Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	T	G	I	Q	I	T	K	A	A	N	D	D	L	L	N	S	F	W	L	L	D	S	E	K	G	E	A	R	C	I	V	A	K	A	G	Y	A	E	D	E	V	V	A	V	S	K	L	G	D	I	E	Y	R	E	V	P	V	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?					?																																	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	K	P	E	V	R	V	E	G	G	Q	H	L	N	V	N	V	L	R	R	E	T	L	E	D	A	V	K	H	P	E	K	Y	P	Q	L	T	I	R	V	S	G	Y	A	V	R	F	N	S	L	T	P	E	Q	Q	R	D	V	I	A
Secondary structure
SS confidence
Disorder																														?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		R	T	F	T	E	S	L
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 1h16 chain A Region: 67 - 127 Aligned: 61 Modelled: 61 Confidence: 100.0% Identity: 79% Fold: PFL-like glycyl radical enzymes Superfamily: PFL-like glycyl radical enzymes Family: PFL-like Phyre2 PDB 2y8n chain C Region: 47 - 125 Aligned: 79 Modelled: 79 Confidence: 100.0% Identity: 29% PDB header:lyase Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit; PDBTitle: crystal structure of glycyl radical enzyme Phyre2 PDB 1r9d chain A Region: 37 - 125 Aligned: 89 Modelled: 89 Confidence: 100.0% Identity: 31% Fold: PFL-like glycyl radical enzymes Superfamily: PFL-like glycyl radical enzymes Family: PFL-like Phyre2 PDB 2f3o chain B Region: 37 - 125 Aligned: 88 Modelled: 89 Confidence: 100.0% Identity: 27% PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus Phyre2 PDB 1ais chain A domain 1 Region: 89 - 99 Aligned: 11 Modelled: 11 Confidence: 26.3% Identity: 27% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1nh2 chain A domain 1 Region: 89 - 101 Aligned: 13 Modelled: 13 Confidence: 25.1% Identity: 15% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1qna chain A domain 1 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 25.0% Identity: 17% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1nh2 chain A domain 2 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 24.8% Identity: 42% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1mp9 chain A domain 1 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 23.8% Identity: 33% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1ais chain A domain 2 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 23.5% Identity: 42% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1qna chain A domain 2 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 22.9% Identity: 42% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1cdw chain A domain 2 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 22.3% Identity: 42% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1mp9 chain A domain 2 Region: 89 - 100 Aligned: 12 Modelled: 12 Confidence: 21.5% Identity: 42% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1cdw chain A domain 1 Region: 89 - 107 Aligned: 19 Modelled: 19 Confidence: 19.4% Identity: 11% Fold: TBP-like Superfamily: TATA-box binding protein-like Family: TATA-box binding protein (TBP), C-terminal domain Phyre2 PDB 1pg5 chain B domain 2 Region: 11 - 46 Aligned: 36 Modelled: 36 Confidence: 18.9% Identity: 17% Fold: Rubredoxin-like Superfamily: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain Family: Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain Phyre2 PDB 1wd6 chain B Region: 15 - 34 Aligned: 20 Modelled: 20 Confidence: 18.8% Identity: 25% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli Phyre2 PDB 3iz5 chain P Region: 11 - 26 Aligned: 16 Modelled: 16 Confidence: 16.9% Identity: 25% PDB header:ribosome Chain: P: PDB Molecule:60s ribosomal protein l15 (l15e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2z1d chain A Region: 32 - 92 Aligned: 61 Modelled: 61 Confidence: 16.3% Identity: 10% PDB header:metal binding protein Chain: A: PDB Molecule:hydrogenase expression/formation protein hypd; PDBTitle: crystal structure of [nife] hydrogenase maturation protein, hypd from2 thermococcus kodakaraensis Phyre2 PDB 2hiq chain A domain 1 Region: 15 - 34 Aligned: 20 Modelled: 20 Confidence: 15.7% Identity: 25% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Hypothetical protein YdhR Phyre2 PDB 1vra chain B Region: 25 - 114 Aligned: 75 Modelled: 81 Confidence: 14.0% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:arginine biosynthesis bifunctional protein argj; PDBTitle: crystal structure of arginine biosynthesis bifunctional protein argj2 (10175521) from bacillus halodurans at 2.00 a resolution Phyre2 1 d1h16a_ 2 c2y8nC_ 3 d1r9da_ 4 c2f3oB_ 5 d1aisa1 6 d1nh2a1 7 d1qnaa1 8 d1nh2a2 9 d1mp9a1 10 d1aisa2 11 d1qnaa2 12 d1cdwa2 13 d1mp9a2 14 d1cdwa1 15 d1pg5b2 16 c1wd6B_ 17 c3iz5P_ 18 c2z1dA_ 19 d2hiqa1 20 c1vraB_ 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 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65

Detailed template information

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

1 d1h16a_ 100.0 79 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like 2 c2y8nC_ 100.0 29 PDB header:lyase Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit; PDBTitle: crystal structure of glycyl radical enzyme 3 d1r9da_ 100.0 31 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like 4 c2f3oB_ 100.0 27 PDB header:unknown function Chain: B: PDB Molecule:pyruvate formate-lyase 2; PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus 5 d1aisa1 26.3 27 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 6 d1nh2a1 25.1 15 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 7 d1qnaa1 25.0 17 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 8 d1nh2a2 24.8 42 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 9 d1mp9a1 23.8 33 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 10 d1aisa2 23.5 42 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 11 d1qnaa2 22.9 42 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 12 d1cdwa2 22.3 42 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 13 d1mp9a2 21.5 42 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 14 d1cdwa1 19.4 11 Fold:TBP-like Superfamily:TATA-box binding protein-like Family:TATA-box binding protein (TBP), C-terminal domain 15 d1pg5b2 18.9 17 Fold:Rubredoxin-like Superfamily:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain Family:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain 16 c1wd6B_ 18.8 25 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein ydhr; PDBTitle: crystal structure of jw1657 from escherichia coli 17 c3iz5P_ 16.9 25 PDB header:ribosome Chain: P: PDB Molecule:60s ribosomal protein l15 (l15e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 18 c2z1dA_ 16.3 10 PDB header:metal binding protein Chain: A: PDB Molecule:hydrogenase expression/formation protein hypd; PDBTitle: crystal structure of [nife] hydrogenase maturation protein, hypd from2 thermococcus kodakaraensis 19 d2hiqa1 15.7 25 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Hypothetical protein YdhR 20 c1vraB_ 14.0 15 PDB header:transferase Chain: B: PDB Molecule:arginine biosynthesis bifunctional protein argj; PDBTitle: crystal structure of arginine biosynthesis bifunctional protein argj2 (10175521) from bacillus halodurans at 2.00 a resolution 21 c1yo8A_ not modelled 12.8 17 PDB header:cell adhesion Chain: A: PDB Molecule:thrombospondin-2; PDBTitle: structure of the c-terminal domain of human thrombospondin-2 22 c3h0mE_ not modelled 12.1 21 PDB header:ligase Chain: E: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase PDBTitle: structure of trna-dependent amidotransferase gatcab from2 aquifex aeolicus 23 d1xlya_ not modelled 11.8 33 Fold:RNA-binding protein She2p Superfamily:RNA-binding protein She2p Family:RNA-binding protein She2p 24 d2fzcb2 not modelled 11.4 15 Fold:Rubredoxin-like Superfamily:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain Family:Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain 25 d1vqom1 not modelled 10.4 24 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 26 c4a1cL_ not modelled 10.3 25 PDB header:ribosome Chain: L: PDB Molecule:ribosomal protein l15; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4. 27 d1jj2l_ not modelled 10.2 24 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 28 c2kwuA_ not modelled 9.9 36 PDB header:protein binding/signaling protein Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution structure of ubm2 of murine polymerase iota in complex with2 ubiquitin 29 d1v82a_ not modelled 9.8 20 Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:1,3-glucuronyltransferase 30 c2vzkD_ not modelled 9.8 15 PDB header:transferase Chain: D: PDB Molecule:glutamate n-acetyltransferase 2 beta chain; PDBTitle: structure of the acyl-enzyme complex of an n-terminal2 nucleophile (ntn) hydrolase, oat2 31 c2z8uQ_ not modelled 9.5 32 PDB header:transcription Chain: Q: PDB Molecule:tata-box-binding protein; PDBTitle: methanococcus jannaschii tbp 32 c2q82A_ not modelled 9.4 43 PDB header:structural protein Chain: A: PDB Molecule:core protein p7; PDBTitle: crystal structure of core protein p7 from pseudomonas phage2 phi12. northeast structural genomics target oc1 33 c1eysH_ not modelled 8.7 11 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 34 d8ruci_ not modelled 8.6 25 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 35 d1gk8i_ not modelled 8.5 17 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 36 c2hx6A_ not modelled 8.4 14 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 37 d1cmwa2 not modelled 8.4 28 Fold:PIN domain-like Superfamily:PIN domain-like Family:5' to 3' exonuclease catalytic domain 38 d1ej7s_ not modelled 8.3 29 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 39 d1tfra2 not modelled 8.3 18 Fold:PIN domain-like Superfamily:PIN domain-like Family:5' to 3' exonuclease catalytic domain 40 d1wdds_ not modelled 7.7 21 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 41 d1ffki_ not modelled 7.6 31 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:L15e 42 c3al0B_ not modelled 7.4 20 PDB header:ligase/rna Chain: B: PDB Molecule:aspartyl/glutamyl-trna(asn/gln) amidotransferase subunit b; PDBTitle: crystal structure of the glutamine transamidosome from thermotoga2 maritima in the glutamylation state. 43 c1d3uA_ not modelled 7.4 42 PDB header:gene regulation/dna Chain: A: PDB Molecule:tata-binding protein; PDBTitle: tata-binding protein/transcription factor (ii)b/bre+tata-2 box complex from pyrococcus woesei 44 c2j6pF_ not modelled 7.3 16 PDB header:oxidoreductase Chain: F: PDB Molecule:sb(v)-as(v) reductase; PDBTitle: structure of as-sb reductase from leishmania major 45 c3eikB_ not modelled 7.3 17 PDB header:transcription Chain: B: PDB Molecule:tata-box-binding protein; PDBTitle: double stranded dna binding protein 46 d2v6ai1 not modelled 7.2 17 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 47 c1mp9B_ not modelled 7.0 33 PDB header:dna binding protein Chain: B: PDB Molecule:tata-binding protein; PDBTitle: tbp from a mesothermophilic archaeon, sulfolobus2 acidocaldarius 48 c3gqjA_ not modelled 6.9 25 PDB header:unknown function Chain: A: PDB Molecule:cell inhibiting factor (cif); PDBTitle: crystal structure of cell inhibiting factor (cif) from photorhabdus2 luminescens 49 d2f2ab2 not modelled 6.9 14 Fold:Glutamine synthetase/guanido kinase Superfamily:Glutamine synthetase/guanido kinase Family:GatB/GatE catalytic domain-like 50 c3f3hA_ not modelled 6.5 27 PDB header:antitumor protein Chain: A: PDB Molecule:immunomodulatory protein ling zhi-8; PDBTitle: crystal structure and anti-tumor activity of lz-8 from the fungus2 ganoderma lucidium 51 d1uzdc1 not modelled 6.5 17 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 52 c3ol0C_ not modelled 6.3 50 PDB header:de novo protein Chain: C: PDB Molecule:de novo designed monomer trefoil-fold sub-domain which PDBTitle: crystal structure of monofoil-4p homo-trimer: de novo designed monomer2 trefoil-fold sub-domain which forms homo-trimer assembly 53 d1v5ra1 not modelled 6.3 33 Fold:N domain of copper amine oxidase-like Superfamily:GAS2 domain-like Family:GAS2 domain 54 c1s1iL_ not modelled 6.1 35 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l15-a; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 55 c3q3jA_ not modelled 6.1 22 PDB header:membrane protein/protein binding Chain: A: PDB Molecule:plexin-a2; PDBTitle: crystal structure of plexin a2 rbd in complex with rnd1 56 c3su8X_ not modelled 6.1 29 PDB header:apoptosis/signaling protein Chain: X: PDB Molecule:plexin-b1; PDBTitle: crystal structure of a truncated intracellular domain of plexin-b1 in2 complex with rac1 57 d2nlua1 not modelled 5.9 39 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:PWWP domain 58 d1eysh1 not modelled 5.8 11 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:Photosynthetic reaction centre, H-chain, cytoplasmic domain 59 c3ajfA_ not modelled 5.6 43 PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: structural insigths into dsrna binding and rna silencing suppression2 by ns3 protein of rice hoja blanca tenuivirus 60 c1ux6A_ not modelled 5.5 19 PDB header:cell adhesion Chain: A: PDB Molecule:thrombospondin-1; PDBTitle: structure of a thrombospondin c-terminal fragment reveals a2 novel calcium core in the type 3 repeats 61 d1xo1a2 not modelled 5.4 22 Fold:PIN domain-like Superfamily:PIN domain-like Family:5' to 3' exonuclease catalytic domain 62 c1zswA_ not modelled 5.1 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:glyoxalase family protein; PDBTitle: crystal structure of bacillus cereus metallo protein from glyoxalase2 family 63 d1v54b1 not modelled 5.1 11 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Periplasmic domain of cytochrome c oxidase subunit II 64 c3bl9B_ not modelled 5.0 16 PDB header:hydrolase Chain: B: PDB Molecule:scavenger mrna-decapping enzyme dcps; PDBTitle: synthetic gene encoded dcps bound to inhibitor dg157493 65 c3gr1A_ not modelled 5.0 22 PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392)

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