Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	T	L	P	A	T	I	S	Q	A	A	K	P	C	L	S	P	V	A	V	W	Q	M	L	L	T	R	L	L	E	Q	H	Y	G	L	T	L	N	D	T	P	F	S	D	E	T	V	I	K	E	H	I	D	A	G	I	T	L	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.
Sequence		D	A	V	N	F	L	V	E	K	Y	E	L	V	R	I	D	H	R	G	F	S	W	Q	Q	Q	S	P	Y	I	S	V	V	D	I	L	R	A	R	R	S	T	G	L	L	K	T	N	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 2fwt chain A Region: 13 - 56 Aligned: 42 Modelled: 44 Confidence: 52.9% Identity: 21% PDB header:electron transport Chain: A: PDB Molecule:dhc, diheme cytochrome c; PDBTitle: crystal structure of dhc purified from rhodobacter2 sphaeroides Phyre2 PDB 2jvw chain A Region: 55 - 92 Aligned: 35 Modelled: 38 Confidence: 43.5% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of uncharacterized protein q5e7h1 from vibrio2 fischeri. northeast structural genomics target vfr117 Phyre2 PDB 1zee chain A domain 1 Region: 22 - 103 Aligned: 47 Modelled: 55 Confidence: 22.1% Identity: 34% Fold: Indolic compounds 2,3-dioxygenase-like Superfamily: Indolic compounds 2,3-dioxygenase-like Family: Indoleamine 2,3-dioxygenase-like Phyre2 PDB 2bh7 chain A Region: 5 - 70 Aligned: 61 Modelled: 66 Confidence: 22.0% Identity: 23% PDB header:hydrolase Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase; PDBTitle: crystal structure of a semet derivative of amid at 2.22 angstroms Phyre2 PDB 2hl7 chain A Region: 46 - 70 Aligned: 25 Modelled: 25 Confidence: 21.6% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa Phyre2 PDB 1yx3 chain A Region: 22 - 68 Aligned: 45 Modelled: 47 Confidence: 20.1% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dsrc; PDBTitle: nmr structure of allochromatium vinosum dsrc: northeast2 structural genomics consortium target op4 Phyre2 PDB 1wj7 chain A domain 1 Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 19.3% Identity: 21% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2dnw chain A Region: 26 - 73 Aligned: 38 Modelled: 48 Confidence: 19.3% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of rsgi ruh-059, an acp domain of acyl2 carrier protein, mitochondrial [precursor] from human cdna Phyre2 PDB 3g2b chain A Region: 36 - 74 Aligned: 35 Modelled: 39 Confidence: 18.8% Identity: 20% PDB header:biosynthetic protein Chain: A: PDB Molecule:coenzyme pqq synthesis protein d; PDBTitle: crystal structure of pqqd from xanthomonas campestris Phyre2 PDB 2kw0 chain A Region: 46 - 70 Aligned: 25 Modelled: 25 Confidence: 18.3% Identity: 20% PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli Phyre2 PDB 1wr1 chain B Region: 13 - 68 Aligned: 47 Modelled: 56 Confidence: 16.6% Identity: 28% PDB header:signaling protein Chain: B: PDB Molecule:ubiquitin-like protein dsk2; PDBTitle: the complex sturcture of dsk2p uba with ubiquitin Phyre2 PDB 1vej chain A domain 1 Region: 2 - 67 Aligned: 57 Modelled: 66 Confidence: 13.5% Identity: 19% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2d86 chain A Region: 13 - 66 Aligned: 53 Modelled: 54 Confidence: 12.8% Identity: 21% PDB header:signaling protein, protein binding Chain: A: PDB Molecule:vav-3 protein; PDBTitle: solution structure of the ch domain from human vav-3 protein Phyre2 PDB 2pby chain B Region: 57 - 97 Aligned: 39 Modelled: 41 Confidence: 11.8% Identity: 15% PDB header:hydrolase Chain: B: PDB Molecule:glutaminase; PDBTitle: probable glutaminase from geobacillus kaustophilus hta426 Phyre2 PDB 1zii chain A Region: 61 - 73 Aligned: 13 Modelled: 13 Confidence: 11.3% Identity: 46% PDB header:leucine zipper Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the dimeric2 state Phyre2 PDB 1zii chain B Region: 61 - 73 Aligned: 13 Modelled: 13 Confidence: 11.3% Identity: 46% PDB header:leucine zipper Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the dimeric2 state Phyre2 PDB 2pjw chain H Region: 39 - 71 Aligned: 33 Modelled: 33 Confidence: 11.1% Identity: 18% PDB header:endocytosis/exocytosis Chain: H: PDB Molecule:uncharacterized protein yhl002w; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting Phyre2 PDB 2ae8 chain C Region: 29 - 86 Aligned: 53 Modelled: 56 Confidence: 11.1% Identity: 28% PDB header:lyase Chain: C: PDB Molecule:imidazoleglycerol-phosphate dehydratase; PDBTitle: crystal structure of imidazoleglycerol-phosphate dehydratase from2 staphylococcus aureus subsp. aureus n315 Phyre2 PDB 1sr9 chain A domain 1 Region: 27 - 38 Aligned: 12 Modelled: 8 Confidence: 10.7% Identity: 25% Fold: RuvA C-terminal domain-like Superfamily: post-HMGL domain-like Family: DmpG/LeuA communication domain-like Phyre2 PDB 1zij chain B Region: 61 - 73 Aligned: 13 Modelled: 13 Confidence: 10.7% Identity: 46% PDB header:leucine zipper Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the trimeric2 state Phyre2 1 c2fwtA_ 2 c2jvwA_ 3 d1zeea1 4 c2bh7A_ 5 c2hl7A_ 6 c1yx3A_ 7 d1wj7a1 8 c2dnwA_ 9 c3g2bA_ 10 c2kw0A_ 11 c1wr1B_ 12 d1veja1 13 c2d86A_ 14 c2pbyB_ 15 c1ziiA_ 16 c1ziiB_ 17 c2pjwH_ 18 c2ae8C_ 19 d1sr9a1 20 c1zijB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Detailed template information

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

1 c2fwtA_ 52.9 21 PDB header:electron transport Chain: A: PDB Molecule:dhc, diheme cytochrome c; PDBTitle: crystal structure of dhc purified from rhodobacter2 sphaeroides 2 c2jvwA_ 43.5 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of uncharacterized protein q5e7h1 from vibrio2 fischeri. northeast structural genomics target vfr117 3 d1zeea1 22.1 34 Fold:Indolic compounds 2,3-dioxygenase-like Superfamily:Indolic compounds 2,3-dioxygenase-like Family:Indoleamine 2,3-dioxygenase-like 4 c2bh7A_ 22.0 23 PDB header:hydrolase Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase; PDBTitle: crystal structure of a semet derivative of amid at 2.22 angstroms 5 c2hl7A_ 21.6 20 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa 6 c1yx3A_ 20.1 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dsrc; PDBTitle: nmr structure of allochromatium vinosum dsrc: northeast2 structural genomics consortium target op4 7 d1wj7a1 19.3 21 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 8 c2dnwA_ 19.3 13 PDB header:transport protein Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of rsgi ruh-059, an acp domain of acyl2 carrier protein, mitochondrial [precursor] from human cdna 9 c3g2bA_ 18.8 20 PDB header:biosynthetic protein Chain: A: PDB Molecule:coenzyme pqq synthesis protein d; PDBTitle: crystal structure of pqqd from xanthomonas campestris 10 c2kw0A_ 18.3 20 PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli 11 c1wr1B_ 16.6 28 PDB header:signaling protein Chain: B: PDB Molecule:ubiquitin-like protein dsk2; PDBTitle: the complex sturcture of dsk2p uba with ubiquitin 12 d1veja1 13.5 19 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 13 c2d86A_ 12.8 21 PDB header:signaling protein, protein binding Chain: A: PDB Molecule:vav-3 protein; PDBTitle: solution structure of the ch domain from human vav-3 protein 14 c2pbyB_ 11.8 15 PDB header:hydrolase Chain: B: PDB Molecule:glutaminase; PDBTitle: probable glutaminase from geobacillus kaustophilus hta426 15 c1ziiA_ 11.3 46 PDB header:leucine zipper Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the dimeric2 state 16 c1ziiB_ 11.3 46 PDB header:leucine zipper Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the dimeric2 state 17 c2pjwH_ 11.1 18 PDB header:endocytosis/exocytosis Chain: H: PDB Molecule:uncharacterized protein yhl002w; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting 18 c2ae8C_ 11.1 28 PDB header:lyase Chain: C: PDB Molecule:imidazoleglycerol-phosphate dehydratase; PDBTitle: crystal structure of imidazoleglycerol-phosphate dehydratase from2 staphylococcus aureus subsp. aureus n315 19 d1sr9a1 10.7 25 Fold:RuvA C-terminal domain-like Superfamily:post-HMGL domain-like Family:DmpG/LeuA communication domain-like 20 c1zijB_ 10.7 46 PDB header:leucine zipper Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the trimeric2 state 21 c1zijA_ not modelled 10.7 46 PDB header:leucine zipper Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the trimeric2 state 22 c1zijC_ not modelled 10.7 46 PDB header:leucine zipper Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant asn16aba in the trimeric2 state 23 d1whra_ not modelled 10.6 13 Fold:IF3-like Superfamily:R3H domain Family:R3H domain 24 d1nq4a_ not modelled 10.5 23 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Acyl-carrier protein (ACP) 25 d1t8ka_ not modelled 9.8 23 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Acyl-carrier protein (ACP) 26 c2g2qB_ not modelled 9.6 30 PDB header:oxidoreductase Chain: B: PDB Molecule:glutaredoxin-2; PDBTitle: the crystal structure of g4, the poxviral disulfide oxidoreductase2 essential for cytoplasmic disulfide bond formation 27 c2cnrA_ not modelled 9.6 7 PDB header:lipid transport Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: structural studies on the interaction of scfas acp with2 acps 28 c2fq2A_ not modelled 9.1 22 PDB header:lipid transport Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of minor conformation of holo-acyl2 carrier protein from malaria parasite plasmodium falciparum 29 d1szpa1 not modelled 8.7 21 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 30 d1q9ja1 not modelled 8.5 18 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:NRPS condensation domain (amide synthase) 31 d1gjja2 not modelled 8.3 14 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 32 c2kwlA_ not modelled 8.2 13 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of acyl carrier protein from borrelia burgdorferi 33 c2kebA_ not modelled 8.2 19 PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit 34 c2yfvC_ not modelled 8.1 31 PDB header:cell cycle Chain: C: PDB Molecule:scm3; PDBTitle: the heterotrimeric complex of kluyveromyces lactis scm3, cse4 and h4 35 c3ce7A_ not modelled 7.8 19 PDB header:biosynthetic protein Chain: A: PDB Molecule:specific mitochodrial acyl carrier protein; PDBTitle: crystal structure of toxoplasma specific mitochodrial acyl2 carrier protein, 59.m03510 36 c3pcqX_ not modelled 7.7 58 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography 37 c1jb0X_ not modelled 7.6 58 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i subunit psax; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 38 d1jb0x_ not modelled 7.6 58 Fold:Single transmembrane helix Superfamily:Subunit PsaX of photosystem I reaction centre Family:Subunit PsaX of photosystem I reaction centre 39 d2hlya1 not modelled 7.2 36 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Atu2299-like 40 d1n7va_ not modelled 7.0 60 Fold:Adsorption protein p2 Superfamily:Adsorption protein p2 Family:Adsorption protein p2 41 c2fvfA_ not modelled 6.8 19 PDB header:biosynthetic protein Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: structure of 10:0-acp (protein with docked fatty acid) 42 c2dakA_ not modelled 6.7 18 PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the second uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) 43 d1vkua_ not modelled 6.4 25 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Acyl-carrier protein (ACP) 44 d1rkta2 not modelled 6.1 21 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 45 d2af8a_ not modelled 6.1 25 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Acyl-carrier protein (ACP) 46 c3ejbC_ not modelled 6.1 23 PDB header:oxidoreductase/lipid transport Chain: C: PDB Molecule:acyl carrier protein; PDBTitle: crystal structure of p450bioi in complex with tetradecanoic2 acid ligated acyl carrier protein 47 d1yo5c1 not modelled 5.9 42 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ets domain 48 d1oqya2 not modelled 5.8 26 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 49 c2lafA_ not modelled 5.8 21 PDB header:membrane protein Chain: A: PDB Molecule:lipoprotein 34; PDBTitle: nmr solution structure of the n-terminal domain of the e. coli2 lipoprotein bamc 50 d1d0qa_ not modelled 5.7 28 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:DNA primase zinc finger 51 c3a58A_ not modelled 5.7 30 PDB header:protein transport/exocytosis Chain: A: PDB Molecule:exocyst complex component sec3; PDBTitle: crystal structure of sec3p - rho1p complex from2 saccharomyces cerevisiae 52 c2l3gA_ not modelled 5.6 20 PDB header:signaling protein Chain: A: PDB Molecule:rho guanine nucleotide exchange factor 7; PDBTitle: solution nmr structure of ch domain of rho guanine nucleotide exchange2 factor 7 from homo sapiens, northeast structural genomics consortium3 target hr4495e 53 d1jjcb6 not modelled 5.5 24 Fold:PheT/TilS domain Superfamily:PheT/TilS domain Family:B3/B4 domain of PheRS, PheT 54 d1wiva_ not modelled 5.4 19 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 55 c2l4bA_ not modelled 5.3 17 PDB header:transferase Chain: A: PDB Molecule:acyl carrier protein; PDBTitle: solution structure of a putative acyl carrier protein from anaplasma2 phagocytophilum. seattle structural genomics center for infectious3 disease target anpha.01018.a 56 d1zcba1 not modelled 5.3 41 Fold:Transducin (alpha subunit), insertion domain Superfamily:Transducin (alpha subunit), insertion domain Family:Transducin (alpha subunit), insertion domain 57 c2l9fA_ not modelled 5.2 19 PDB header:transferase Chain: A: PDB Molecule:cale8; PDBTitle: nmr solution structure of meacp 58 c2dagA_ not modelled 5.1 23 PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the first uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) 59 d1sknp_ not modelled 5.1 17 Fold:A DNA-binding domain in eukaryotic transcription factors Superfamily:A DNA-binding domain in eukaryotic transcription factors Family:A DNA-binding domain in eukaryotic transcription factors 60 d1hfes_ not modelled 5.0 30 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Fe-only hydrogenase smaller subunit Family:Fe-only hydrogenase smaller subunit

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

---

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