Secondary structure and disorder prediction

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Sequence		M	N	F	I	R	Q	G	L	G	I	A	L	Q	P	E	L	T	L	K	S	I	A	G	E	L	C	S	V	P	L	E	P	T	F	Y	R	Q	I	S	L	L	A	K	E	K	P	V	E	G	S	P	L	F	L	L	Q	M	C	M	E
Secondary structure
SS confidence
Disorder		?	?	?		?	?								?	?																											?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		Q	L	V	A	I	G	K	I
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 2h9q chain C Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 53.2% Identity: 19% PDB header:transcription Chain: C: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: crystal structure of the effector binding domain of a catm2 variant (r156h) Phyre2 PDB 3fd3 chain A Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 52.6% Identity: 23% PDB header:transcription regulator Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein; PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58. Phyre2 PDB 2hxr chain A Region: 1 - 62 Aligned: 61 Modelled: 62 Confidence: 45.6% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator cynr; PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism Phyre2 PDB 3jv9 chain B Region: 1 - 41 Aligned: 41 Modelled: 41 Confidence: 39.1% Identity: 22% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis Phyre2 PDB 2f7c chain A Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 39.0% Identity: 19% PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate Phyre2 PDB 2h9b chain B Region: 2 - 67 Aligned: 66 Modelled: 66 Confidence: 33.2% Identity: 21% PDB header:transcription Chain: B: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of the effector binding domain of a benm variant2 (benm r156h/t157s) Phyre2 PDB 1koh chain A domain 2 Region: 9 - 36 Aligned: 27 Modelled: 28 Confidence: 30.5% Identity: 26% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Non-canonical RBD domain Phyre2 PDB 1ixc chain A domain 2 Region: 2 - 67 Aligned: 62 Modelled: 66 Confidence: 28.6% Identity: 13% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 2f78 chain A Region: 1 - 66 Aligned: 66 Modelled: 66 Confidence: 20.2% Identity: 23% PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate Phyre2 PDB 1al3 chain A Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 18.7% Identity: 13% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 1al3 chain A Region: 2 - 41 Aligned: 40 Modelled: 40 Confidence: 18.7% Identity: 13% PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes Phyre2 PDB 1iz1 chain B Region: 1 - 32 Aligned: 32 Modelled: 32 Confidence: 18.5% Identity: 6% PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator Phyre2 PDB 3onm chain B Region: 1 - 17 Aligned: 17 Modelled: 17 Confidence: 18.4% Identity: 29% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator lrha; PDBTitle: effector binding domain of lysr-type transcription factor rovm from y.2 pseudotuberculosis Phyre2 PDB 3t1b chain B Region: 1 - 31 Aligned: 31 Modelled: 31 Confidence: 16.9% Identity: 32% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant Phyre2 PDB 1ft8 chain A domain 2 Region: 9 - 36 Aligned: 27 Modelled: 28 Confidence: 16.4% Identity: 30% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Non-canonical RBD domain Phyre2 PDB 3fzj chain C Region: 1 - 31 Aligned: 31 Modelled: 31 Confidence: 12.4% Identity: 19% PDB header:transcription regulator Chain: C: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: tsar low resolution crystal structure, tetragonal form Phyre2 PDB 3kk4 chain B Region: 20 - 45 Aligned: 26 Modelled: 26 Confidence: 11.8% Identity: 27% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i Phyre2 PDB 3kos chain A Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 10.5% Identity: 9% PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator ampr; PDBTitle: structure of the ampr effector binding domain from citrobacter2 freundii Phyre2 PDB 2esn chain A domain 2 Region: 2 - 31 Aligned: 30 Modelled: 30 Confidence: 10.1% Identity: 13% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 3a5d chain B Region: 35 - 68 Aligned: 34 Modelled: 34 Confidence: 9.4% Identity: 32% PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase alpha chain; PDBTitle: inter-subunit interaction and quaternary rearrangement2 defined by the central stalk of prokaryotic v1-atpase Phyre2 1 c2h9qC_ 2 c3fd3A_ 3 c2hxrA_ 4 c3jv9B_ 5 c2f7cA_ 6 c2h9bB_ 7 d1koha2 8 d1ixca2 9 c2f78A_ 10 d1al3a_ 11 c1al3A_ 12 c1iz1B_ 13 c3onmB_ 14 c3t1bB_ 15 d1ft8a2 16 c3fzjC_ 17 c3kk4B_ 18 c3kosA_ 19 d2esna2 20 c3a5dB_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 c2h9qC_ 53.2 19 PDB header:transcription Chain: C: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: crystal structure of the effector binding domain of a catm2 variant (r156h) 2 c3fd3A_ 52.6 23 PDB header:transcription regulator Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein; PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58. 3 c2hxrA_ 45.6 20 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator cynr; PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism 4 c3jv9B_ 39.1 22 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis 5 c2f7cA_ 39.0 19 PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate 6 c2h9bB_ 33.2 21 PDB header:transcription Chain: B: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of the effector binding domain of a benm variant2 (benm r156h/t157s) 7 d1koha2 30.5 26 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD domain 8 d1ixca2 28.6 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 9 c2f78A_ 20.2 23 PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate 10 d1al3a_ 18.7 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 11 c1al3A_ 18.7 13 PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes 12 c1iz1B_ 18.5 6 PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator 13 c3onmB_ 18.4 29 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator lrha; PDBTitle: effector binding domain of lysr-type transcription factor rovm from y.2 pseudotuberculosis 14 c3t1bB_ 16.9 32 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant 15 d1ft8a2 16.4 30 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Non-canonical RBD domain 16 c3fzjC_ 12.4 19 PDB header:transcription regulator Chain: C: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: tsar low resolution crystal structure, tetragonal form 17 c3kk4B_ 11.8 27 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i 18 c3kosA_ 10.5 9 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator ampr; PDBTitle: structure of the ampr effector binding domain from citrobacter2 freundii 19 d2esna2 10.1 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 20 c3a5dB_ 9.4 32 PDB header:hydrolase Chain: B: PDB Molecule:v-type atp synthase alpha chain; PDBTitle: inter-subunit interaction and quaternary rearrangement2 defined by the central stalk of prokaryotic v1-atpase 21 c3ispA_ not modelled 8.5 28 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator PDBTitle: crystal structure of argp from mycobacterium tuberculosis 22 d1dwka2 not modelled 8.0 56 Fold:Cyanase C-terminal domain Superfamily:Cyanase C-terminal domain Family:Cyanase C-terminal domain 23 d2b0ja1 not modelled 6.4 35 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:HMD dimerization domain-like 24 c2esnC_ not modelled 6.1 13 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa 25 c2iv1J_ not modelled 5.9 40 PDB header:lyase Chain: J: PDB Molecule:cyanate hydratase; PDBTitle: site directed mutagenesis of key residues involved in the2 catalytic mechanism of cyanase 26 c1w0jB_ not modelled 5.8 32 PDB header:hydrolase Chain: B: PDB Molecule:atp synthase alpha chain heart isoform, PDBTitle: beryllium fluoride inhibited bovine f1-atpase 27 c3ho7A_ not modelled 5.7 23 PDB header:transcription Chain: A: PDB Molecule:oxyr; PDBTitle: crystal structure of oxyr from porphyromonas gingivalis 28 d1f6fa_ not modelled 5.6 33 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Long-chain cytokines

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