Secondary structure and disorder prediction

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Sequence		M	A	Y	F	L	D	F	D	E	R	A	L	K	E	W	R	K	L	G	S	T	V	R	E	Q	L	K	K	K	L	V	E	V	L	E	S	P	R	I	E	A	N	K	L	R	G	M	P	D	C	Y	K	I	K	L	R	S	S	G	Y
Secondary structure
SS confidence
Disorder		?	?															?	?																			?	?	?	?	?	?	?	?	?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.
Sequence		R	L	V	Y	Q	V	I	D	E	K	V	V	V	F	V	I	S	V	G	K	R	E	R	S	E	V	Y	S	E	A	V	K	R	I	L
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 3kix chain Y Region: 2 - 95 Aligned: 94 Modelled: 94 Confidence: 100.0% Identity: 100% PDB header:ribosome Chain: Y: PDB Molecule: PDBTitle: structure of rele nuclease bound to the 70s ribosome2 (postcleavage state; part 3 of 4) Phyre2 PDB 1wmi chain A domain 1 Region: 1 - 83 Aligned: 83 Modelled: 83 Confidence: 99.9% Identity: 20% Fold: RelE-like Superfamily: RelE-like Family: RelE-like Phyre2 PDB 2khe chain A Region: 1 - 88 Aligned: 86 Modelled: 88 Confidence: 99.9% Identity: 34% PDB header:hydrolase Chain: A: PDB Molecule:toxin-like protein; PDBTitle: solution structure of the bacterial toxin rele from thermus2 thermophilus hb8 Phyre2 PDB 3g5o chain C Region: 1 - 83 Aligned: 82 Modelled: 83 Confidence: 99.9% Identity: 22% PDB header:toxin/antitoxin Chain: C: PDB Molecule:uncharacterized protein rv2866; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis Phyre2 PDB 3bpq chain D Region: 5 - 88 Aligned: 78 Modelled: 84 Confidence: 99.8% Identity: 21% PDB header:toxin Chain: D: PDB Molecule:toxin rele3; PDBTitle: crystal structure of relb-rele antitoxin-toxin complex from2 methanococcus jannaschii Phyre2 PDB 2otr chain A Region: 3 - 87 Aligned: 82 Modelled: 85 Confidence: 99.3% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein hp0892; PDBTitle: solution structure of conserved hypothetical protein hp0892 from2 helicobacter pylori Phyre2 PDB 3oei chain H Region: 3 - 80 Aligned: 75 Modelled: 78 Confidence: 99.1% Identity: 21% PDB header:toxin, protein binding Chain: H: PDB Molecule:relk (toxin rv3358); PDBTitle: crystal structure of mycobacterium tuberculosis reljk (rv3357-rv3358-2 relbe3) Phyre2 PDB 2a6s chain A domain 1 Region: 4 - 74 Aligned: 70 Modelled: 71 Confidence: 99.0% Identity: 16% Fold: RelE-like Superfamily: RelE-like Family: YoeB/Txe-like Phyre2 PDB 1z8m chain A domain 1 Region: 3 - 87 Aligned: 80 Modelled: 85 Confidence: 98.4% Identity: 21% Fold: RelE-like Superfamily: RelE-like Family: RelE-like Phyre2 PDB 3kxe chain B Region: 4 - 80 Aligned: 72 Modelled: 77 Confidence: 97.6% Identity: 15% PDB header:protein binding Chain: B: PDB Molecule:toxin protein pare-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex Phyre2 PDB 2kru chain A Region: 5 - 34 Aligned: 30 Modelled: 30 Confidence: 81.2% Identity: 23% PDB header:oxidoreductase Chain: A: PDB Molecule:light-independent protochlorophyllide reductase PDBTitle: solution nmr structure of the pcp_red domain of light-2 independent protochlorophyllide reductase subunit b from3 chlorobium tepidum. northeast structural genomics4 consortium target ctr69a (casp target) Phyre2 PDB 2l09 chain A Region: 5 - 34 Aligned: 30 Modelled: 30 Confidence: 73.1% Identity: 17% PDB header:oxidoreductase Chain: A: PDB Molecule:asr4154 protein; PDBTitle: solution nmr structure of protein asr4154 from nostoc sp. pcc71202 northeast structural genomics consortium target id nsr143 Phyre2 PDB 2apn chain A Region: 1 - 18 Aligned: 18 Modelled: 18 Confidence: 16.1% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure Phyre2 PDB 1ugj chain A Region: 59 - 81 Aligned: 23 Modelled: 23 Confidence: 10.1% Identity: 17% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: RIKEN cDNA 2310057j16 protein (KIAA1543) Phyre2 PDB 1v9x chain A Region: 15 - 51 Aligned: 37 Modelled: 37 Confidence: 10.1% Identity: 8% PDB header:transferase Chain: A: PDB Molecule:poly (adp-ribose) polymerase; PDBTitle: solution structure of the first zn-finger domain of2 poly(adp-ribose) polymerase-1 Phyre2 PDB 2dmj chain A Region: 15 - 37 Aligned: 23 Modelled: 23 Confidence: 8.8% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:poly (adp-ribose) polymerase family, member 1; PDBTitle: solution structure of the first zf-parp domain of human2 poly(adp-ribose)polymerase-1 Phyre2 PDB 1v85 chain A Region: 7 - 37 Aligned: 31 Modelled: 31 Confidence: 8.2% Identity: 19% PDB header:apoptosis Chain: A: PDB Molecule:similar to ring finger protein 36; PDBTitle: sterile alpha motif (sam) domain of mouse bifunctional2 apoptosis regulator Phyre2 PDB 1efa chain A domain 1 Region: 9 - 48 Aligned: 40 Modelled: 40 Confidence: 7.7% Identity: 20% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1wix chain A Region: 9 - 41 Aligned: 33 Modelled: 33 Confidence: 7.3% Identity: 12% Fold: CH domain-like Superfamily: Hook domain Family: Hook domain Phyre2 PDB 1nwb chain A Region: 5 - 18 Aligned: 14 Modelled: 14 Confidence: 7.0% Identity: 21% Fold: HesB-like domain Superfamily: HesB-like domain Family: HesB-like domain Phyre2 1 c3kixy_ 2 d1wmia1 3 c2kheA_ 4 c3g5oC_ 5 c3bpqD_ 6 c2otrA_ 7 c3oeiH_ 8 d2a6sa1 9 d1z8ma1 10 c3kxeB_ 11 c2kruA_ 12 c2l09A_ 13 c2apnA_ 14 d1ugja_ 15 c1v9xA_ 16 c2dmjA_ 17 c1v85A_ 18 d1efaa1 19 d1wixa_ 20 d1nwba_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 c3kixy_ 100.0 100 PDB header:ribosome Chain: Y: PDB Molecule: PDBTitle: structure of rele nuclease bound to the 70s ribosome2 (postcleavage state; part 3 of 4) 2 d1wmia1 99.9 20 Fold:RelE-like Superfamily:RelE-like Family:RelE-like 3 c2kheA_ 99.9 34 PDB header:hydrolase Chain: A: PDB Molecule:toxin-like protein; PDBTitle: solution structure of the bacterial toxin rele from thermus2 thermophilus hb8 4 c3g5oC_ 99.9 22 PDB header:toxin/antitoxin Chain: C: PDB Molecule:uncharacterized protein rv2866; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 5 c3bpqD_ 99.8 21 PDB header:toxin Chain: D: PDB Molecule:toxin rele3; PDBTitle: crystal structure of relb-rele antitoxin-toxin complex from2 methanococcus jannaschii 6 c2otrA_ 99.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein hp0892; PDBTitle: solution structure of conserved hypothetical protein hp0892 from2 helicobacter pylori 7 c3oeiH_ 99.1 21 PDB header:toxin, protein binding Chain: H: PDB Molecule:relk (toxin rv3358); PDBTitle: crystal structure of mycobacterium tuberculosis reljk (rv3357-rv3358-2 relbe3) 8 d2a6sa1 99.0 16 Fold:RelE-like Superfamily:RelE-like Family:YoeB/Txe-like 9 d1z8ma1 98.4 21 Fold:RelE-like Superfamily:RelE-like Family:RelE-like 10 c3kxeB_ 97.6 15 PDB header:protein binding Chain: B: PDB Molecule:toxin protein pare-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 11 c2kruA_ 81.2 23 PDB header:oxidoreductase Chain: A: PDB Molecule:light-independent protochlorophyllide reductase PDBTitle: solution nmr structure of the pcp_red domain of light-2 independent protochlorophyllide reductase subunit b from3 chlorobium tepidum. northeast structural genomics4 consortium target ctr69a (casp target) 12 c2l09A_ 73.1 17 PDB header:oxidoreductase Chain: A: PDB Molecule:asr4154 protein; PDBTitle: solution nmr structure of protein asr4154 from nostoc sp. pcc71202 northeast structural genomics consortium target id nsr143 13 c2apnA_ 16.1 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure 14 d1ugja_ 10.1 17 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:RIKEN cDNA 2310057j16 protein (KIAA1543) 15 c1v9xA_ 10.1 8 PDB header:transferase Chain: A: PDB Molecule:poly (adp-ribose) polymerase; PDBTitle: solution structure of the first zn-finger domain of2 poly(adp-ribose) polymerase-1 16 c2dmjA_ 8.8 17 PDB header:transferase Chain: A: PDB Molecule:poly (adp-ribose) polymerase family, member 1; PDBTitle: solution structure of the first zf-parp domain of human2 poly(adp-ribose)polymerase-1 17 c1v85A_ 8.2 19 PDB header:apoptosis Chain: A: PDB Molecule:similar to ring finger protein 36; PDBTitle: sterile alpha motif (sam) domain of mouse bifunctional2 apoptosis regulator 18 d1efaa1 7.7 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 19 d1wixa_ 7.3 12 Fold:CH domain-like Superfamily:Hook domain Family:Hook domain 20 d1nwba_ 7.0 21 Fold:HesB-like domain Superfamily:HesB-like domain Family:HesB-like domain 21 d1zdna1 not modelled 6.9 10 Fold:UBC-like Superfamily:UBC-like Family:UBC-related 22 c2eamA_ not modelled 6.6 19 PDB header:signaling protein Chain: A: PDB Molecule:putative 47 kda protein; PDBTitle: solution structure of the n-terminal sam-domain of a human2 putative 47 kda protein 23 d1v38a_ not modelled 6.5 23 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 24 c1hk7A_ not modelled 6.5 16 PDB header:chaperone Chain: A: PDB Molecule:heat shock protein hsp82; PDBTitle: middle domain of hsp90 25 c2dl0A_ not modelled 6.4 17 PDB header:signaling protein Chain: A: PDB Molecule:sam and sh3 domain-containing protein 1; PDBTitle: solution structure of the sam-domain of the sam and sh32 domain containing protein 1 26 c2lc0A_ not modelled 6.3 8 PDB header:protein binding Chain: A: PDB Molecule:putative uncharacterized protein tb39.8; PDBTitle: rv0020c_nter structure 27 c1x0gA_ not modelled 6.2 21 PDB header:metal binding protein Chain: A: PDB Molecule:isca; PDBTitle: crystal structure of isca with the [2fe-2s] cluster 28 c3djmA_ not modelled 5.9 19 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein duf427; PDBTitle: crystal structure of a protein of unknown function from duf427 family2 (rsph17029_0682) from rhodobacter sphaeroides 2.4.1 at 2.51 a3 resolution 29 d1ykha1 not modelled 5.8 18 Fold:Mediator hinge subcomplex-like Superfamily:Mediator hinge subcomplex-like Family:MED7 hinge region 30 c2d2aA_ not modelled 5.6 29 PDB header:metal transport Chain: A: PDB Molecule:sufa protein; PDBTitle: crystal structure of escherichia coli sufa involved in2 biosynthesis of iron-sulfur clusters 31 d2hsga1 not modelled 5.6 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 32 d1nexa2 not modelled 5.2 12 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 33 d1qpza1 not modelled 5.1 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator

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