Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	V	Q	Q	F	F	V	V	A	V	F	F	L	I	P	I	F	C	F	R	E	A	W	K	G	W	R	A	G	A	I	D	K	R	V	K	N	A	P	E	P	V	Y	V	W	R	A	K	N	P	G	L	F	F	A	Y	M	V	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?																												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.
Sequence		Y	I	G	F	G	I	L	S	I	G	M	I	V	Y	L	I	F	Y	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 1qp6 chain B Region: 20 - 37 Aligned: 18 Modelled: 18 Confidence: 30.7% Identity: 50% PDB header:de novo protein Chain: B: PDB Molecule:protein (alpha2d); PDBTitle: solution structure of alpha2d Phyre2 PDB 1xfj chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 23.3% Identity: 27% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: YfiH-like Phyre2 PDB 1rw0 chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 19.8% Identity: 27% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: YfiH-like Phyre2 PDB 2a6q chain B domain 1 Region: 30 - 51 Aligned: 22 Modelled: 22 Confidence: 17.8% Identity: 14% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 1xaf chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 17.5% Identity: 33% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: YfiH-like Phyre2 PDB 1t8h chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 16.6% Identity: 27% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: YfiH-like Phyre2 PDB 3hs2 chain H Region: 29 - 51 Aligned: 21 Modelled: 23 Confidence: 16.3% Identity: 14% PDB header:antitoxin Chain: H: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd truncated to residue 57 in an orthorhombic2 space group Phyre2 PDB 3hry chain A Region: 29 - 51 Aligned: 21 Modelled: 23 Confidence: 16.3% Identity: 14% PDB header:antitoxin Chain: A: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd in a trigonal space group and partially2 disordered Phyre2 PDB 1bxn chain A domain 1 Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 13.8% Identity: 9% Fold: TIM beta/alpha-barrel Superfamily: RuBisCo, C-terminal domain Family: RuBisCo, large subunit, C-terminal domain Phyre2 PDB 1ykw chain A domain 1 Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 13.2% Identity: 32% Fold: TIM beta/alpha-barrel Superfamily: RuBisCo, C-terminal domain Family: RuBisCo, large subunit, C-terminal domain Phyre2 PDB 1rv9 chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 12.9% Identity: 20% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: YfiH-like Phyre2 PDB 3g5o chain A Region: 34 - 51 Aligned: 18 Modelled: 18 Confidence: 11.1% Identity: 11% PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis Phyre2 PDB 2ip6 chain A Region: 31 - 42 Aligned: 12 Modelled: 12 Confidence: 10.9% Identity: 33% PDB header:antimicrobial protein Chain: A: PDB Molecule:papb; PDBTitle: crystal structure of pedb Phyre2 PDB 2zt9 chain E Region: 58 - 77 Aligned: 20 Modelled: 20 Confidence: 10.8% Identity: 50% PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 Phyre2 PDB 2j5d chain A Region: 66 - 75 Aligned: 10 Modelled: 10 Confidence: 9.6% Identity: 40% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles Phyre2 PDB 2job chain A Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 9.3% Identity: 30% PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site Phyre2 PDB 3fy6 chain A Region: 20 - 33 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 57% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of v. cholerae.2 integron cassette protein vch_cass3 Phyre2 PDB 1ldd chain A Region: 53 - 60 Aligned: 8 Modelled: 8 Confidence: 8.8% Identity: 0% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: SCF ubiquitin ligase complex WHB domain Phyre2 PDB 1wwc chain A Region: 35 - 50 Aligned: 16 Modelled: 16 Confidence: 8.6% Identity: 25% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 PDB 1rcx chain H Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 8.2% Identity: 32% PDB header:lyase (carbon-carbon) Chain: H: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase; PDBTitle: non-activated spinach rubisco in complex with its substrate2 ribulose-1,5-bisphosphate Phyre2 1 c1qp6B_ 2 d1xfja_ 3 d1rw0a_ 4 d2a6qb1 5 d1xafa_ 6 d1t8ha_ 7 c3hs2H_ 8 c3hryA_ 9 d1bxna1 10 d1ykwa1 11 d1rv9a_ 12 c3g5oA_ 13 c2ip6A_ 14 c2zt9E_ 15 c2j5dA_ 16 c2jobA_ 17 c3fy6A_ 18 d1ldda_ 19 d1wwca_ 20 c1rcxH_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 c1qp6B_ 30.7 50 PDB header:de novo protein Chain: B: PDB Molecule:protein (alpha2d); PDBTitle: solution structure of alpha2d 2 d1xfja_ 23.3 27 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:YfiH-like 3 d1rw0a_ 19.8 27 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:YfiH-like 4 d2a6qb1 17.8 14 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 5 d1xafa_ 17.5 33 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:YfiH-like 6 d1t8ha_ 16.6 27 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:YfiH-like 7 c3hs2H_ 16.3 14 PDB header:antitoxin Chain: H: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd truncated to residue 57 in an orthorhombic2 space group 8 c3hryA_ 16.3 14 PDB header:antitoxin Chain: A: PDB Molecule:prevent host death protein; PDBTitle: crystal structure of phd in a trigonal space group and partially2 disordered 9 d1bxna1 13.8 9 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 10 d1ykwa1 13.2 32 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 11 d1rv9a_ 12.9 20 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:YfiH-like 12 c3g5oA_ 11.1 11 PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 13 c2ip6A_ 10.9 33 PDB header:antimicrobial protein Chain: A: PDB Molecule:papb; PDBTitle: crystal structure of pedb 14 c2zt9E_ 10.8 50 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 15 c2j5dA_ 9.6 40 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles 16 c2jobA_ 9.3 30 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 17 c3fy6A_ 9.2 57 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:integron cassette protein; PDBTitle: structure from the mobile metagenome of v. cholerae.2 integron cassette protein vch_cass3 18 d1ldda_ 8.8 0 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:SCF ubiquitin ligase complex WHB domain 19 d1wwca_ 8.6 25 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 20 c1rcxH_ 8.2 32 PDB header:lyase (carbon-carbon) Chain: H: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase; PDBTitle: non-activated spinach rubisco in complex with its substrate2 ribulose-1,5-bisphosphate 21 d2q9oa1 not modelled 8.1 42 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 22 d2a6qa1 not modelled 7.9 11 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 23 c1bwvA_ not modelled 7.6 14 PDB header:lyase Chain: A: PDB Molecule:protein (ribulose bisphosphate carboxylase); PDBTitle: activated ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco)2 complexed with the reaction intermediate analogue 2-carboxyarabinitol3 1,5-bisphosphate 24 d1vcaa2 not modelled 7.3 19 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 25 d1geha1 not modelled 6.8 27 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 26 d1bwva1 not modelled 6.7 18 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 27 d8ruca1 not modelled 6.6 32 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 28 d1wdda1 not modelled 6.5 32 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 29 c2jmvA_ not modelled 6.5 41 PDB header:antiviral protein Chain: A: PDB Molecule:scytovirin; PDBTitle: solution structure of scytovirin refined against residual2 dipolar couplings 30 d1ej7l1 not modelled 6.2 32 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 31 d1svda1 not modelled 6.2 27 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 32 c1vf5R_ not modelled 6.2 16 PDB header:photosynthesis Chain: R: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 33 c2e75E_ not modelled 6.2 16 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus 34 c2e74E_ not modelled 6.2 16 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus 35 d2e74e1 not modelled 6.2 16 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 36 c2e76E_ not modelled 6.2 16 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 37 d1wwwx_ not modelled 6.1 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 38 c1telA_ not modelled 6.0 32 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribulose bisphosphate carboxylase, large subunit; PDBTitle: crystal structure of a rubisco-like protein from chlorobium2 tepidum 39 c2w0cR_ not modelled 5.9 31 PDB header:virus Chain: R: PDB Molecule:protein p3; PDBTitle: x-ray structure of the entire lipid-containing2 bacteriophage pm2 40 c3nwrA_ not modelled 5.9 32 PDB header:lyase Chain: A: PDB Molecule:a rubisco-like protein; PDBTitle: crystal structure of a rubisco-like protein from burkholderia fungorum 41 d1kbva1 not modelled 5.8 33 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 42 c2qygC_ not modelled 5.7 32 PDB header:unknown function Chain: C: PDB Molecule:ribulose bisphosphate carboxylase-like protein 2; PDBTitle: crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas2 palustris 43 c2rq2A_ not modelled 5.6 45 PDB header:antibiotic Chain: A: PDB Molecule:big defensin; PDBTitle: the solution structure of the n-terminal fragment of big2 defensin

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