Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	Q	A	D	A	Y	G	G	Y	R	A	L	Y	E	S	G	R	I	T	E	A	A	C	M	A	H	A	R	R	K	I	H	D	V	H	A	R	A	P	T	D	V	T	T	E	A	L	Q	R	I	S	E	L	Y	A	I	E	V	A
Secondary structure
SS confidence
Disorder		?			?	?																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110
Sequence		V	R	G	C	S	A	E	Q	R	L	A	A	R	K	A	R	P	A	P	L	M	Q	S	L	Y	D	W	I	Q	T	Q	M	K	T	L	A	R	H	S	D	T	A	K	A	F	A	Y	L	L	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 1gm5 chain A domain 1 Region: 39 - 87 Aligned: 48 Modelled: 49 Confidence: 39.1% Identity: 13% Fold: Four-helical up-and-down bundle Superfamily: RecG, N-terminal domain Family: RecG, N-terminal domain Phyre2 PDB 3bhp chain A Region: 42 - 89 Aligned: 47 Modelled: 47 Confidence: 30.7% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 Phyre2 PDB 2rf4 chain B Region: 31 - 66 Aligned: 35 Modelled: 36 Confidence: 17.9% Identity: 23% PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 Phyre2 PDB 2f23 chain A domain 2 Region: 94 - 105 Aligned: 12 Modelled: 12 Confidence: 17.9% Identity: 25% Fold: FKBP-like Superfamily: FKBP-like Family: GreA transcript cleavage factor, C-terminal domain Phyre2 PDB 2etn chain A Region: 94 - 105 Aligned: 12 Modelled: 12 Confidence: 17.5% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:anti-cleavage anti-grea transcription factor PDBTitle: crystal structure of thermus aquaticus gfh1 Phyre2 PDB 2etn chain A domain 2 Region: 94 - 105 Aligned: 12 Modelled: 12 Confidence: 16.1% Identity: 25% Fold: FKBP-like Superfamily: FKBP-like Family: GreA transcript cleavage factor, C-terminal domain Phyre2 PDB 1w0b chain A Region: 58 - 99 Aligned: 42 Modelled: 42 Confidence: 14.2% Identity: 12% Fold: Spectrin repeat-like Superfamily: Alpha-hemoglobin stabilizing protein AHSP Family: Alpha-hemoglobin stabilizing protein AHSP Phyre2 PDB 1grj chain A Region: 94 - 105 Aligned: 12 Modelled: 12 Confidence: 12.4% Identity: 17% PDB header:transcription regulation Chain: A: PDB Molecule:grea protein; PDBTitle: grea transcript cleavage factor from escherichia coli Phyre2 PDB 1uny chain A Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 11.9% Identity: 38% PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles Phyre2 PDB 1u9g chain A Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 11.4% Identity: 38% PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) Phyre2 PDB 1u9g chain B Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 11.4% Identity: 38% PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) Phyre2 PDB 1unv chain A Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 11.4% Identity: 38% PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles Phyre2 PDB 2p4v chain A Region: 94 - 105 Aligned: 12 Modelled: 12 Confidence: 11.2% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor greb; PDBTitle: crystal structure of the transcript cleavage factor, greb2 at 2.6a resolution Phyre2 PDB 1unv chain B Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 11.2% Identity: 38% PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles Phyre2 PDB 1n1b chain A domain 1 Region: 79 - 109 Aligned: 31 Modelled: 31 Confidence: 10.7% Identity: 3% Fold: alpha/alpha toroid Superfamily: Terpenoid cyclases/Protein prenyltransferases Family: Terpenoid cyclase N-terminal domain Phyre2 PDB 1grj chain A domain 2 Region: 92 - 105 Aligned: 14 Modelled: 14 Confidence: 10.5% Identity: 14% Fold: FKBP-like Superfamily: FKBP-like Family: GreA transcript cleavage factor, C-terminal domain Phyre2 PDB 1u7n chain A Region: 1 - 9 Aligned: 9 Modelled: 9 Confidence: 10.3% Identity: 22% Fold: Isocitrate/Isopropylmalate dehydrogenase-like Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like Family: PlsX-like Phyre2 PDB 1x4q chain A Region: 77 - 97 Aligned: 21 Modelled: 21 Confidence: 10.3% Identity: 19% PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) Phyre2 PDB 1unz chain A Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 10.1% Identity: 38% PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles Phyre2 PDB 1unz chain B Region: 49 - 61 Aligned: 13 Modelled: 13 Confidence: 10.1% Identity: 38% PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles Phyre2 1 d1gm5a1 2 c3bhpA_ 3 c2rf4B_ 4 d2f23a2 5 c2etnA_ 6 d2etna2 7 d1w0ba_ 8 c1grjA_ 9 c1unyA_ 10 c1u9gA_ 11 c1u9gB_ 12 c1unvA_ 13 c2p4vA_ 14 c1unvB_ 15 d1n1ba1 16 d1grja2 17 d1u7na_ 18 c1x4qA_ 19 c1unzA_ 20 c1unzB_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 d1gm5a1 39.1 13 Fold:Four-helical up-and-down bundle Superfamily:RecG, N-terminal domain Family:RecG, N-terminal domain 2 c3bhpA_ 30.7 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 3 c2rf4B_ 17.9 23 PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 4 d2f23a2 17.9 25 Fold:FKBP-like Superfamily:FKBP-like Family:GreA transcript cleavage factor, C-terminal domain 5 c2etnA_ 17.5 25 PDB header:transcription Chain: A: PDB Molecule:anti-cleavage anti-grea transcription factor PDBTitle: crystal structure of thermus aquaticus gfh1 6 d2etna2 16.1 25 Fold:FKBP-like Superfamily:FKBP-like Family:GreA transcript cleavage factor, C-terminal domain 7 d1w0ba_ 14.2 12 Fold:Spectrin repeat-like Superfamily:Alpha-hemoglobin stabilizing protein AHSP Family:Alpha-hemoglobin stabilizing protein AHSP 8 c1grjA_ 12.4 17 PDB header:transcription regulation Chain: A: PDB Molecule:grea protein; PDBTitle: grea transcript cleavage factor from escherichia coli 9 c1unyA_ 11.9 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 10 c1u9gA_ 11.4 38 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) 11 c1u9gB_ 11.4 38 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: heterocyclic peptide backbone modification in gcn4-pli based coiled2 coils: replacement of k(8)l(9) 12 c1unvA_ 11.4 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 13 c2p4vA_ 11.2 25 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor greb; PDBTitle: crystal structure of the transcript cleavage factor, greb2 at 2.6a resolution 14 c1unvB_ 11.2 38 PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 15 d1n1ba1 10.7 3 Fold:alpha/alpha toroid Superfamily:Terpenoid cyclases/Protein prenyltransferases Family:Terpenoid cyclase N-terminal domain 16 d1grja2 10.5 14 Fold:FKBP-like Superfamily:FKBP-like Family:GreA transcript cleavage factor, C-terminal domain 17 d1u7na_ 10.3 22 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:PlsX-like 18 c1x4qA_ 10.3 19 PDB header:rna binding protein Chain: A: PDB Molecule:u4/u6 small nuclear ribonucleoprotein prp3; PDBTitle: solution structure of pwi domain in u4/u6 small nuclear2 ribonucleoprotein prp3(hprp3) 19 c1unzA_ 10.1 38 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 20 c1unzB_ 10.1 38 PDB header:four helix bundle Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 21 d1am9a_ not modelled 9.9 16 Fold:HLH-like Superfamily:HLH, helix-loop-helix DNA-binding domain Family:HLH, helix-loop-helix DNA-binding domain 22 d2ovra1 not modelled 9.9 19 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 23 c1n20A_ not modelled 9.4 3 PDB header:isomerase Chain: A: PDB Molecule:(+)-bornyl diphosphate synthase; PDBTitle: (+)-bornyl diphosphate synthase: complex with mg and 3-aza-2 2,3-dihydrogeranyl diphosphate 24 c2jvdA_ not modelled 7.9 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 25 d1ee8a1 not modelled 7.3 15 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 26 c2g9pA_ not modelled 7.3 38 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 27 c1u2uB_ not modelled 7.1 50 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: nmr solution structure of a designed heterodimeric leucine2 zipper 28 c3if8A_ not modelled 6.7 7 PDB header:cell cycle Chain: A: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex 29 d2cg4a1 not modelled 6.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 30 d1iega_ not modelled 5.7 19 Fold:Herpes virus serine proteinase, assemblin Superfamily:Herpes virus serine proteinase, assemblin Family:Herpes virus serine proteinase, assemblin 31 c1u7mB_ not modelled 5.6 24 PDB header:de novo protein Chain: B: PDB Molecule:four-helix bundle model; PDBTitle: solution structure of a diiron protein model: due ferri(ii)2 turn mutant 32 d2v0ea1 not modelled 5.4 25 Fold:GYF/BRK domain-like Superfamily:BRK domain-like Family:BRK domain-like 33 c1r7gA_ not modelled 5.4 8 PDB header:membrane protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: nmr structure of the membrane anchor domain (1-31) of the2 nonstructural protein 5a (ns5a) of hepatitis c virus3 (minimized average structure, sample in 100mm dpc)

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