Secondary structure and disorder prediction

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Sequence		M	S	T	P	D	F	S	T	A	E	N	N	Q	E	L	A	N	E	V	S	C	L	K	A	M	L	T	L	M	L	Q	A	M	G	Q	A	D	A	G	R	V	M	L	K	M	E	K	Q	L	A	L	I	E	D	E	T	Q	A	A	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																																								?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.
Sequence		F	S	K	T	V	K	Q	I	K	Q	A	Y	R	Q
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 2oxl chain A Region: 15 - 68 Aligned: 54 Modelled: 54 Confidence: 58.9% Identity: 20% PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance Phyre2 PDB 2dt7 chain A Region: 48 - 74 Aligned: 27 Modelled: 27 Confidence: 39.7% Identity: 33% PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor 3a subunit 3; PDBTitle: solution structure of the second surp domain of human2 splicing factor sf3a120 in complex with a fragment of3 human splicing factor sf3a60 Phyre2 PDB 3cl3 chain D Region: 43 - 60 Aligned: 18 Modelled: 18 Confidence: 32.2% Identity: 39% PDB header:viral protein/signaling protein Chain: D: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: crystal structure of a vflip-ikkgamma complex: insights2 into viral activation of the ikk signalosome Phyre2 PDB 2k6o chain A Region: 55 - 73 Aligned: 19 Modelled: 19 Confidence: 16.8% Identity: 32% PDB header:antimicrobial protein Chain: A: PDB Molecule:cathelicidin antimicrobial peptide; PDBTitle: human ll-37 structure Phyre2 PDB 2fcg chain F Region: 61 - 73 Aligned: 13 Modelled: 13 Confidence: 15.2% Identity: 38% PDB header:antimicrobial protein Chain: F: PDB Molecule:antibacterial protein fall-39, core peptide; PDBTitle: solution structure of the c-terminal fragment of human ll-37 Phyre2 PDB 1ij2 chain C Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 13.4% Identity: 40% PDB header:transcription Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvtl coiled-coil trimer with threonine at the a(16)2 position Phyre2 PDB 1zta chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 13.3% Identity: 47% PDB header:dna-binding motif Chain: A: PDB Molecule:leucine zipper monomer; PDBTitle: the solution structure of a leucine-zipper motif peptide Phyre2 PDB 1ij2 chain B Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.5% Identity: 40% PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvtl coiled-coil trimer with threonine at the a(16)2 position Phyre2 PDB 1ij3 chain B Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.1% Identity: 40% PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvsl coiled-coil trimer with serine at the a(16)2 position Phyre2 PDB 1ij3 chain C Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.1% Identity: 40% PDB header:transcription Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvsl coiled-coil trimer with serine at the a(16)2 position Phyre2 PDB 1rb6 chain C Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% PDB header:dna binding protein Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: antiparallel trimer of gcn4-leucine zipper core mutant as2 n16a tetragonal form Phyre2 PDB 3k7z chain B Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% PDB header:dna binding protein Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution Phyre2 PDB 3k7z chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% PDB header:dna binding protein Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution Phyre2 PDB 1rb1 chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% PDB header:dna binding protein Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution Phyre2 PDB 1rb1 chain B Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 12.0% Identity: 40% PDB header:dna binding protein Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution Phyre2 PDB 1swi chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 11.4% Identity: 40% PDB header:leucine zipper Chain: A: PDB Molecule:gcn4p1; PDBTitle: gcn4-leucine zipper core mutant as n16a complexed with2 benzene Phyre2 PDB 2l5g chain A Region: 42 - 57 Aligned: 16 Modelled: 16 Confidence: 11.4% Identity: 31% PDB header:transcription regulator Chain: A: PDB Molecule:g protein pathway suppressor 2; PDBTitle: co-ordinates and 1h, 13c and 15n chemical shift assignments for the2 complex of gps2 53-90 and smrt 167-207 Phyre2 PDB 1gh6 chain A Region: 65 - 74 Aligned: 10 Modelled: 10 Confidence: 9.7% Identity: 20% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 2l6l chain A Region: 64 - 74 Aligned: 11 Modelled: 11 Confidence: 9.5% Identity: 27% PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 24; PDBTitle: solution structure of human j-protein co-chaperone, dph4 Phyre2 PDB 1ce0 chain B Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 9.5% Identity: 33% PDB header:hiv-1 envelope protein Chain: B: PDB Molecule:protein (leucine zipper model h38-p1); PDBTitle: trimerization specificity in hiv-1 gp41: analysis with a2 gcn4 leucine zipper model Phyre2 1 c2oxlA_ 2 c2dt7A_ 3 c3cl3D_ 4 c2k6oA_ 5 c2fcgF_ 6 c1ij2C_ 7 c1ztaA_ 8 c1ij2B_ 9 c1ij3B_ 10 c1ij3C_ 11 c1rb6C_ 12 c3k7zB_ 13 c3k7zA_ 14 c1rb1A_ 15 c1rb1B_ 16 c1swiA_ 17 c2l5gA_ 18 d1gh6a_ 19 c2l6lA_ 20 c1ce0B_ 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

Detailed template information

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

1 c2oxlA_ 58.9 20 PDB header:gene regulation Chain: A: PDB Molecule:hypothetical protein ymgb; PDBTitle: structure and function of the e. coli protein ymgb: a protein critical2 for biofilm formation and acid resistance 2 c2dt7A_ 39.7 33 PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor 3a subunit 3; PDBTitle: solution structure of the second surp domain of human2 splicing factor sf3a120 in complex with a fragment of3 human splicing factor sf3a60 3 c3cl3D_ 32.2 39 PDB header:viral protein/signaling protein Chain: D: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: crystal structure of a vflip-ikkgamma complex: insights2 into viral activation of the ikk signalosome 4 c2k6oA_ 16.8 32 PDB header:antimicrobial protein Chain: A: PDB Molecule:cathelicidin antimicrobial peptide; PDBTitle: human ll-37 structure 5 c2fcgF_ 15.2 38 PDB header:antimicrobial protein Chain: F: PDB Molecule:antibacterial protein fall-39, core peptide; PDBTitle: solution structure of the c-terminal fragment of human ll-37 6 c1ij2C_ 13.4 40 PDB header:transcription Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvtl coiled-coil trimer with threonine at the a(16)2 position 7 c1ztaA_ 13.3 47 PDB header:dna-binding motif Chain: A: PDB Molecule:leucine zipper monomer; PDBTitle: the solution structure of a leucine-zipper motif peptide 8 c1ij2B_ 12.5 40 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvtl coiled-coil trimer with threonine at the a(16)2 position 9 c1ij3B_ 12.1 40 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvsl coiled-coil trimer with serine at the a(16)2 position 10 c1ij3C_ 12.1 40 PDB header:transcription Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-pvsl coiled-coil trimer with serine at the a(16)2 position 11 c1rb6C_ 12.0 40 PDB header:dna binding protein Chain: C: PDB Molecule:general control protein gcn4; PDBTitle: antiparallel trimer of gcn4-leucine zipper core mutant as2 n16a tetragonal form 12 c3k7zB_ 12.0 40 PDB header:dna binding protein Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution 13 c3k7zA_ 12.0 40 PDB header:dna binding protein Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution 14 c1rb1A_ 12.0 40 PDB header:dna binding protein Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution 15 c1rb1B_ 12.0 40 PDB header:dna binding protein Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: gcn4-leucine zipper core mutant as n16a trigonal automatic2 solution 16 c1swiA_ 11.4 40 PDB header:leucine zipper Chain: A: PDB Molecule:gcn4p1; PDBTitle: gcn4-leucine zipper core mutant as n16a complexed with2 benzene 17 c2l5gA_ 11.4 31 PDB header:transcription regulator Chain: A: PDB Molecule:g protein pathway suppressor 2; PDBTitle: co-ordinates and 1h, 13c and 15n chemical shift assignments for the2 complex of gps2 53-90 and smrt 167-207 18 d1gh6a_ 9.7 20 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 19 c2l6lA_ 9.5 27 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 24; PDBTitle: solution structure of human j-protein co-chaperone, dph4 20 c1ce0B_ 9.5 33 PDB header:hiv-1 envelope protein Chain: B: PDB Molecule:protein (leucine zipper model h38-p1); PDBTitle: trimerization specificity in hiv-1 gp41: analysis with a2 gcn4 leucine zipper model 21 c2ovcA_ not modelled 9.4 64 PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily kqt member 4; PDBTitle: crystal structure of a coiled-coil tetramerization domain from kv7.42 channels 22 d2bcgg2 not modelled 8.9 21 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:GDI-like N domain 23 c2khfA_ not modelled 8.7 20 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in dpc-micelles 24 c2w0cR_ not modelled 8.4 71 PDB header:virus Chain: R: PDB Molecule:protein p3; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 25 c2voiB_ not modelled 8.2 33 PDB header:apoptosis Chain: B: PDB Molecule:bh3-interacting domain death agonist p13; PDBTitle: structure of mouse a1 bound to the bid bh3-domain 26 d1nz6a_ not modelled 8.2 45 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 27 c2o37A_ not modelled 8.1 27 PDB header:chaperone Chain: A: PDB Molecule:protein sis1; PDBTitle: j-domain of sis1 protein, hsp40 co-chaperone from2 saccharomyces cerevisiae. 28 c2g7rA_ not modelled 7.7 29 PDB header:hydrolase Chain: A: PDB Molecule:mucosa-associated lymphoid tissue lymphoma translocation PDBTitle: x-ray structure of the death domain of the human mucosa associated2 lymphoid tissue lymphoma translocation protein 1 29 c3ag7A_ not modelled 7.2 11 PDB header:plant protein Chain: A: PDB Molecule:putative uncharacterized protein f9e10.5; PDBTitle: an auxilin-like j-domain containing protein, jac1 j-domain 30 c2ys8A_ not modelled 7.2 27 PDB header:protein binding Chain: A: PDB Molecule:rab-related gtp-binding protein rabj; PDBTitle: solution structure of the dnaj-like domain from human ras-2 associated protein rap1 31 c2l06A_ not modelled 7.0 86 PDB header:protein binding Chain: A: PDB Molecule:phycobilisome lcm core-membrane linker polypeptide; PDBTitle: solution nmr structure of the pbs linker polypeptide domain (fragment2 254-400) of phycobilisome linker protein apce from synechocystis sp.3 pcc 6803. northeast structural genomics consortium target sgr209c 32 c2guzO_ not modelled 6.8 36 PDB header:chaperone, protein transport Chain: O: PDB Molecule:mitochondrial import inner membrane translocase PDBTitle: structure of the tim14-tim16 complex of the mitochondrial2 protein import motor 33 c2ochA_ not modelled 6.8 36 PDB header:chaperone Chain: A: PDB Molecule:hypothetical protein dnj-12; PDBTitle: j-domain of dnj-12 from caenorhabditis elegans 34 c2ctrA_ not modelled 6.6 36 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily b member 9; PDBTitle: solution structure of j-domain from human dnaj subfamily b2 menber 9 35 c2ky4A_ not modelled 6.4 56 PDB header:photosynthesis Chain: A: PDB Molecule:phycobilisome linker polypeptide; PDBTitle: solution nmr structure of the pbs linker domain of phycobilisome2 linker polypeptide from anabaena sp. northeast structural genomics3 consortium target nsr123e 36 d1fd3a_ not modelled 6.4 67 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 37 c2xzrA_ not modelled 6.3 24 PDB header:cell adhesion Chain: A: PDB Molecule:immunoglobulin-binding protein eibd; PDBTitle: escherichia coli immunoglobulin-binding protein eibd 391-438 fused2 to gcn4 adaptors 38 c2dn9A_ not modelled 6.3 55 PDB header:apoptosis, chaperone Chain: A: PDB Molecule:dnaj homolog subfamily a member 3; PDBTitle: solution structure of j-domain from the dnaj homolog, human2 tid1 protein 39 c2khgA_ not modelled 6.3 20 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe 40 d1xbla_ not modelled 6.1 27 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 41 c1bq0A_ not modelled 6.1 27 PDB header:chaperone Chain: A: PDB Molecule:dnaj; PDBTitle: j-domain (residues 1-77) of the escherichia coli n-terminal2 fragment (residues 1-104) of the molecular chaperone dnaj,3 nmr, 20 structures 42 c2d96A_ not modelled 6.0 29 PDB header:transcription Chain: A: PDB Molecule:nuclear factor nf-kappa-b p100 subunit; PDBTitle: solution structure of the death domain of nuclear factor nf-2 kappa-b p100 43 d1fafa_ not modelled 6.0 36 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 44 d1ni7a_ not modelled 5.8 20 Fold:SufE/NifU Superfamily:SufE/NifU Family:SufE-like 45 d1qmga2 not modelled 5.8 28 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:6-phosphogluconate dehydrogenase-like, N-terminal domain 46 c2ctqA_ not modelled 5.7 27 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 12; PDBTitle: solution structure of j-domain from human dnaj subfamily c2 menber 12 47 c2pjwV_ not modelled 5.7 22 PDB header:endocytosis/exocytosis Chain: V: PDB Molecule:vacuolar protein sorting-associated protein 27; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting 48 d1e3ha6 not modelled 5.6 17 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 49 c2a3dA_ not modelled 5.4 35 PDB header:three-helix bundle Chain: A: PDB Molecule:protein (de novo three-helix bundle); PDBTitle: solution structure of a de novo designed single chain three-2 helix bundle (a3d) 50 c2o7hF_ not modelled 5.4 33 PDB header:transcription Chain: F: PDB Molecule:general control protein gcn4; PDBTitle: crystal structure of trimeric coiled coil gcn4 leucine zipper 51 c2cugA_ not modelled 5.3 36 PDB header:chaperone Chain: A: PDB Molecule:mkiaa0962 protein; PDBTitle: solution structure of the j domain of the pseudo dnaj2 protein, mouse hypothetical mkiaa0962

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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