	S	L	F	K	S	V	L	F	L	G	A	G	S	V	W	F	R	T	G	H	R	D	I	E	K	L	G	G
Secondary structure
SS confidence
Disorder									?	?	?	?	?	?	?	?		?																																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	G	K	K	M	P	V	I	S	I	A	M	L	V	G	L	M	A	M	A	A	L	P	P	L	N	G	F	A	G	E	W	V	I	Y	Q	S	F	F	K	L	S	N	S	G	A	F	V	A	R	L	L	G	P	L	L	A	V	G	L
Secondary structure
SS confidence
Disorder																																												?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		A	I	T	G	A	L	A	V	M	C	M	A	K	V	Y	G	V	T	F	L	G	A	P	R	T	K	E	A	E	N	A	T	C	A	P	L	L	M	S	V	S	V	V	A	L	A	I	C	C	V	I	G	G	V	A	A	P	W	L	L
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		P	M	L	S	A	A	V	P	L	P	L	E	P	A	N	T	T	V	S	Q	P	M	I	T	L	L	L	I	A	C	P	L	L	P	F	I	I	M	A	I	C	K	G	D	R	L	P	S	R	S	R	G	A	A	W	V	C	G	Y	D
Secondary structure
SS confidence
Disorder																	?		?			?																									?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence		H	E	K	S	M	V	I	T	A	H	G	F	A	M	P	V	K	Q	A	F	A	P	V	L	K	L	R	K	W	L	N	P	V	S	L	V	P	G	W	Q	C	E	G	S	A	L	L	F	R	R	M	A	L	V	E	L	A	V	L	V
Secondary structure
SS confidence
Disorder																																?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		V	I	I	V	S	R	G	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 3rko chain L Region: 4 - 592 Aligned: 546 Modelled: 575 Confidence: 100.0% Identity: 21% PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain M Region: 6 - 489 Aligned: 461 Modelled: 484 Confidence: 100.0% Identity: 21% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain N Region: 1 - 488 Aligned: 456 Modelled: 487 Confidence: 100.0% Identity: 18% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain K Region: 107 - 186 Aligned: 80 Modelled: 80 Confidence: 33.2% Identity: 16% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2l3i chain A Region: 278 - 289 Aligned: 12 Modelled: 12 Confidence: 24.2% Identity: 42% PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide Phyre2 PDB 1s1q chain A Region: 212 - 227 Aligned: 16 Modelled: 16 Confidence: 24.0% Identity: 19% Fold: UBC-like Superfamily: UBC-like Family: UEV domain Phyre2 PDB 1a6q chain A domain 1 Region: 367 - 400 Aligned: 34 Modelled: 34 Confidence: 19.3% Identity: 12% Fold: Another 3-helical bundle Superfamily: Protein serine/threonine phosphatase 2C, C-terminal domain Family: Protein serine/threonine phosphatase 2C, C-terminal domain Phyre2 PDB 1o8b chain B domain 1 Region: 281 - 306 Aligned: 23 Modelled: 26 Confidence: 14.4% Identity: 17% Fold: NagB/RpiA/CoA transferase-like Superfamily: NagB/RpiA/CoA transferase-like Family: D-ribose-5-phosphate isomerase (RpiA), catalytic domain Phyre2 PDB 3na2 chain C Region: 217 - 228 Aligned: 12 Modelled: 12 Confidence: 10.5% Identity: 25% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein of unknown function from mine drainage2 metagenome leptospirillum rubarum Phyre2 PDB 1j4n chain A Region: 329 - 453 Aligned: 106 Modelled: 125 Confidence: 9.3% Identity: 16% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 3d37 chain A domain 2 Region: 216 - 223 Aligned: 8 Modelled: 8 Confidence: 8.3% Identity: 38% Fold: Phage tail proteins Superfamily: Phage tail proteins Family: Baseplate protein-like Phyre2 PDB 2yrk chain A domain 1 Region: 537 - 555 Aligned: 19 Modelled: 19 Confidence: 6.9% Identity: 26% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: HkH motif-containing C2H2 finger Phyre2 PDB 2c1h chain A domain 1 Region: 536 - 559 Aligned: 24 Modelled: 24 Confidence: 6.6% Identity: 21% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) Phyre2 PDB 1l6s chain A Region: 536 - 559 Aligned: 24 Modelled: 24 Confidence: 6.3% Identity: 25% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) Phyre2 PDB 1gzg chain A Region: 536 - 559 Aligned: 24 Modelled: 24 Confidence: 6.2% Identity: 25% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) Phyre2 PDB 2q09 chain A domain 1 Region: 535 - 547 Aligned: 11 Modelled: 13 Confidence: 5.7% Identity: 36% Fold: Composite domain of metallo-dependent hydrolases Superfamily: Composite domain of metallo-dependent hydrolases Family: Imidazolonepropionase-like Phyre2 PDB 2z84 chain A Region: 535 - 539 Aligned: 5 Modelled: 5 Confidence: 5.4% Identity: 80% PDB header:hydrolase Chain: A: PDB Molecule:ufm1-specific protease 1; PDBTitle: insights from crystal and solution structures of mouse ufsp1 Phyre2 PDB 2imr chain A domain 1 Region: 530 - 542 Aligned: 13 Modelled: 13 Confidence: 5.4% Identity: 38% Fold: Composite domain of metallo-dependent hydrolases Superfamily: Composite domain of metallo-dependent hydrolases Family: DR0824-like Phyre2 1 c3rkoL_ 2 c3rkoM_ 3 c3rkoN_ 4 c3rkoK_ 5 c2l3iA_ 6 d1s1qa_ 7 d1a6qa1 8 d1o8bb1 9 c3na2C_ 10 d1j4na_ 11 d3d37a2 12 d2yrka1 13 d2c1ha1 14 d1l6sa_ 15 d1gzga_ 16 d2q09a1 17 c2z84A_ 18 d2imra1

Detailed template information

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

1 c3rkoL_ 100.0 21 PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 c3rkoM_ 100.0 21 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 c3rkoN_ 100.0 18 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 4 c3rkoK_ 33.2 16 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 5 c2l3iA_ 24.2 42 PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide 6 d1s1qa_ 24.0 19 Fold:UBC-like Superfamily:UBC-like Family:UEV domain 7 d1a6qa1 19.3 12 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 8 d1o8bb1 14.4 17 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:D-ribose-5-phosphate isomerase (RpiA), catalytic domain 9 c3na2C_ 10.5 25 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein of unknown function from mine drainage2 metagenome leptospirillum rubarum 10 d1j4na_ 9.3 16 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 11 d3d37a2 8.3 38 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:Baseplate protein-like 12 d2yrka1 6.9 26 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:HkH motif-containing C2H2 finger 13 d2c1ha1 6.6 21 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) 14 d1l6sa_ 6.3 25 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) 15 d1gzga_ 6.2 25 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase) 16 d2q09a1 5.7 36 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:Imidazolonepropionase-like 17 c2z84A_ 5.4 80 PDB header:hydrolase Chain: A: PDB Molecule:ufm1-specific protease 1; PDBTitle: insights from crystal and solution structures of mouse ufsp1 18 d2imra1 5.4 38 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:DR0824-like

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