Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	K	V	N	L	Y	I	S	N	D	A	Y	E	K	I	N	A	I	I	E	K	R	R	Q	E	G	A	R	E	K	D	V	S	F	S	A	T	A	S	M	L	L	E	L	G	L	R	V	H	E	A	Q	M	E	R	K	E	S	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																				?	?	?	?	?	?	?																							?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	N	Q	T	E	F	N	K	L	L	L	E	C	V	V	K	T	Q	S	S	V	A	K	I	L	G	I	E	S	L	S	P	H	V	S	G	N	S	K	F	E	Y	A	N	M	V	E	D	I	R	E	K	V	S	S	E	M	E	R	F
Secondary structure
SS confidence
Disorder		?	?													?	?	?												?	?	?			?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		F	P	K	N	D	D	E
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 3on0 chain D Region: 2 - 121 Aligned: 107 Modelled: 120 Confidence: 100.0% Identity: 39% PDB header:dna binding protein/dna Chain: D: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram-sbma complex Phyre2 PDB 2g7o chain A domain 1 Region: 60 - 127 Aligned: 68 Modelled: 68 Confidence: 99.9% Identity: 100% Fold: TraM-like Superfamily: TraM-like Family: TraM-like Phyre2 PDB 1dp3 chain A Region: 2 - 56 Aligned: 55 Modelled: 55 Confidence: 99.9% Identity: 64% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: DNA-binding domain (fragment?) of the TraM protein Phyre2 PDB 3omy chain B Region: 2 - 53 Aligned: 50 Modelled: 51 Confidence: 99.9% Identity: 48% PDB header:dna binding protein Chain: B: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram n-terminal domain Phyre2 PDB 1tlh chain A Region: 9 - 86 Aligned: 71 Modelled: 78 Confidence: 42.5% Identity: 15% Fold: Anti-sigma factor AsiA Superfamily: Anti-sigma factor AsiA Family: Anti-sigma factor AsiA Phyre2 PDB 2qwt chain A Region: 10 - 49 Aligned: 40 Modelled: 40 Confidence: 23.8% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of the tetr transcription regulatory2 protein from mycobacterium vanbaalenii Phyre2 PDB 2jvd chain A Region: 8 - 32 Aligned: 25 Modelled: 25 Confidence: 15.1% Identity: 28% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 Phyre2 PDB 3bhp chain A Region: 7 - 32 Aligned: 26 Modelled: 25 Confidence: 14.7% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 Phyre2 PDB 2l53 chain B Region: 63 - 76 Aligned: 14 Modelled: 14 Confidence: 14.4% Identity: 36% PDB header:ca-binding protein/proton transport Chain: B: PDB Molecule:voltage-gated sodium channel type v alpha isoform b PDBTitle: solution nmr structure of apo-calmodulin in complex with the iq motif2 of human cardiac sodium channel nav1.5 Phyre2 PDB 1oys chain A domain 2 Region: 53 - 84 Aligned: 32 Modelled: 32 Confidence: 13.2% Identity: 25% Fold: Ribonuclease PH domain 2-like Superfamily: Ribonuclease PH domain 2-like Family: Ribonuclease PH domain 2-like Phyre2 PDB 1x2l chain A domain 1 Region: 49 - 107 Aligned: 56 Modelled: 59 Confidence: 11.5% Identity: 18% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: CUT domain Phyre2 PDB 3bpq chain C Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 11.1% Identity: 32% PDB header:toxin Chain: C: PDB Molecule:antitoxin relb3; PDBTitle: crystal structure of relb-rele antitoxin-toxin complex from2 methanococcus jannaschii Phyre2 PDB 2r17 chain C Region: 11 - 114 Aligned: 84 Modelled: 84 Confidence: 10.8% Identity: 14% PDB header:protein transport Chain: C: PDB Molecule:vacuolar protein sorting-associated protein 35; PDBTitle: functional architecture of the retromer cargo-recognition complex Phyre2 PDB 3r9l chain A Region: 110 - 125 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of nucleoside diphosphate kinase from giardia2 lamblia featuring a disordered dinucleotide binding site Phyre2 PDB 2v7q chain I domain 1 Region: 24 - 47 Aligned: 22 Modelled: 24 Confidence: 10.2% Identity: 23% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Epsilon subunit of mitochondrial F1F0-ATP synthase Family: Epsilon subunit of mitochondrial F1F0-ATP synthase Phyre2 PDB 2jdq chain B Region: 107 - 126 Aligned: 20 Modelled: 20 Confidence: 9.9% Identity: 25% PDB header:protein transport Chain: B: PDB Molecule:importin alpha-1 subunit; PDBTitle: c-terminal domain of influenza a virus polymerase pb22 subunit in complex with human importin alpha5 Phyre2 PDB 2cp8 chain A Region: 60 - 73 Aligned: 14 Modelled: 14 Confidence: 8.4% Identity: 29% PDB header:protein binding Chain: A: PDB Molecule:next to brca1 gene 1 protein; PDBTitle: solution structure of the rsgi ruh-046, a uba domain from2 human next to brca1 gene 1 protein (kiaa0049 protein)3 r923h variant Phyre2 PDB 1zkd chain A domain 1 Region: 30 - 66 Aligned: 29 Modelled: 37 Confidence: 8.4% Identity: 28% Fold: S-adenosyl-L-methionine-dependent methyltransferases Superfamily: S-adenosyl-L-methionine-dependent methyltransferases Family: RPA4359-like Phyre2 PDB 1l7d chain A domain 2 Region: 37 - 68 Aligned: 32 Modelled: 32 Confidence: 7.3% Identity: 16% Fold: Flavodoxin-like Superfamily: Formate/glycerate dehydrogenase catalytic domain-like Family: L-alanine dehydrogenase-like Phyre2 PDB 2kxw chain B Region: 63 - 76 Aligned: 14 Modelled: 14 Confidence: 7.2% Identity: 36% PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 Phyre2 1 c3on0D_ 2 d2g7oa1 3 d1dp3a_ 4 c3omyB_ 5 d1tlha_ 6 c2qwtA_ 7 c2jvdA_ 8 c3bhpA_ 9 c2l53B_ 10 d1oysa2 11 d1x2la1 12 c3bpqC_ 13 c2r17C_ 14 c3r9lA_ 15 d2v7qi1 16 c2jdqB_ 17 c2cp8A_ 18 d1zkda1 19 d1l7da2 20 c2kxwB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 c3on0D_ 100.0 39 PDB header:dna binding protein/dna Chain: D: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram-sbma complex 2 d2g7oa1 99.9 100 Fold:TraM-like Superfamily:TraM-like Family:TraM-like 3 d1dp3a_ 99.9 64 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:DNA-binding domain (fragment?) of the TraM protein 4 c3omyB_ 99.9 48 PDB header:dna binding protein Chain: B: PDB Molecule:protein tram; PDBTitle: crystal structure of the ped208 tram n-terminal domain 5 d1tlha_ 42.5 15 Fold:Anti-sigma factor AsiA Superfamily:Anti-sigma factor AsiA Family:Anti-sigma factor AsiA 6 c2qwtA_ 23.8 20 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of the tetr transcription regulatory2 protein from mycobacterium vanbaalenii 7 c2jvdA_ 15.1 28 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 8 c3bhpA_ 14.7 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 9 c2l53B_ 14.4 36 PDB header:ca-binding protein/proton transport Chain: B: PDB Molecule:voltage-gated sodium channel type v alpha isoform b PDBTitle: solution nmr structure of apo-calmodulin in complex with the iq motif2 of human cardiac sodium channel nav1.5 10 d1oysa2 13.2 25 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 11 d1x2la1 11.5 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:CUT domain 12 c3bpqC_ 11.1 32 PDB header:toxin Chain: C: PDB Molecule:antitoxin relb3; PDBTitle: crystal structure of relb-rele antitoxin-toxin complex from2 methanococcus jannaschii 13 c2r17C_ 10.8 14 PDB header:protein transport Chain: C: PDB Molecule:vacuolar protein sorting-associated protein 35; PDBTitle: functional architecture of the retromer cargo-recognition complex 14 c3r9lA_ 10.4 13 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of nucleoside diphosphate kinase from giardia2 lamblia featuring a disordered dinucleotide binding site 15 d2v7qi1 10.2 23 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Epsilon subunit of mitochondrial F1F0-ATP synthase Family:Epsilon subunit of mitochondrial F1F0-ATP synthase 16 c2jdqB_ 9.9 25 PDB header:protein transport Chain: B: PDB Molecule:importin alpha-1 subunit; PDBTitle: c-terminal domain of influenza a virus polymerase pb22 subunit in complex with human importin alpha5 17 c2cp8A_ 8.4 29 PDB header:protein binding Chain: A: PDB Molecule:next to brca1 gene 1 protein; PDBTitle: solution structure of the rsgi ruh-046, a uba domain from2 human next to brca1 gene 1 protein (kiaa0049 protein)3 r923h variant 18 d1zkda1 8.4 28 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:RPA4359-like 19 d1l7da2 7.3 16 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:L-alanine dehydrogenase-like 20 c2kxwB_ 7.2 36 PDB header:calcium-binding protein/metal transport Chain: B: PDB Molecule:sodium channel protein type 2 subunit alpha; PDBTitle: structure of the c-domain fragment of apo calmodulin bound to the iq2 motif of nav1.2 21 c3mtuE_ not modelled 7.1 28 PDB header:contractile protein Chain: E: PDB Molecule:head morphogenesis protein, tropomyosin alpha-1 chain; PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle 22 d1f7ca_ not modelled 6.9 14 Fold:GTPase activation domain, GAP Superfamily:GTPase activation domain, GAP Family:BCR-homology GTPase activation domain (BH-domain) 23 c1f7cA_ not modelled 6.9 14 PDB header:signaling protein Chain: A: PDB Molecule:rhogap protein; PDBTitle: crystal structure of the bh domain from graf, the gtpase2 regulator associated with focal adhesion kinase 24 c3izcR_ not modelled 6.4 24 PDB header:ribosome Chain: R: PDB Molecule:60s ribosomal protein rpl18 (l18e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 25 d1nhkl_ not modelled 6.2 25 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 26 c3pk1A_ not modelled 6.2 20 PDB header:apoptosis/apoptosis regulator Chain: A: PDB Molecule:induced myeloid leukemia cell differentiation protein mcl- PDBTitle: crystal structure of mcl-1 in complex with the baxbh3 domain 27 d1kx5b_ not modelled 6.0 21 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 28 d2o4aa1 not modelled 6.0 23 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:CUT domain 29 d1xiqa_ not modelled 6.0 13 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 30 c2hurF_ not modelled 5.9 27 PDB header:signaling protein,transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: escherichia coli nucleoside diphosphate kinase 31 c2imuA_ not modelled 5.8 22 PDB header:viral protein Chain: A: PDB Molecule:structural polyprotein (pp) p1; PDBTitle: nmr structure of pep46 from the infectious bursal disease2 virus (ibdv) in dodecylphosphocholin (dpc). 32 d1ehwa_ not modelled 5.7 20 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 33 c3knyA_ not modelled 5.5 39 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein bt_3535; PDBTitle: crystal structure of a two domain protein with unknown function2 (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 a3 resolution 34 c2o01J_ not modelled 5.4 63 PDB header:photosynthesis Chain: J: PDB Molecule:photosystem i reaction center subunit ix; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

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