Secondary structure and disorder prediction

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Sequence		M	E	K	L	T	T	E	L	H	S	L	S	E	M	D	R	R	H	V	V	S	I	L	A	E	I	A	N	G	Y	D	D	F	N	D	M	L	I	Y	L	E	F	Y	P	N	H	K	I	L	I	S
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 1s4k chain A Region: 7 - 49 Aligned: 43 Modelled: 43 Confidence: 21.4% Identity: 21% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: YdiL-like Phyre2 PDB 3pue chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 11.7% Identity: 28% PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of the complex of dhydrodipicolinate synthase from2 acinetobacter baumannii with lysine at 2.6a resolution Phyre2 PDB 1plo chain A Region: 31 - 49 Aligned: 19 Modelled: 19 Confidence: 10.8% Identity: 32% Fold: Snake toxin-like Superfamily: Snake toxin-like Family: Extracellular domain of cell surface receptors Phyre2 PDB 3fkk chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 10.6% Identity: 16% PDB header:lyase Chain: A: PDB Molecule:l-2-keto-3-deoxyarabonate dehydratase; PDBTitle: structure of l-2-keto-3-deoxyarabonate dehydratase Phyre2 PDB 2gsc chain A domain 1 Region: 7 - 31 Aligned: 25 Modelled: 25 Confidence: 10.3% Identity: 40% Fold: Bromodomain-like Superfamily: IVS-encoded protein-like Family: IVS-encoded protein-like Phyre2 PDB 3h5d chain D Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 9.5% Identity: 20% PDB header:lyase Chain: D: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: dihydrodipicolinate synthase from drug-resistant streptococcus2 pneumoniae Phyre2 PDB 3g0s chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 9.4% Identity: 36% PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: dihydrodipicolinate synthase from salmonella typhimurium lt2 Phyre2 PDB 3qfe chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 9.1% Identity: 12% PDB header:lyase Chain: B: PDB Molecule:putative dihydrodipicolinate synthase family protein; PDBTitle: crystal structures of a putative dihydrodipicolinate synthase family2 protein from coccidioides immitis Phyre2 PDB 2a6n chain A domain 1 Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 28% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: Class I aldolase Phyre2 PDB 1f74 chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 8.8% Identity: 24% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: Class I aldolase Phyre2 PDB 3d0c chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 8.7% Identity: 28% PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from2 oceanobacillus iheyensis at 1.9 a resolution Phyre2 PDB 3bi8 chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 8.5% Identity: 20% PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: structure of dihydrodipicolinate synthase from clostridium2 botulinum Phyre2 PDB 3na8 chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 8.3% Identity: 24% PDB header:lyase Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase; PDBTitle: crystal structure of a putative dihydrodipicolinate synthetase from2 pseudomonas aeruginosa Phyre2 PDB 1hl2 chain A Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 8.2% Identity: 40% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: Class I aldolase Phyre2 PDB 2v9d chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 12% PDB header:lyase Chain: B: PDB Molecule:yage; PDBTitle: crystal structure of yage, a prophage protein belonging to2 the dihydrodipicolinic acid synthase family from e. coli3 k12 Phyre2 PDB 3n2x chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 12% PDB header:lyase Chain: B: PDB Molecule:uncharacterized protein yage; PDBTitle: crystal structure of yage, a prophage protein belonging to the2 dihydrodipicolinic acid synthase family from e. coli k12 in complex3 with pyruvate Phyre2 PDB 3b4u chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.7% Identity: 20% PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from agrobacterium2 tumefaciens str. c58 Phyre2 PDB 1z3x chain A domain 1 Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 7.5% Identity: 17% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: GUN4-associated domain Phyre2 PDB 1ki1 chain B domain 2 Region: 33 - 39 Aligned: 7 Modelled: 7 Confidence: 7.2% Identity: 57% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Pleckstrin-homology domain (PH domain) Phyre2 PDB 3si9 chain B Region: 5 - 29 Aligned: 25 Modelled: 25 Confidence: 7.1% Identity: 16% PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from bartonella2 henselae Phyre2 1 d1s4ka_ 2 c3pueA_ 3 d1ploa_ 4 c3fkkA_ 5 d2gsca1 6 c3h5dD_ 7 c3g0sA_ 8 c3qfeB_ 9 d2a6na1 10 d1f74a_ 11 c3d0cB_ 12 c3bi8A_ 13 c3na8A_ 14 d1hl2a_ 15 c2v9dB_ 16 c3n2xB_ 17 c3b4uB_ 18 d1z3xa1 19 d1ki1b2 20 c3si9B_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d1s4ka_ 21.4 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:YdiL-like 2 c3pueA_ 11.7 28 PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of the complex of dhydrodipicolinate synthase from2 acinetobacter baumannii with lysine at 2.6a resolution 3 d1ploa_ 10.8 32 Fold:Snake toxin-like Superfamily:Snake toxin-like Family:Extracellular domain of cell surface receptors 4 c3fkkA_ 10.6 16 PDB header:lyase Chain: A: PDB Molecule:l-2-keto-3-deoxyarabonate dehydratase; PDBTitle: structure of l-2-keto-3-deoxyarabonate dehydratase 5 d2gsca1 10.3 40 Fold:Bromodomain-like Superfamily:IVS-encoded protein-like Family:IVS-encoded protein-like 6 c3h5dD_ 9.5 20 PDB header:lyase Chain: D: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: dihydrodipicolinate synthase from drug-resistant streptococcus2 pneumoniae 7 c3g0sA_ 9.4 36 PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: dihydrodipicolinate synthase from salmonella typhimurium lt2 8 c3qfeB_ 9.1 12 PDB header:lyase Chain: B: PDB Molecule:putative dihydrodipicolinate synthase family protein; PDBTitle: crystal structures of a putative dihydrodipicolinate synthase family2 protein from coccidioides immitis 9 d2a6na1 9.0 28 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 10 d1f74a_ 8.8 24 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 11 c3d0cB_ 8.7 28 PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from2 oceanobacillus iheyensis at 1.9 a resolution 12 c3bi8A_ 8.5 20 PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: structure of dihydrodipicolinate synthase from clostridium2 botulinum 13 c3na8A_ 8.3 24 PDB header:lyase Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase; PDBTitle: crystal structure of a putative dihydrodipicolinate synthetase from2 pseudomonas aeruginosa 14 d1hl2a_ 8.2 40 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 15 c2v9dB_ 7.9 12 PDB header:lyase Chain: B: PDB Molecule:yage; PDBTitle: crystal structure of yage, a prophage protein belonging to2 the dihydrodipicolinic acid synthase family from e. coli3 k12 16 c3n2xB_ 7.9 12 PDB header:lyase Chain: B: PDB Molecule:uncharacterized protein yage; PDBTitle: crystal structure of yage, a prophage protein belonging to the2 dihydrodipicolinic acid synthase family from e. coli k12 in complex3 with pyruvate 17 c3b4uB_ 7.7 20 PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from agrobacterium2 tumefaciens str. c58 18 d1z3xa1 7.5 17 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:GUN4-associated domain 19 d1ki1b2 7.2 57 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain) 20 c3si9B_ 7.1 16 PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from bartonella2 henselae 21 c3qwmA_ not modelled 6.9 57 PDB header:signaling protein Chain: A: PDB Molecule:iq motif and sec7 domain-containing protein 1; PDBTitle: crystal structure of gep100, the plextrin homology domain of iq motif2 and sec7 domain-containing protein 1 isoform a 22 d1xkya1 not modelled 6.9 12 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 23 c3eb2A_ not modelled 6.8 32 PDB header:lyase Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase; PDBTitle: crystal structure of dihydrodipicolinate synthase from2 rhodopseudomonas palustris at 2.0a resolution 24 c3fluD_ not modelled 6.3 20 PDB header:lyase Chain: D: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from the pathogen2 neisseria meningitidis 25 c3noeA_ not modelled 6.2 24 PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from pseudomonas2 aeruginosa 26 c2yxgD_ not modelled 5.6 28 PDB header:lyase Chain: D: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihyrodipicolinate synthase (dapa) 27 c2vc6A_ not modelled 5.6 40 PDB header:lyase Chain: A: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: structure of mosa from s. meliloti with pyruvate bound 28 c2jnsA_ not modelled 5.6 21 PDB header:unknown function Chain: A: PDB Molecule:bromodomain-containing protein 4; PDBTitle: solution structure of the bromodomain-containing protein 42 et domain 29 d1o5ka_ not modelled 5.6 36 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 30 d1txda2 not modelled 5.6 33 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain) 31 d1xcga2 not modelled 5.6 33 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain)

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