Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	M	I	A	L	D	G	A	Q	G	E	G	G	G	Q	I	L	R	S	A	L	S	L	S	M	I	T	G	Q	P	F	T	I	T	S	I	R	A	G	R	A	K	P	G	L	L	R	Q	H	L	T	A	V	K	A	A	T	E
Secondary structure
SS confidence
Disorder		?	?	?	?		?	?																							?	?							?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	C	G	A	T	V	E	G	A	E	L	G	S	Q	R	L	L	F	R	P	G	T	V	R	G	G	D	Y	R	F	A	I	G	S	A	G	S	C	T	L	V	L	Q	T	V	L	P	A	L	W	F	A	D	G	P	S	R	V	E	V
Secondary structure
SS confidence
Disorder												?																																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	G	G	T	D	N	P	S	A	P	P	A	D	F	I	R	R	V	L	E	P	L	L	A	K	I	G	I	H	Q	Q	T	T	L	L	R	H	G	F	Y	P	A	G	G	G	V	V	A	T	E	V	S	P	V	A	S	F	N	T	L
Secondary structure
SS confidence
Disorder																																																					?		?	?		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Q	L	G	E	R	G	N	I	V	Q	M	R	G	E	V	L	L	A	G	V	P	R	H	V	A	E	R	E	I	A	T	L	A	G	S	F	S	L	H	E	Q	N	I	H	N	L	P	R	D	Q	G	P	G	N	T	V	S	L	E	V
Secondary structure
SS confidence
Disorder		?		?	?		?															?																									?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	S	E	N	I	T	E	R	F	F	V	V	G	E	K	R	V	S	A	E	V	V	A	A	Q	L	V	K	E	V	K	R	Y	L	A	S	T	A	A	V	G	E	Y	L	A	D	Q	L	V	L	P	M	A	L	A	G	A	G	E	F
Secondary structure
SS confidence
Disorder																?	?		?																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.
Sequence		T	V	A	H	P	S	C	H	L	L	T	N	I	A	V	V	E	R	F	L	P	V	R	F	S	L	I	E	T	D	G	V	T	R	V	S	I	E
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 1qmi chain C Region: 5 - 338 Aligned: 334 Modelled: 334 Confidence: 100.0% Identity: 99% PDB header:rna 3'-terminal phosphate cyclase Chain: C: PDB Molecule:rna 3'-terminal phosphate cyclase; PDBTitle: crystal structure of rna 3'-terminal phosphate cyclase, an2 ubiquitous enzyme with unusual topology Phyre2 PDB 3pqv chain D Region: 15 - 338 Aligned: 324 Modelled: 324 Confidence: 100.0% Identity: 18% PDB header:unknown function Chain: D: PDB Molecule:rcl1 protein; PDBTitle: cyclase homolog Phyre2 PDB 1qmh chain A domain 2 Region: 4 - 337 Aligned: 239 Modelled: 239 Confidence: 100.0% Identity: 100% Fold: IF3-like Superfamily: EPT/RTPC-like Family: RNA 3'-terminal phosphate cyclase, RPTC Phyre2 PDB 1qmh chain A domain 1 Region: 184 - 278 Aligned: 95 Modelled: 95 Confidence: 99.9% Identity: 100% Fold: Thioredoxin fold Superfamily: RNA 3'-terminal phosphate cyclase, RPTC, insert domain Family: RNA 3'-terminal phosphate cyclase, RPTC, insert domain Phyre2 PDB 1p88 chain A Region: 16 - 153 Aligned: 123 Modelled: 136 Confidence: 95.7% Identity: 15% Fold: IF3-like Superfamily: EPT/RTPC-like Family: Enolpyruvate transferase, EPT Phyre2 PDB 2o0z chain A Region: 16 - 183 Aligned: 139 Modelled: 162 Confidence: 94.7% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: mycobacterium tuberculosis epsp synthase in complex with2 product (eps) Phyre2 PDB 1uae chain A Region: 23 - 168 Aligned: 124 Modelled: 146 Confidence: 94.5% Identity: 17% Fold: IF3-like Superfamily: EPT/RTPC-like Family: Enolpyruvate transferase, EPT Phyre2 PDB 1g6s chain A Region: 16 - 169 Aligned: 139 Modelled: 154 Confidence: 93.0% Identity: 21% Fold: IF3-like Superfamily: EPT/RTPC-like Family: Enolpyruvate transferase, EPT Phyre2 PDB 2pqd chain A Region: 16 - 183 Aligned: 139 Modelled: 164 Confidence: 92.0% Identity: 17% PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: a100g cp4 epsps liganded with (r)-difluoromethyl tetrahedral reaction2 intermediate analog Phyre2 PDB 3roi chain A Region: 16 - 183 Aligned: 127 Modelled: 152 Confidence: 91.8% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: 2.20 angstrom resolution structure of 3-phosphoshikimate 1-2 carboxyvinyltransferase (aroa) from coxiella burnetii Phyre2 PDB 3rmt chain B Region: 16 - 183 Aligned: 135 Modelled: 162 Confidence: 91.7% Identity: 21% PDB header:transferase Chain: B: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase 1; PDBTitle: crystal structure of putative 5-enolpyruvoylshikimate-3-phosphate2 synthase from bacillus halodurans c-125 Phyre2 PDB 2yvw chain A Region: 23 - 168 Aligned: 124 Modelled: 146 Confidence: 87.1% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:udp-n-acetylglucosamine 1-carboxyvinyltransferase; PDBTitle: crystal structure of udp-n-acetylglucosamine 1-carboxyvinyltransferase2 from aquifex aeolicus vf5 Phyre2 PDB 1ejd chain A Region: 16 - 163 Aligned: 123 Modelled: 137 Confidence: 81.4% Identity: 17% Fold: IF3-like Superfamily: EPT/RTPC-like Family: Enolpyruvate transferase, EPT Phyre2 PDB 3r38 chain A Region: 2 - 153 Aligned: 127 Modelled: 152 Confidence: 73.0% Identity: 11% PDB header:transferase Chain: A: PDB Molecule:udp-n-acetylglucosamine 1-carboxyvinyltransferase 1; PDBTitle: 2.23 angstrom resolution crystal structure of udp-n-acetylglucosamine2 1-carboxyvinyltransferase (mura) from listeria monocytogenes egd-e Phyre2 PDB 1rf6 chain A Region: 5 - 183 Aligned: 145 Modelled: 179 Confidence: 69.6% Identity: 13% Fold: IF3-like Superfamily: EPT/RTPC-like Family: Enolpyruvate transferase, EPT Phyre2 PDB 1ul7 chain A Region: 112 - 213 Aligned: 94 Modelled: 102 Confidence: 46.3% Identity: 14% Fold: TBP-like Superfamily: KA1-like Family: Kinase associated domain 1, KA1 Phyre2 PDB 3cvo chain A Region: 3 - 29 Aligned: 19 Modelled: 27 Confidence: 34.5% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution Phyre2 PDB 2uwj chain E Region: 264 - 288 Aligned: 25 Modelled: 25 Confidence: 34.3% Identity: 24% PDB header:chaperone Chain: E: PDB Molecule:type iii export protein psce; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation Phyre2 PDB 1hsk chain A Region: 132 - 162 Aligned: 31 Modelled: 31 Confidence: 28.2% Identity: 23% PDB header:oxidoreductase Chain: A: PDB Molecule:udp-n-acetylenolpyruvoylglucosamine reductase; PDBTitle: crystal structure of s. aureus murb Phyre2 PDB 2e1b chain A domain 1 Region: 159 - 166 Aligned: 8 Modelled: 8 Confidence: 26.7% Identity: 75% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: AlaX-M N-terminal domain-like Phyre2 1 c1qmiC_ 2 c3pqvD_ 3 d1qmha2 4 d1qmha1 5 d1p88a_ 6 c2o0zA_ 7 d1uaea_ 8 d1g6sa_ 9 c2pqdA_ 10 c3roiA_ 11 c3rmtB_ 12 c2yvwA_ 13 d1ejda_ 14 c3r38A_ 15 d1rf6a_ 16 d1ul7a_ 17 c3cvoA_ 18 c2uwjE_ 19 c1hskA_ 20 d2e1ba1 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 49

Detailed template information

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

1 c1qmiC_ 100.0 99 PDB header:rna 3'-terminal phosphate cyclase Chain: C: PDB Molecule:rna 3'-terminal phosphate cyclase; PDBTitle: crystal structure of rna 3'-terminal phosphate cyclase, an2 ubiquitous enzyme with unusual topology 2 c3pqvD_ 100.0 18 PDB header:unknown function Chain: D: PDB Molecule:rcl1 protein; PDBTitle: cyclase homolog 3 d1qmha2 100.0 100 Fold:IF3-like Superfamily:EPT/RTPC-like Family:RNA 3'-terminal phosphate cyclase, RPTC 4 d1qmha1 99.9 100 Fold:Thioredoxin fold Superfamily:RNA 3'-terminal phosphate cyclase, RPTC, insert domain Family:RNA 3'-terminal phosphate cyclase, RPTC, insert domain 5 d1p88a_ 95.7 15 Fold:IF3-like Superfamily:EPT/RTPC-like Family:Enolpyruvate transferase, EPT 6 c2o0zA_ 94.7 20 PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: mycobacterium tuberculosis epsp synthase in complex with2 product (eps) 7 d1uaea_ 94.5 17 Fold:IF3-like Superfamily:EPT/RTPC-like Family:Enolpyruvate transferase, EPT 8 d1g6sa_ 93.0 21 Fold:IF3-like Superfamily:EPT/RTPC-like Family:Enolpyruvate transferase, EPT 9 c2pqdA_ 92.0 17 PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: a100g cp4 epsps liganded with (r)-difluoromethyl tetrahedral reaction2 intermediate analog 10 c3roiA_ 91.8 21 PDB header:transferase Chain: A: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase; PDBTitle: 2.20 angstrom resolution structure of 3-phosphoshikimate 1-2 carboxyvinyltransferase (aroa) from coxiella burnetii 11 c3rmtB_ 91.7 21 PDB header:transferase Chain: B: PDB Molecule:3-phosphoshikimate 1-carboxyvinyltransferase 1; PDBTitle: crystal structure of putative 5-enolpyruvoylshikimate-3-phosphate2 synthase from bacillus halodurans c-125 12 c2yvwA_ 87.1 21 PDB header:transferase Chain: A: PDB Molecule:udp-n-acetylglucosamine 1-carboxyvinyltransferase; PDBTitle: crystal structure of udp-n-acetylglucosamine 1-carboxyvinyltransferase2 from aquifex aeolicus vf5 13 d1ejda_ 81.4 17 Fold:IF3-like Superfamily:EPT/RTPC-like Family:Enolpyruvate transferase, EPT 14 c3r38A_ 73.0 11 PDB header:transferase Chain: A: PDB Molecule:udp-n-acetylglucosamine 1-carboxyvinyltransferase 1; PDBTitle: 2.23 angstrom resolution crystal structure of udp-n-acetylglucosamine2 1-carboxyvinyltransferase (mura) from listeria monocytogenes egd-e 15 d1rf6a_ 69.6 13 Fold:IF3-like Superfamily:EPT/RTPC-like Family:Enolpyruvate transferase, EPT 16 d1ul7a_ 46.3 14 Fold:TBP-like Superfamily:KA1-like Family:Kinase associated domain 1, KA1 17 c3cvoA_ 34.5 21 PDB header:transferase Chain: A: PDB Molecule:methyltransferase-like protein of unknown function; PDBTitle: crystal structure of a methyltransferase-like protein (spo2022) from2 silicibacter pomeroyi dss-3 at 1.80 a resolution 18 c2uwjE_ 34.3 24 PDB header:chaperone Chain: E: PDB Molecule:type iii export protein psce; PDBTitle: structure of the heterotrimeric complex which regulates2 type iii secretion needle formation 19 c1hskA_ 28.2 23 PDB header:oxidoreductase Chain: A: PDB Molecule:udp-n-acetylenolpyruvoylglucosamine reductase; PDBTitle: crystal structure of s. aureus murb 20 d2e1ba1 26.7 75 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:AlaX-M N-terminal domain-like 21 d1hska2 not modelled 23.6 23 Fold:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain Superfamily:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain Family:Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain 22 d1f46a_ not modelled 22.2 12 Fold:TBP-like Superfamily:Cell-division protein ZipA, C-terminal domain Family:Cell-division protein ZipA, C-terminal domain 23 c2e1bA_ not modelled 16.0 75 PDB header:ligase, hydrolase Chain: A: PDB Molecule:216aa long hypothetical alanyl-trna synthetase; PDBTitle: crystal structure of the alax-m trans-editing enzyme from2 pyrococcus horikoshii 24 c2q1kA_ not modelled 13.2 29 PDB header:chaperone Chain: A: PDB Molecule:asce; PDBTitle: cyrstal structure of asce from aeromonas hydrophilla 25 d2q07a3 not modelled 11.4 38 Fold:Cystatin-like Superfamily:Pre-PUA domain Family:AF0587 pre C-terminal domain-like 26 d1h72c1 not modelled 10.9 16 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:GHMP Kinase, N-terminal domain 27 d2od4a1 not modelled 10.9 21 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Marine metagenome family DABB2 28 d1mp9a1 not modelled 10.7 23 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 29 d1hh2p3 not modelled 9.9 5 Fold:Alpha-lytic protease prodomain-like Superfamily:Prokaryotic type KH domain (KH-domain type II) Family:Prokaryotic type KH domain (KH-domain type II) 30 d2zdra1 not modelled 9.8 12 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 31 d1nh2a1 not modelled 9.4 28 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 32 c2xi5D_ not modelled 9.4 13 PDB header:transferase Chain: D: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein 33 c2xi7B_ not modelled 9.3 13 PDB header:transferase Chain: B: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein 34 d2a9sa1 not modelled 9.3 5 Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like 35 d1ul1x1 not modelled 9.1 12 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 36 d1nwpa_ not modelled 9.0 21 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 37 d1cuoa_ not modelled 8.3 13 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 38 c2ch4A_ not modelled 7.8 18 PDB header:transferase/chemotaxis Chain: A: PDB Molecule:chemotaxis protein chea; PDBTitle: complex between bacterial chemotaxis histidine kinase chea2 domains p4 and p5 and receptor-adaptor protein chew 39 d1cf2o2 not modelled 7.4 36 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:GAPDH-like 40 d1rkra_ not modelled 7.3 21 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 41 d1qnaa1 not modelled 7.3 20 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 42 c1fwlD_ not modelled 7.0 16 PDB header:transferase Chain: D: PDB Molecule:homoserine kinase; PDBTitle: crystal structure of homoserine kinase 43 d1aisa1 not modelled 6.7 26 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 44 c1gmuB_ not modelled 6.6 31 PDB header:metallochaperone Chain: B: PDB Molecule:uree; PDBTitle: structure of uree 45 d1cc3a_ not modelled 6.4 17 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 46 d1mp9a2 not modelled 5.8 14 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 47 c2rrnA_ not modelled 5.8 14 PDB header:protein transport Chain: A: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: solution structure of secdf periplasmic domain p4 48 d1cdwa1 not modelled 5.4 18 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 49 d1gmua2 not modelled 5.3 30 Fold:Ferredoxin-like Superfamily:Urease metallochaperone UreE, C-terminal domain Family:Urease metallochaperone UreE, C-terminal 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