Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	Q	L	T	A	Q	A	P	V	D	P	I	V	L	G	K	M	G	S	S	Y	G	I	R	G	W	L	R	V	F	S	S	T	E	D	A	E	S	I	F	D	Y	Q	P	W	F	I	Q	K	A	G	Q	W	Q	Q	V	Q	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	S	W	K	H	H	N	Q	D	M	I	I	K	L	K	G	V	D	D	R	D	A	A	N	L	L	T	N	C	E	I	V	V	D	S	S	Q	L	P	Q	L	E	E	G	D	Y	Y	W	K	D	L	M	G	C	Q	V	V	T	T	E
Secondary structure
SS confidence
Disorder																																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	Y	D	L	G	K	V	V	D	M	M	E	T	G	S	N	D	V	L	V	I	K	A	N	L	K	D	A	F	G	I	K	E	R	L	V	P	F	L	D	G	Q	V	I	K	K	V	D	L	T	T	R	S	I	E	V	D	W	D	P
Secondary structure
SS confidence
Disorder																										?	?	?	?	?	?																											?		?	?
Disorder confidence
		.	.
Sequence		G	F
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 3h9n chain A Region: 12 - 182 Aligned: 171 Modelled: 171 Confidence: 100.0% Identity: 66% PDB header:ribosomal protein Chain: A: PDB Molecule:ribosome maturation factor rimm; PDBTitle: crystal structure of the ribosome maturation factor rimm2 (hi0203) from h.influenzae. northeast structural genomics3 consortium target ir66. Phyre2 PDB 2f1l chain A Region: 12 - 182 Aligned: 164 Modelled: 171 Confidence: 100.0% Identity: 38% PDB header:unknown function Chain: A: PDB Molecule:16s rrna processing protein; PDBTitle: crystal structure of a putative 16s ribosomal rna processing protein2 rimm (pa3744) from pseudomonas aeruginosa at 2.46 a resolution Phyre2 PDB 2qgg chain A Region: 8 - 181 Aligned: 172 Modelled: 174 Confidence: 100.0% Identity: 38% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:16s rrna-processing protein rimm; PDBTitle: x-ray structure of the protein q6f7i0 from acinetobacter2 calcoaceticus amms 248. northeast structural genomics3 consortium target asr73. Phyre2 PDB 2dyi chain A Region: 11 - 181 Aligned: 159 Modelled: 171 Confidence: 100.0% Identity: 30% PDB header:ribosome Chain: A: PDB Molecule:probable 16s rrna-processing protein rimm; PDBTitle: crystal structure of 16s ribosomal rna processing protein rimm from2 thermus thermophilus hb8 Phyre2 PDB 2f1l chain A domain 2 Region: 12 - 99 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 39% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: RimM N-terminal domain-like Phyre2 PDB 2dog chain A Region: 11 - 102 Aligned: 85 Modelled: 92 Confidence: 99.9% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:probable 16s rrna-processing protein rimm; PDBTitle: solution structure of the n-terminal domain of rimm from thermus2 thermophilus hb8 Phyre2 PDB 2f1l chain A domain 1 Region: 106 - 182 Aligned: 75 Modelled: 77 Confidence: 99.9% Identity: 39% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: RimM C-terminal domain-like Phyre2 PDB 3htr chain B Region: 99 - 178 Aligned: 76 Modelled: 78 Confidence: 97.9% Identity: 12% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein; PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris Phyre2 PDB 1eys chain H domain 1 Region: 110 - 177 Aligned: 60 Modelled: 68 Confidence: 97.4% Identity: 27% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: Photosynthetic reaction centre, H-chain, cytoplasmic domain Phyre2 PDB 1eys chain H Region: 110 - 177 Aligned: 60 Modelled: 68 Confidence: 97.4% Identity: 27% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 1rzh chain H domain 1 Region: 110 - 158 Aligned: 44 Modelled: 49 Confidence: 96.9% Identity: 27% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: Photosynthetic reaction centre, H-chain, cytoplasmic domain Phyre2 PDB 1k6n chain H Region: 110 - 158 Aligned: 44 Modelled: 49 Confidence: 96.8% Identity: 27% PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides Phyre2 PDB 2i5n chain H domain 1 Region: 110 - 158 Aligned: 45 Modelled: 49 Confidence: 96.8% Identity: 24% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: Photosynthetic reaction centre, H-chain, cytoplasmic domain Phyre2 PDB 2i5n chain H Region: 110 - 158 Aligned: 45 Modelled: 49 Confidence: 96.7% Identity: 24% PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique Phyre2 PDB 1pm3 chain A Region: 108 - 180 Aligned: 63 Modelled: 70 Confidence: 94.4% Identity: 22% Fold: PRC-barrel domain Superfamily: PRC-barrel domain Family: MTH1895 Phyre2 PDB 1sqr chain A Region: 66 - 93 Aligned: 28 Modelled: 28 Confidence: 81.4% Identity: 36% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Ribosomal protein L35ae Phyre2 PDB 4a1d chain H Region: 53 - 93 Aligned: 41 Modelled: 41 Confidence: 80.5% Identity: 10% PDB header:ribosome Chain: H: PDB Molecule:rpl35a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4. Phyre2 PDB 3izc chain J Region: 66 - 91 Aligned: 26 Modelled: 26 Confidence: 72.0% Identity: 23% PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein rpl12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 3iz5 chain J Region: 66 - 93 Aligned: 28 Modelled: 28 Confidence: 70.9% Identity: 11% PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2hvy chain B Region: 112 - 156 Aligned: 45 Modelled: 45 Confidence: 68.6% Identity: 18% PDB header:isomerase/biosynthetic protein/rna Chain: B: PDB Molecule:small nucleolar rnp similar to gar1; PDBTitle: crystal structure of an h/aca box rnp from pyrococcus furiosus Phyre2 1 c3h9nA_ 2 c2f1lA_ 3 c2qggA_ 4 c2dyiA_ 5 d2f1la2 6 c2dogA_ 7 d2f1la1 8 c3htrB_ 9 d1eysh1 10 c1eysH_ 11 d1rzhh1 12 c1k6nH_ 13 d2i5nh1 14 c2i5nH_ 15 d1pm3a_ 16 d1sqra_ 17 c4a1dH_ 18 c3izcj_ 19 c3iz5j_ 20 c2hvyB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

Detailed template information

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

1 c3h9nA_ 100.0 66 PDB header:ribosomal protein Chain: A: PDB Molecule:ribosome maturation factor rimm; PDBTitle: crystal structure of the ribosome maturation factor rimm2 (hi0203) from h.influenzae. northeast structural genomics3 consortium target ir66. 2 c2f1lA_ 100.0 38 PDB header:unknown function Chain: A: PDB Molecule:16s rrna processing protein; PDBTitle: crystal structure of a putative 16s ribosomal rna processing protein2 rimm (pa3744) from pseudomonas aeruginosa at 2.46 a resolution 3 c2qggA_ 100.0 38 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:16s rrna-processing protein rimm; PDBTitle: x-ray structure of the protein q6f7i0 from acinetobacter2 calcoaceticus amms 248. northeast structural genomics3 consortium target asr73. 4 c2dyiA_ 100.0 30 PDB header:ribosome Chain: A: PDB Molecule:probable 16s rrna-processing protein rimm; PDBTitle: crystal structure of 16s ribosomal rna processing protein rimm from2 thermus thermophilus hb8 5 d2f1la2 100.0 39 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:RimM N-terminal domain-like 6 c2dogA_ 99.9 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:probable 16s rrna-processing protein rimm; PDBTitle: solution structure of the n-terminal domain of rimm from thermus2 thermophilus hb8 7 d2f1la1 99.9 39 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:RimM C-terminal domain-like 8 c3htrB_ 97.9 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized prc-barrel domain protein; PDBTitle: crystal structure of prc-barrel domain protein from2 rhodopseudomonas palustris 9 d1eysh1 97.4 27 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:Photosynthetic reaction centre, H-chain, cytoplasmic domain 10 c1eysH_ 97.4 27 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 11 d1rzhh1 96.9 27 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:Photosynthetic reaction centre, H-chain, cytoplasmic domain 12 c1k6nH_ 96.8 27 PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides 13 d2i5nh1 96.8 24 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:Photosynthetic reaction centre, H-chain, cytoplasmic domain 14 c2i5nH_ 96.7 24 PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique 15 d1pm3a_ 94.4 22 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:MTH1895 16 d1sqra_ 81.4 36 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Ribosomal protein L35ae 17 c4a1dH_ 80.5 10 PDB header:ribosome Chain: H: PDB Molecule:rpl35a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4. 18 c3izcj_ 72.0 23 PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein rpl12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 19 c3iz5j_ 70.9 11 PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l12 (l11p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 20 c2hvyB_ 68.6 18 PDB header:isomerase/biosynthetic protein/rna Chain: B: PDB Molecule:small nucleolar rnp similar to gar1; PDBTitle: crystal structure of an h/aca box rnp from pyrococcus furiosus 21 d2ey4c1 not modelled 63.4 18 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Gar1-like SnoRNP 22 c3uaiC_ not modelled 60.5 13 PDB header:isomerase/chaperone Chain: C: PDB Molecule:h/aca ribonucleoprotein complex subunit 1; PDBTitle: structure of the shq1-cbf5-nop10-gar1 complex from saccharomyces2 cerevisiae 23 c2ro0A_ not modelled 53.5 10 PDB header:transferase Chain: A: PDB Molecule:histone acetyltransferase esa1; PDBTitle: solution structure of the knotted tudor domain of the yeast2 histone acetyltransferase, esa1 24 c2kk4A_ not modelled 40.2 34 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein af_2094; PDBTitle: solution nmr structure of protein af2094 from archaeoglobus2 fulgidus. northeast structural genomics consotium (nesg)3 target gt2 25 c2eqnA_ not modelled 22.4 12 PDB header:transcription Chain: A: PDB Molecule:hypothetical protein loc92345; PDBTitle: solution structure of the naf1 domain of hypothetical2 protein bc008207 [homo sapiens] 26 d1wb1a2 not modelled 15.2 36 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 27 d1fxkc_ not modelled 13.8 27 Fold:Long alpha-hairpin Superfamily:Prefoldin Family:Prefoldin 28 d1qhka_ not modelled 11.7 13 Fold:MbtH/L9 domain-like Superfamily:L9 N-domain-like Family:N-terminal domain of RNase HI 29 c3h9wA_ not modelled 11.6 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:diguanylate cyclase with pas/pac sensor; PDBTitle: crystal structure of the n-terminal domain of diguanylate cyclase with2 pas/pac sensor (maqu_2914) from marinobacter aquaeolei, northeast3 structural genomics consortium target mqr66c 30 d2b78a1 not modelled 10.4 21 Fold:PUA domain-like Superfamily:PUA domain-like Family:Hypothetical RNA methyltransferase domain (HRMD) 31 c2rnzA_ not modelled 9.2 11 PDB header:transferase Chain: A: PDB Molecule:histone acetyltransferase esa1; PDBTitle: solution structure of the presumed chromodomain of the2 yeast histone acetyltransferase, esa1 32 c2pdtD_ not modelled 9.2 15 PDB header:circadian clock protein Chain: D: PDB Molecule:vivid pas protein vvd; PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid 33 c2v3mF_ not modelled 9.0 15 PDB header:ribosomal protein Chain: F: PDB Molecule:naf1; PDBTitle: structure of the gar1 domain of naf1 34 c3ml6D_ not modelled 8.8 18 PDB header:protein transport Chain: D: PDB Molecule:chimeric complex between protein dishevlled2 homolog dvl-2 PDBTitle: a complex between dishevlled2 and clathrin adaptor ap-2 35 d1bywa_ not modelled 7.3 10 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Flavin-binding PAS domain 36 c2l4rA_ not modelled 7.2 9 PDB header:transport protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily h member 2; PDBTitle: nmr solution structure of the n-terminal pas domain of herg 37 c3ewkA_ not modelled 7.0 16 PDB header:flavoprotein Chain: A: PDB Molecule:sensor protein; PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos 38 c2gj3A_ not modelled 6.5 15 PDB header:transferase Chain: A: PDB Molecule:nitrogen fixation regulatory protein; PDBTitle: crystal structure of the fad-containing pas domain of the2 protein nifl from azotobacter vinelandii. 39 c3mxqC_ not modelled 6.1 11 PDB header:transferase Chain: C: PDB Molecule:sensor protein; PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae 40 d1n9la_ not modelled 5.8 21 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Flavin-binding PAS domain 41 c3kxrA_ not modelled 5.7 27 PDB header:transport protein Chain: A: PDB Molecule:magnesium transporter, putative; PDBTitle: structure of the cystathionine beta-synthase pair domain of the2 putative mg2+ transporter so5017 from shewanella oneidensis mr-1. 42 d2f5ka1 not modelled 5.6 4 Fold:SH3-like barrel Superfamily:Chromo domain-like Family:Chromo barrel domain 43 c3gbyA_ not modelled 5.6 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ct1051; PDBTitle: crystal structure of a protein with unknown function ct10512 from chlorobium tepidum 44 c2w7aA_ not modelled 5.6 14 PDB header:rna-binding protein Chain: A: PDB Molecule:line-1 orf1p; PDBTitle: structure of the human line-1 orf1p central domain 45 c3luqC_ not modelled 5.4 18 PDB header:transferase Chain: C: PDB Molecule:sensor protein; PDBTitle: the crystal structure of a pas domain from a sensory box2 histidine kinase regulator from geobacter sulfurreducens to3 2.5a 46 c2zdiC_ not modelled 5.4 27 PDB header:chaperone Chain: C: PDB Molecule:prefoldin subunit alpha; PDBTitle: crystal structure of prefoldin from pyrococcus horikoshii2 ot3 47 c3l31B_ not modelled 5.2 13 PDB header:hydrolase Chain: B: PDB Molecule:probable manganase-dependent inorganic PDBTitle: crystal structure of the cbs and drtgg domains of the2 regulatory region of clostridium perfringens3 pyrophosphatase complexed with the inhibitor, amp 48 c3oi8B_ not modelled 5.1 27 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: the crystal structure of functionally unknown conserved protein domain2 from neisseria meningitidis mc58

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