Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	W	L	V	K	K	S	C	C	N	K	Q	D	N	R	H	V	L	M	L	C	D	A	G	G	A	I	K	M	I	A	E	V	K	S	D	F	A	V	K	V	G	D	L	L	S	P	L	Q	N	A	L	Y	C	I	N	R	E	K
Secondary structure
SS confidence
Disorder		?	?	?		?																														?	?		?		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.
Sequence		L	H	T	V	K	V	L	S	A	S	S	Y	S	P	D	E	W	E	R	Q	C	K	V	A	G	K	T	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 2jso chain A Region: 1 - 88 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 100% PDB header:signaling protein Chain: A: PDB Molecule:polymyxin resistance protein pmrd; PDBTitle: antimicrobial resistance protein Phyre2 PDB 2rqx chain A Region: 1 - 82 Aligned: 80 Modelled: 82 Confidence: 100.0% Identity: 38% PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae Phyre2 PDB 1lwh chain A domain 1 Region: 12 - 50 Aligned: 39 Modelled: 39 Confidence: 28.7% Identity: 23% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2l66 chain B Region: 32 - 46 Aligned: 15 Modelled: 15 Confidence: 22.8% Identity: 47% PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, abrb family; PDBTitle: the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb2 superfamily from archaea. Phyre2 PDB 1v9j chain A Region: 67 - 82 Aligned: 16 Modelled: 16 Confidence: 13.2% Identity: 25% Fold: Alpha-lytic protease prodomain-like Superfamily: BolA-like Family: BolA-like Phyre2 PDB 1ny8 chain A Region: 67 - 85 Aligned: 19 Modelled: 19 Confidence: 12.1% Identity: 42% Fold: Alpha-lytic protease prodomain-like Superfamily: BolA-like Family: BolA-like Phyre2 PDB 1vc4 chain A Region: 11 - 50 Aligned: 40 Modelled: 40 Confidence: 10.5% Identity: 18% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: Tryptophan biosynthesis enzymes Phyre2 PDB 3hcj chain B Region: 53 - 84 Aligned: 29 Modelled: 29 Confidence: 9.5% Identity: 14% PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase; PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form) Phyre2 PDB 1hyo chain A domain 2 Region: 29 - 46 Aligned: 18 Modelled: 18 Confidence: 9.3% Identity: 22% Fold: FAH Superfamily: FAH Family: FAH Phyre2 PDB 2dhm chain A Region: 72 - 82 Aligned: 11 Modelled: 11 Confidence: 9.0% Identity: 36% PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli Phyre2 PDB 3anw chain A Region: 12 - 66 Aligned: 55 Modelled: 55 Confidence: 8.7% Identity: 13% PDB header:replication Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: a protein complex essential initiation of dna replication Phyre2 PDB 1hyo chain B Region: 29 - 46 Aligned: 18 Modelled: 18 Confidence: 7.8% Identity: 22% PDB header:hydrolase Chain: B: PDB Molecule:fumarylacetoacetate hydrolase; PDBTitle: crystal structure of fumarylacetoacetate hydrolase2 complexed with 4-(hydroxymethylphosphinoyl)-3-oxo-butanoic3 acid Phyre2 PDB 1uij chain A Region: 37 - 67 Aligned: 31 Modelled: 31 Confidence: 7.6% Identity: 19% PDB header:sugar binding protein Chain: A: PDB Molecule:beta subunit of beta conglycinin; PDBTitle: crystal structure of soybean beta-conglycinin beta2 homotrimer (i122m/k124w) Phyre2 PDB 3gdw chain A Region: 18 - 33 Aligned: 15 Modelled: 16 Confidence: 7.5% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:sigma-54 interaction domain protein; PDBTitle: crystal structure of sigma-54 interaction domain protein from2 enterococcus faecalis Phyre2 PDB 1fx0 chain B domain 2 Region: 40 - 67 Aligned: 28 Modelled: 28 Confidence: 7.5% Identity: 18% Fold: Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily: N-terminal domain of alpha and beta subunits of F1 ATP synthase Family: N-terminal domain of alpha and beta subunits of F1 ATP synthase Phyre2 PDB 1g5v chain A Region: 37 - 49 Aligned: 13 Modelled: 13 Confidence: 7.1% Identity: 38% PDB header:translation Chain: A: PDB Molecule:survival motor neuron protein 1; PDBTitle: solution structure of the tudor domain of the human smn2 protein Phyre2 PDB 1m2s chain A Region: 73 - 88 Aligned: 16 Modelled: 16 Confidence: 7.0% Identity: 38% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 3eps chain B Region: 25 - 46 Aligned: 18 Modelled: 22 Confidence: 6.1% Identity: 39% PDB header:transferase, hydrolase Chain: B: PDB Molecule:isocitrate dehydrogenase kinase/phosphatase; PDBTitle: the crystal structure of isocitrate dehydrogenase kinase/phosphatase2 from e. coli Phyre2 PDB 2vxa chain L Region: 61 - 84 Aligned: 24 Modelled: 24 Confidence: 6.0% Identity: 25% PDB header:flavoprotein Chain: L: PDB Molecule:dodecin; PDBTitle: h.halophila dodecin in complex with riboflavin Phyre2 PDB 3lzk chain C Region: 29 - 46 Aligned: 18 Modelled: 18 Confidence: 6.0% Identity: 11% PDB header:hydrolase Chain: C: PDB Molecule:fumarylacetoacetate hydrolase family protein; PDBTitle: the crystal structure of a probably aromatic amino acid2 degradation protein from sinorhizobium meliloti 1021 Phyre2 1 c2jsoA_ 2 c2rqxA_ 3 d1lwha1 4 c2l66B_ 5 d1v9ja_ 6 d1ny8a_ 7 d1vc4a_ 8 c3hcjB_ 9 d1hyoa2 10 c2dhmA_ 11 c3anwA_ 12 c1hyoB_ 13 c1uijA_ 14 c3gdwA_ 15 d1fx0b2 16 c1g5vA_ 17 d1m2sa_ 18 c3epsB_ 19 c2vxaL_ 20 c3lzkC_ 21 22 23 24 25

Detailed template information

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

1 c2jsoA_ 100.0 100 PDB header:signaling protein Chain: A: PDB Molecule:polymyxin resistance protein pmrd; PDBTitle: antimicrobial resistance protein 2 c2rqxA_ 100.0 38 PDB header:signaling protein Chain: A: PDB Molecule:polymyxin b resistance protein; PDBTitle: solution nmr structure of pmrd from klebsiella pneumoniae 3 d1lwha1 28.7 23 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 4 c2l66B_ 22.8 47 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, abrb family; PDBTitle: the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb2 superfamily from archaea. 5 d1v9ja_ 13.2 25 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 6 d1ny8a_ 12.1 42 Fold:Alpha-lytic protease prodomain-like Superfamily:BolA-like Family:BolA-like 7 d1vc4a_ 10.5 18 Fold:TIM beta/alpha-barrel Superfamily:Ribulose-phoshate binding barrel Family:Tryptophan biosynthesis enzymes 8 c3hcjB_ 9.5 14 PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase; PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form) 9 d1hyoa2 9.3 22 Fold:FAH Superfamily:FAH Family:FAH 10 c2dhmA_ 9.0 36 PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli 11 c3anwA_ 8.7 13 PDB header:replication Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: a protein complex essential initiation of dna replication 12 c1hyoB_ 7.8 22 PDB header:hydrolase Chain: B: PDB Molecule:fumarylacetoacetate hydrolase; PDBTitle: crystal structure of fumarylacetoacetate hydrolase2 complexed with 4-(hydroxymethylphosphinoyl)-3-oxo-butanoic3 acid 13 c1uijA_ 7.6 19 PDB header:sugar binding protein Chain: A: PDB Molecule:beta subunit of beta conglycinin; PDBTitle: crystal structure of soybean beta-conglycinin beta2 homotrimer (i122m/k124w) 14 c3gdwA_ 7.5 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:sigma-54 interaction domain protein; PDBTitle: crystal structure of sigma-54 interaction domain protein from2 enterococcus faecalis 15 d1fx0b2 7.5 18 Fold:Domain of alpha and beta subunits of F1 ATP synthase-like Superfamily:N-terminal domain of alpha and beta subunits of F1 ATP synthase Family:N-terminal domain of alpha and beta subunits of F1 ATP synthase 16 c1g5vA_ 7.1 38 PDB header:translation Chain: A: PDB Molecule:survival motor neuron protein 1; PDBTitle: solution structure of the tudor domain of the human smn2 protein 17 d1m2sa_ 7.0 38 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 18 c3epsB_ 6.1 39 PDB header:transferase, hydrolase Chain: B: PDB Molecule:isocitrate dehydrogenase kinase/phosphatase; PDBTitle: the crystal structure of isocitrate dehydrogenase kinase/phosphatase2 from e. coli 19 c2vxaL_ 6.0 25 PDB header:flavoprotein Chain: L: PDB Molecule:dodecin; PDBTitle: h.halophila dodecin in complex with riboflavin 20 c3lzkC_ 6.0 11 PDB header:hydrolase Chain: C: PDB Molecule:fumarylacetoacetate hydrolase family protein; PDBTitle: the crystal structure of a probably aromatic amino acid2 degradation protein from sinorhizobium meliloti 1021 21 c3o2eA_ not modelled 5.9 14 PDB header:unknown function Chain: A: PDB Molecule:bola-like protein; PDBTitle: crystal structure of a bol-like protein from babesia bovis 22 d2cqaa1 not modelled 5.8 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:TIP49 domain 23 c2kaoA_ not modelled 5.7 18 PDB header:oxidoreductase Chain: A: PDB Molecule:methionine-r-sulfoxide reductase b1; PDBTitle: structure of reduced mouse methionine sulfoxide reductase b12 (sec95cys mutant) 24 d2aw2a1 not modelled 5.7 29 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 25 c1v60A_ not modelled 5.6 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:riken cdna 1810037g04; PDBTitle: solution structure of bola1 protein from mus musculus

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