Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	F	F	R	T	V	L	F	G	S	L	M	A	V	C	A	N	S	Y	A	L	S	E	S	E	A	E	D	M	A	D	L	T	A	V	F	V	F	L	K	N	D	C	G	Y	Q	N	L	P	N	G	Q	I	R	R	A	L	V
Secondary structure
SS confidence
Disorder		?	?	?														?	?	?					?	?	?	?																					?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.
Sequence		F	F	A	Q	Q	N	Q	W	D	L	S	N	Y	D	T	F	D	M	K	A	L	G	E	D	S	Y	R	D	L	S	G	I	G	I	P	V	A	K	K	C	K	A	L	A	R	D	S	L	S	L	L	A	Y	V	K
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 3utk chain A Region: 27 - 105 Aligned: 77 Modelled: 79 Confidence: 95.5% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:lipoprotein outs; PDBTitle: structure of the pilotin of the type ii secretion system Phyre2 PDB 3sol chain A Region: 27 - 105 Aligned: 77 Modelled: 79 Confidence: 93.1% Identity: 25% PDB header:protein transport Chain: A: PDB Molecule:type ii secretion pathway related protein; PDBTitle: crystal structure of the type 2 secretion system pilotin gsps Phyre2 PDB 4a56 chain A Region: 27 - 105 Aligned: 77 Modelled: 79 Confidence: 92.2% Identity: 26% PDB header:protein transport Chain: A: PDB Molecule:pullulanase secretion protein puls; PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca Phyre2 PDB 2al6 chain A domain 2 Region: 24 - 44 Aligned: 21 Modelled: 21 Confidence: 42.5% Identity: 43% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Third domain of FERM Phyre2 PDB 3pnt chain D Region: 30 - 77 Aligned: 47 Modelled: 48 Confidence: 20.2% Identity: 28% PDB header:hydrolase/hydrolase inhibitor Chain: D: PDB Molecule:immunity factor for spn; PDBTitle: crystal structure of the streptococcus pyogenes nad+ glycohydrolase2 spn in complex with ifs, the immunity factor for spn Phyre2 PDB 1q0q chain A domain 1 Region: 32 - 59 Aligned: 27 Modelled: 28 Confidence: 15.3% Identity: 19% Fold: Left-handed superhelix Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Phyre2 PDB 1wn4 chain A Region: 48 - 64 Aligned: 17 Modelled: 17 Confidence: 14.1% Identity: 41% PDB header:plant protein Chain: A: PDB Molecule:vontr protein; PDBTitle: nmr structure of vontr Phyre2 PDB 3qb2 chain A Region: 30 - 67 Aligned: 37 Modelled: 38 Confidence: 13.5% Identity: 24% PDB header:hydrolase inhibitor Chain: A: PDB Molecule:immunity factor for spn; PDBTitle: the crystal structure of immunity factor for spn (ifs) Phyre2 PDB 1r0k chain A domain 1 Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 11.6% Identity: 29% Fold: Left-handed superhelix Superfamily: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family: 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Phyre2 PDB 1mi1 chain A Region: 68 - 99 Aligned: 32 Modelled: 32 Confidence: 11.5% Identity: 28% PDB header:signaling protein Chain: A: PDB Molecule:neurobeachin; PDBTitle: crystal structure of the ph-beach domain of human2 neurobeachin Phyre2 PDB 1t77 chain A domain 1 Region: 68 - 90 Aligned: 23 Modelled: 23 Confidence: 10.9% Identity: 30% Fold: BEACH domain Superfamily: BEACH domain Family: BEACH domain Phyre2 PDB 3dal chain A Region: 74 - 108 Aligned: 34 Modelled: 35 Confidence: 9.7% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:pr domain zinc finger protein 1; PDBTitle: methyltransferase domain of human pr domain-containing2 protein 1 Phyre2 PDB 2i2x chain O Region: 44 - 49 Aligned: 6 Modelled: 6 Confidence: 8.5% Identity: 83% PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri Phyre2 PDB 3frw chain F Region: 23 - 53 Aligned: 31 Modelled: 31 Confidence: 8.0% Identity: 13% PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum Phyre2 PDB 1mi1 chain A domain 1 Region: 68 - 106 Aligned: 39 Modelled: 39 Confidence: 7.9% Identity: 23% Fold: BEACH domain Superfamily: BEACH domain Family: BEACH domain Phyre2 PDB 3a14 chain B Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 7.8% Identity: 33% PDB header:oxidoreductase Chain: B: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: crystal structure of dxr from thermotoga maritima, in complex with2 nadph Phyre2 PDB 3kor chain D Region: 23 - 53 Aligned: 31 Modelled: 31 Confidence: 7.5% Identity: 13% PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus Phyre2 PDB 2wx3 chain A Region: 31 - 38 Aligned: 8 Modelled: 8 Confidence: 7.0% Identity: 50% PDB header:structural protein Chain: A: PDB Molecule:mrna-decapping enzyme 1a; PDBTitle: asymmetric trimer of the human dcp1a c-terminal domain Phyre2 PDB 3mcr chain A Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 6.1% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:nadh dehydrogenase, subunit c; PDBTitle: crystal structure of nadh dehydrogenase subunit c (tfu_2693) from2 thermobifida fusca yx-er1 at 2.65 a resolution Phyre2 PDB 2jcy chain A Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 6.0% Identity: 24% PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis Phyre2 1 c3utkA_ 2 c3solA_ 3 c4a56A_ 4 d2al6a2 5 c3pntD_ 6 d1q0qa1 7 c1wn4A_ 8 c3qb2A_ 9 d1r0ka1 10 c1mi1A_ 11 d1t77a1 12 c3dalA_ 13 c2i2xO_ 14 c3frwF_ 15 d1mi1a1 16 c3a14B_ 17 c3korD_ 18 c2wx3A_ 19 c3mcrA_ 20 c2jcyA_ 21 22 23

Detailed template information

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

1 c3utkA_ 95.5 31 PDB header:protein transport Chain: A: PDB Molecule:lipoprotein outs; PDBTitle: structure of the pilotin of the type ii secretion system 2 c3solA_ 93.1 25 PDB header:protein transport Chain: A: PDB Molecule:type ii secretion pathway related protein; PDBTitle: crystal structure of the type 2 secretion system pilotin gsps 3 c4a56A_ 92.2 26 PDB header:protein transport Chain: A: PDB Molecule:pullulanase secretion protein puls; PDBTitle: crystal structure of the type 2 secretion system pilotin2 from klebsiella oxytoca 4 d2al6a2 42.5 43 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Third domain of FERM 5 c3pntD_ 20.2 28 PDB header:hydrolase/hydrolase inhibitor Chain: D: PDB Molecule:immunity factor for spn; PDBTitle: crystal structure of the streptococcus pyogenes nad+ glycohydrolase2 spn in complex with ifs, the immunity factor for spn 6 d1q0qa1 15.3 19 Fold:Left-handed superhelix Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 7 c1wn4A_ 14.1 41 PDB header:plant protein Chain: A: PDB Molecule:vontr protein; PDBTitle: nmr structure of vontr 8 c3qb2A_ 13.5 24 PDB header:hydrolase inhibitor Chain: A: PDB Molecule:immunity factor for spn; PDBTitle: the crystal structure of immunity factor for spn (ifs) 9 d1r0ka1 11.6 29 Fold:Left-handed superhelix Superfamily:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain Family:1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 10 c1mi1A_ 11.5 28 PDB header:signaling protein Chain: A: PDB Molecule:neurobeachin; PDBTitle: crystal structure of the ph-beach domain of human2 neurobeachin 11 d1t77a1 10.9 30 Fold:BEACH domain Superfamily:BEACH domain Family:BEACH domain 12 c3dalA_ 9.7 21 PDB header:transferase Chain: A: PDB Molecule:pr domain zinc finger protein 1; PDBTitle: methyltransferase domain of human pr domain-containing2 protein 1 13 c2i2xO_ 8.5 83 PDB header:transferase Chain: O: PDB Molecule:methyltransferase 1; PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri 14 c3frwF_ 8.0 13 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 15 d1mi1a1 7.9 23 Fold:BEACH domain Superfamily:BEACH domain Family:BEACH domain 16 c3a14B_ 7.8 33 PDB header:oxidoreductase Chain: B: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: crystal structure of dxr from thermotoga maritima, in complex with2 nadph 17 c3korD_ 7.5 13 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 18 c2wx3A_ 7.0 50 PDB header:structural protein Chain: A: PDB Molecule:mrna-decapping enzyme 1a; PDBTitle: asymmetric trimer of the human dcp1a c-terminal domain 19 c3mcrA_ 6.1 19 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh dehydrogenase, subunit c; PDBTitle: crystal structure of nadh dehydrogenase subunit c (tfu_2693) from2 thermobifida fusca yx-er1 at 2.65 a resolution 20 c2jcyA_ 6.0 24 PDB header:oxidoreductase Chain: A: PDB Molecule:1-deoxy-d-xylulose 5-phosphate reductoisomerase; PDBTitle: x-ray structure of mutant 1-deoxy-d-xylulose 5-phosphate2 reductoisomerase, dxr, rv2870c, from mycobacterium3 tuberculosis 21 d2p8ta1 not modelled 6.0 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PH0730 N-terminal domain-like 22 c3hk0B_ not modelled 5.6 17 PDB header:signaling protein Chain: B: PDB Molecule:growth factor receptor-bound protein 10; PDBTitle: crystal structure of the ra and ph domains of grb10 23 c2hm2Q_ not modelled 5.5 21 PDB header:apoptosis Chain: Q: PDB Molecule:pyrin-only protein 1; PDBTitle: solution structure of asc2

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