Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	M	Y	A	T	L	E	E	A	I	D	A	A	R	E	E	F	L	A	D	N	P	G	I	D	A	E	D	A	N	V	Q	Q	F	N	A	Q	K	Y	V	L	Q	D	G	D	I	M	W	Q	V	E	F	F	A	D	E	G	E	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?													?	?	?	?				?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	E	C	L	P	M	L	S	G	E	A	A	Q	S	V	F	D	G	D	Y	D	E	I	E	I	R	Q	E	W	Q	E	E	N	T	L	H	E	W	D	E	G	E	F	Q	L	E	P	P	L	D	T	E	E	G	R	A	A	A	D	E
Secondary structure
SS confidence
Disorder																?		?													?	?	?	?	?	?		?		?	?	?	?	?								?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.
Sequence		W	D	E	R
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 1jal chain A domain 2 Region: 40 - 48 Aligned: 9 Modelled: 9 Confidence: 39.1% Identity: 67% Fold: beta-Grasp (ubiquitin-like) Superfamily: TGS-like Family: G domain-linked domain Phyre2 PDB 1ni3 chain A domain 2 Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 38.6% Identity: 18% Fold: beta-Grasp (ubiquitin-like) Superfamily: TGS-like Family: G domain-linked domain Phyre2 PDB 2hj1 chain A Region: 5 - 46 Aligned: 40 Modelled: 42 Confidence: 36.2% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a 3d domain-swapped dimer of protein hi0395 from2 haemophilus influenzae Phyre2 PDB 2hj1 chain A domain 1 Region: 5 - 46 Aligned: 40 Modelled: 42 Confidence: 36.2% Identity: 33% Fold: beta-Grasp (ubiquitin-like) Superfamily: MoaD/ThiS Family: HI0395-like Phyre2 PDB 1ni3 chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 25.6% Identity: 18% PDB header:hydrolase Chain: A: PDB Molecule:ychf gtp-binding protein; PDBTitle: structure of the schizosaccharomyces pombe ychf gtpase Phyre2 PDB 2ohf chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 25.3% Identity: 24% PDB header:hydrolase Chain: A: PDB Molecule:gtp-binding protein 9; PDBTitle: crystal structure of human ola1 in complex with amppcp Phyre2 PDB 1jal chain A Region: 16 - 48 Aligned: 33 Modelled: 33 Confidence: 21.4% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ychf protein; PDBTitle: ychf protein (hi0393) Phyre2 PDB 2dwq chain B Region: 40 - 48 Aligned: 9 Modelled: 9 Confidence: 18.7% Identity: 56% PDB header:hydrolase Chain: B: PDB Molecule:gtp-binding protein; PDBTitle: thermus thermophilus ychf gtp-binding protein Phyre2 PDB 2i9c chain A domain 1 Region: 93 - 106 Aligned: 14 Modelled: 13 Confidence: 11.9% Identity: 29% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: RPA1889-like Phyre2 PDB 1hrt chain I Region: 54 - 83 Aligned: 30 Modelled: 30 Confidence: 9.3% Identity: 33% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Leech antihemostatic proteins Family: Hirudin-like Phyre2 PDB 1wxq chain A Region: 25 - 48 Aligned: 24 Modelled: 24 Confidence: 9.1% Identity: 29% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:gtp-binding protein; PDBTitle: crystal structure of gtp binding protein from pyrococcus horikoshii2 ot3 Phyre2 PDB 3b49 chain A Region: 62 - 115 Aligned: 54 Modelled: 54 Confidence: 8.0% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2189 protein; PDBTitle: crystal structure of an uncharacterized conserved protein from2 listeria innocua Phyre2 PDB 3cs5 chain B Region: 33 - 47 Aligned: 15 Modelled: 15 Confidence: 8.0% Identity: 60% PDB header:photosynthesis Chain: B: PDB Molecule:phycobilisome degradation protein nbla; PDBTitle: nbla protein from synechococcus elongatus pcc 7942 Phyre2 PDB 3rh3 chain A Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 7.3% Identity: 35% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized duf3829-like protein; PDBTitle: crystal structure of an uncharacterized duf3829-like protein (bt_1908)2 from bacteroides thetaiotaomicron vpi-5482 at 2.10 a resolution Phyre2 PDB 1nh2 chain B Region: 7 - 26 Aligned: 18 Modelled: 20 Confidence: 7.1% Identity: 39% Fold: Transcription factor IIA (TFIIA), alpha-helical domain Superfamily: Transcription factor IIA (TFIIA), alpha-helical domain Family: Transcription factor IIA (TFIIA), alpha-helical domain Phyre2 PDB 3d6n chain B Region: 63 - 96 Aligned: 30 Modelled: 34 Confidence: 6.6% Identity: 17% PDB header:hydrolase/transferase Chain: B: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: crystal structure of aquifex dihydroorotase activated by aspartate2 transcarbamoylase Phyre2 PDB 2kd3 chain A Region: 60 - 66 Aligned: 7 Modelled: 7 Confidence: 6.6% Identity: 43% PDB header:protein binding Chain: A: PDB Molecule:sclerostin; PDBTitle: nmr structure of the wnt modulator protein sclerostin Phyre2 PDB 2iay chain A domain 1 Region: 101 - 118 Aligned: 18 Modelled: 18 Confidence: 6.6% Identity: 39% Fold: Lp2179-like Superfamily: Lp2179-like Family: Lp2179-like Phyre2 PDB 2qqr chain A domain 2 Region: 39 - 53 Aligned: 15 Modelled: 15 Confidence: 6.2% Identity: 40% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: Tudor domain Phyre2 PDB 2qqs chain A domain 2 Region: 39 - 53 Aligned: 15 Modelled: 15 Confidence: 6.1% Identity: 47% Fold: SH3-like barrel Superfamily: Tudor/PWWP/MBT Family: Tudor domain Phyre2 1 d1jala2 2 d1ni3a2 3 c2hj1A_ 4 d2hj1a1 5 c1ni3A_ 6 c2ohfA_ 7 c1jalA_ 8 c2dwqB_ 9 d2i9ca1 10 d1hrti_ 11 c1wxqA_ 12 c3b49A_ 13 c3cs5B_ 14 c3rh3A_ 15 d1nh2b_ 16 c3d6nB_ 17 c2kd3A_ 18 d2iaya1 19 d2qqra2 20 d2qqsa2 21 22 23

Detailed template information

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

1 d1jala2 39.1 67 Fold:beta-Grasp (ubiquitin-like) Superfamily:TGS-like Family:G domain-linked domain 2 d1ni3a2 38.6 18 Fold:beta-Grasp (ubiquitin-like) Superfamily:TGS-like Family:G domain-linked domain 3 c2hj1A_ 36.2 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a 3d domain-swapped dimer of protein hi0395 from2 haemophilus influenzae 4 d2hj1a1 36.2 33 Fold:beta-Grasp (ubiquitin-like) Superfamily:MoaD/ThiS Family:HI0395-like 5 c1ni3A_ 25.6 18 PDB header:hydrolase Chain: A: PDB Molecule:ychf gtp-binding protein; PDBTitle: structure of the schizosaccharomyces pombe ychf gtpase 6 c2ohfA_ 25.3 24 PDB header:hydrolase Chain: A: PDB Molecule:gtp-binding protein 9; PDBTitle: crystal structure of human ola1 in complex with amppcp 7 c1jalA_ 21.4 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ychf protein; PDBTitle: ychf protein (hi0393) 8 c2dwqB_ 18.7 56 PDB header:hydrolase Chain: B: PDB Molecule:gtp-binding protein; PDBTitle: thermus thermophilus ychf gtp-binding protein 9 d2i9ca1 11.9 29 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:RPA1889-like 10 d1hrti_ 9.3 33 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Leech antihemostatic proteins Family:Hirudin-like 11 c1wxqA_ 9.1 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:gtp-binding protein; PDBTitle: crystal structure of gtp binding protein from pyrococcus horikoshii2 ot3 12 c3b49A_ 8.0 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2189 protein; PDBTitle: crystal structure of an uncharacterized conserved protein from2 listeria innocua 13 c3cs5B_ 8.0 60 PDB header:photosynthesis Chain: B: PDB Molecule:phycobilisome degradation protein nbla; PDBTitle: nbla protein from synechococcus elongatus pcc 7942 14 c3rh3A_ 7.3 35 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized duf3829-like protein; PDBTitle: crystal structure of an uncharacterized duf3829-like protein (bt_1908)2 from bacteroides thetaiotaomicron vpi-5482 at 2.10 a resolution 15 d1nh2b_ 7.1 39 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 16 c3d6nB_ 6.6 17 PDB header:hydrolase/transferase Chain: B: PDB Molecule:aspartate carbamoyltransferase; PDBTitle: crystal structure of aquifex dihydroorotase activated by aspartate2 transcarbamoylase 17 c2kd3A_ 6.6 43 PDB header:protein binding Chain: A: PDB Molecule:sclerostin; PDBTitle: nmr structure of the wnt modulator protein sclerostin 18 d2iaya1 6.6 39 Fold:Lp2179-like Superfamily:Lp2179-like Family:Lp2179-like 19 d2qqra2 6.2 40 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 20 d2qqsa2 6.1 47 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 21 c2ekiA_ not modelled 5.8 33 PDB header:signaling protein Chain: A: PDB Molecule:developmentally-regulated gtp-binding protein 1; PDBTitle: solution structures of the tgs domain of human2 developmentally-regulated gtp-binding protein 1 22 c1aikC_ not modelled 5.7 43 PDB header:viral protein Chain: C: PDB Molecule:hiv-1 gp41 glycoprotein; PDBTitle: hiv gp41 core structure 23 c3iuoA_ not modelled 5.6 47 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent dna helicase recq; PDBTitle: the crystal structure of the c-terminal domain of the atp-dependent2 dna helicase recq from porphyromonas gingivalis to 1.6a

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