Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	R	V	K	R	G	V	I	A	R	A	R	H	K	K	I	L	K	Q	A	K	G	Y	Y	G	A	R	S	R	V	Y	R	V	A	F	Q	A	V	I	K	A	G	Q	Y	A	Y	R	D	R	R	Q	R	K	R	Q	F	R	Q	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.
Sequence		W	I	A	R	I	N	A	A	A	R	Q	N	G	I	S	Y	S	K	F	I	N	G	L	K	K	A	S	V	E	I	D	R	K	I	L	A	D	I	A	V	F	D	K	V	A	F	T	A	L	V	E	K	A	K	A	A	L	A
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 2zjr chain N domain 1 Region: 2 - 117 Aligned: 116 Modelled: 116 Confidence: 100.0% Identity: 55% Fold: PABP domain-like Superfamily: Ribosomal protein L20 Family: Ribosomal protein L20 Phyre2 PDB 2j01 chain U domain 1 Region: 2 - 117 Aligned: 116 Modelled: 116 Confidence: 100.0% Identity: 59% Fold: PABP domain-like Superfamily: Ribosomal protein L20 Family: Ribosomal protein L20 Phyre2 PDB 3bbo chain S Region: 1 - 116 Aligned: 116 Modelled: 116 Confidence: 100.0% Identity: 47% PDB header:ribosome Chain: S: PDB Molecule:ribosomal protein l20; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2ghj chain D Region: 20 - 118 Aligned: 99 Modelled: 99 Confidence: 100.0% Identity: 64% PDB header:structural protein Chain: D: PDB Molecule:50s ribosomal protein l20; PDBTitle: crystal structure of folded and partially unfolded forms of2 aquifex aeolicus ribosomal protein l20 Phyre2 PDB 2ftc chain L Region: 1 - 116 Aligned: 115 Modelled: 116 Confidence: 100.0% Identity: 35% PDB header:ribosome Chain: L: PDB Molecule:mrpl20 protein; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome Phyre2 PDB 2gyc chain O domain 1 Region: 3 - 117 Aligned: 115 Modelled: 115 Confidence: 100.0% Identity: 100% Fold: PABP domain-like Superfamily: Ribosomal protein L20 Family: Ribosomal protein L20 Phyre2 PDB 1gyz chain A Region: 61 - 118 Aligned: 58 Modelled: 58 Confidence: 99.9% Identity: 66% Fold: PABP domain-like Superfamily: Ribosomal protein L20 Family: Ribosomal protein L20 Phyre2 PDB 2cob chain A domain 1 Region: 65 - 92 Aligned: 28 Modelled: 28 Confidence: 48.8% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Psq domain Phyre2 PDB 2k53 chain A Region: 65 - 86 Aligned: 22 Modelled: 22 Confidence: 38.6% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 Phyre2 PDB 3deu chain A domain 1 Region: 55 - 116 Aligned: 62 Modelled: 62 Confidence: 31.5% Identity: 8% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MarR-like transcriptional regulators Phyre2 PDB 1fip chain A Region: 65 - 89 Aligned: 25 Modelled: 25 Confidence: 29.3% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 65 - 90 Aligned: 26 Modelled: 26 Confidence: 26.6% Identity: 19% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 PDB 3fm5 chain D Region: 55 - 111 Aligned: 57 Modelled: 57 Confidence: 24.4% Identity: 12% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator; PDBTitle: x-ray crystal structure of transcriptional regulator (marr family)2 from rhodococcus sp. rha1 Phyre2 PDB 2p9x chain B Region: 97 - 112 Aligned: 16 Modelled: 16 Confidence: 20.6% Identity: 31% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 Phyre2 PDB 1ku9 chain A Region: 56 - 116 Aligned: 61 Modelled: 58 Confidence: 20.5% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DNA-binding protein Mj223 Phyre2 PDB 3deu chain B Region: 55 - 116 Aligned: 62 Modelled: 62 Confidence: 18.6% Identity: 8% PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator slya; PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands Phyre2 PDB 2k5e chain A Region: 65 - 85 Aligned: 21 Modelled: 21 Confidence: 18.6% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195 Phyre2 PDB 1eto chain B Region: 65 - 88 Aligned: 24 Modelled: 24 Confidence: 17.3% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 65 - 89 Aligned: 25 Modelled: 25 Confidence: 17.1% Identity: 28% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2cg4 chain A domain 1 Region: 89 - 113 Aligned: 25 Modelled: 25 Confidence: 16.2% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 1 d2zjrn1 2 d2j01u1 3 c3bboS_ 4 c2ghjD_ 5 c2ftcL_ 6 d2gyco1 7 d1gyza_ 8 d2coba1 9 c2k53A_ 10 d3deua1 11 d1fipa_ 12 c3e7lD_ 13 c3fm5D_ 14 c2p9xB_ 15 d1ku9a_ 16 c3deuB_ 17 c2k5eA_ 18 d1etob_ 19 d1ntca_ 20 d2cg4a1 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

Detailed template information

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

1 d2zjrn1 100.0 55 Fold:PABP domain-like Superfamily:Ribosomal protein L20 Family:Ribosomal protein L20 2 d2j01u1 100.0 59 Fold:PABP domain-like Superfamily:Ribosomal protein L20 Family:Ribosomal protein L20 3 c3bboS_ 100.0 47 PDB header:ribosome Chain: S: PDB Molecule:ribosomal protein l20; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 4 c2ghjD_ 100.0 64 PDB header:structural protein Chain: D: PDB Molecule:50s ribosomal protein l20; PDBTitle: crystal structure of folded and partially unfolded forms of2 aquifex aeolicus ribosomal protein l20 5 c2ftcL_ 100.0 35 PDB header:ribosome Chain: L: PDB Molecule:mrpl20 protein; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome 6 d2gyco1 100.0 100 Fold:PABP domain-like Superfamily:Ribosomal protein L20 Family:Ribosomal protein L20 7 d1gyza_ 99.9 66 Fold:PABP domain-like Superfamily:Ribosomal protein L20 Family:Ribosomal protein L20 8 d2coba1 48.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 9 c2k53A_ 38.6 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:a3dk08 protein; PDBTitle: nmr solution structure of a3dk08 protein from clostridium2 thermocellum: northeast structural genomics consortium3 target cmr9 10 d3deua1 31.5 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 11 d1fipa_ 29.3 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 c3e7lD_ 26.6 19 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 13 c3fm5D_ 24.4 12 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator; PDBTitle: x-ray crystal structure of transcriptional regulator (marr family)2 from rhodococcus sp. rha1 14 c2p9xB_ 20.6 31 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0832; PDBTitle: crystal structure of ph0832 from pyrococcus horikoshii ot3 15 d1ku9a_ 20.5 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DNA-binding protein Mj223 16 c3deuB_ 18.6 8 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator slya; PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands 17 c2k5eA_ 18.6 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195 18 d1etob_ 17.3 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 d1ntca_ 17.1 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 20 d2cg4a1 16.2 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 21 d2cyya1 not modelled 15.1 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 22 d1etxa_ not modelled 14.3 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 23 c2ijlB_ not modelled 14.1 29 PDB header:transcription Chain: B: PDB Molecule:molybdenum-binding transcriptional repressor; PDBTitle: the structure of a putative mode from agrobacterium tumefaciens. 24 d2cfxa1 not modelled 12.9 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 25 c3g3rA_ not modelled 12.5 23 PDB header:biosynthetic protein Chain: A: PDB Molecule:vacuolar transporter chaperone 4; PDBTitle: crystal structure of a eukaryotic polyphosphate polymerase2 in complex with appnhp-mn2+ 26 d1y0ua_ not modelled 11.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 27 c2l4aA_ not modelled 10.9 26 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 28 c3jw4C_ not modelled 10.2 14 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator, marr/emrr family; PDBTitle: the structure of a putative marr family transcriptional regulator from2 clostridium acetobutylicum 29 c3g3oA_ not modelled 9.8 20 PDB header:biosynthetic protein Chain: A: PDB Molecule:vacuolar transporter chaperone 2; PDBTitle: crystal structure of the cytoplasmic tunnel domain in yeast2 vtc2p 30 d1i1ga1 not modelled 9.3 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 31 c2ee7A_ not modelled 8.9 12 PDB header:structural protein Chain: A: PDB Molecule:sperm flagellar protein 1; PDBTitle: solution structure of the ch domain from human sperm2 flagellar protein 1 32 d1umqa_ not modelled 8.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 33 c1umqA_ not modelled 8.4 21 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 34 d1g2ha_ not modelled 8.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 35 d1pc6a_ not modelled 8.0 25 Fold:NinB Superfamily:NinB Family:NinB 36 d2hepa1 not modelled 7.3 67 Fold:Long alpha-hairpin Superfamily:YnzC-like Family:YznC-like 37 c2hepA_ not modelled 7.3 67 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. 38 d1b9ma1 not modelled 6.9 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of molybdate-dependent transcriptional regulator ModE 39 c3cdhB_ not modelled 6.2 12 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of the marr family transcriptional regulator spo14532 from silicibacter pomeroyi dss-3 40 d2d5ra1 not modelled 5.9 19 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:CAF1-like ribonuclease 41 d2cpta1 not modelled 5.6 19 Fold:Spectrin repeat-like Superfamily:MIT domain Family:MIT domain 42 d2fi0a1 not modelled 5.4 15 Fold:SP0561-like Superfamily:SP0561-like Family:SP0561-like 43 d1qpza1 not modelled 5.4 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 44 c3s2wB_ not modelled 5.2 18 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1 45 d1lcda_ not modelled 5.2 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator

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

---

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