Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	K	L	G	E	N	V	P	L	L	I	D	K	A	V	D	F	M	A	S	S	Q	A	F	R	E	Y	L	K	K	L	P	P	R	N	A	I	P	S	G	I	P	D	E	S	V	P	L	Y	L	Q	R	L	E	Y	Y	R	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																															?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		Y	R	P	K	Q	V	E	G	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 2ae9 chain A domain 1 Region: 16 - 58 Aligned: 43 Modelled: 43 Confidence: 82.0% Identity: 26% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ido chain B domain 1 Region: 16 - 58 Aligned: 43 Modelled: 43 Confidence: 79.6% Identity: 28% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 1se7 chain A Region: 16 - 58 Aligned: 43 Modelled: 43 Confidence: 79.0% Identity: 28% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2eyq chain A domain 6 Region: 38 - 60 Aligned: 23 Modelled: 23 Confidence: 52.5% Identity: 39% Fold: TRCF domain-like Superfamily: TRCF domain-like Family: TRCF domain Phyre2 PDB 2qsr chain A Region: 38 - 60 Aligned: 23 Modelled: 23 Confidence: 44.3% Identity: 22% PDB header:transcription Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of c-terminal domain of transcription-repair2 coupling factor Phyre2 PDB 1zxh chain A Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 18.3% Identity: 44% PDB header:immune system/protein binding Chain: A: PDB Molecule:immunoglobulin g binding protein g; PDBTitle: g311 mutant protein Phyre2 PDB 1mvk chain A Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 17.5% Identity: 14% Fold: beta-Grasp (ubiquitin-like) Superfamily: Immunoglobulin-binding domains Family: Immunoglobulin-binding domains Phyre2 PDB 1urq chain A Region: 5 - 32 Aligned: 28 Modelled: 27 Confidence: 17.4% Identity: 18% PDB header:transport protein Chain: A: PDB Molecule:m-tomosyn isoform; PDBTitle: crystal structure of neuronal q-snares in complex with2 r-snare motif of tomosyn Phyre2 PDB 1em7 chain A Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 17.3% Identity: 44% Fold: beta-Grasp (ubiquitin-like) Superfamily: Immunoglobulin-binding domains Family: Immunoglobulin-binding domains Phyre2 PDB 3gxq chain B Region: 17 - 31 Aligned: 15 Modelled: 15 Confidence: 16.3% Identity: 67% PDB header:dna binding protein/dna Chain: B: PDB Molecule:putative regulator of transfer genes arta; PDBTitle: structure of arta and dna complex Phyre2 PDB 1x9f chain C Region: 11 - 57 Aligned: 47 Modelled: 47 Confidence: 16.0% Identity: 15% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 PDB 1x9f chain A Region: 5 - 57 Aligned: 53 Modelled: 53 Confidence: 15.2% Identity: 9% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 PDB 1gl2 chain A Region: 5 - 32 Aligned: 28 Modelled: 27 Confidence: 13.7% Identity: 36% PDB header:membrane protein Chain: A: PDB Molecule:endobrevin; PDBTitle: crystal structure of an endosomal snare core complex Phyre2 PDB 2eyq chain A Region: 38 - 60 Aligned: 23 Modelled: 23 Confidence: 13.5% Identity: 39% PDB header:hydrolase Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor Phyre2 PDB 1k6m chain A Region: 43 - 63 Aligned: 21 Modelled: 21 Confidence: 12.4% Identity: 29% PDB header:transferase, hydrolase Chain: A: PDB Molecule:6-phosphofructo-2-kinase/fructose-2,6- PDBTitle: crystal structure of human liver 6-phosphofructo-2-2 kinase/fructose-2,6-bisphosphatase Phyre2 PDB 2iea chain A domain 1 Region: 19 - 69 Aligned: 51 Modelled: 51 Confidence: 12.2% Identity: 24% Fold: Thiamin diphosphate-binding fold (THDP-binding) Superfamily: Thiamin diphosphate-binding fold (THDP-binding) Family: TK-like Pyr module Phyre2 PDB 1q3m chain A Region: 55 - 63 Aligned: 9 Modelled: 9 Confidence: 11.2% Identity: 67% Fold: GLA-domain Superfamily: GLA-domain Family: GLA-domain Phyre2 PDB 2i1v chain B Region: 43 - 63 Aligned: 21 Modelled: 21 Confidence: 11.2% Identity: 24% PDB header:transferase, hydrolase Chain: B: PDB Molecule:6-phosphofructo-2-kinase/fructose-2,6- PDBTitle: crystal structure of pfkfb3 in complex with adp and2 fructose-2,6-bisphosphate Phyre2 PDB 3qf7 chain D Region: 25 - 31 Aligned: 7 Modelled: 7 Confidence: 10.5% Identity: 86% PDB header:hydrolase Chain: D: PDB Molecule:mre11; PDBTitle: the mre11:rad50 complex forms an atp dependent molecular clamp in dna2 double-strand break repair Phyre2 PDB 1bif chain A Region: 43 - 63 Aligned: 21 Modelled: 21 Confidence: 9.6% Identity: 29% PDB header:bifunctional enzyme Chain: A: PDB Molecule:6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase; PDBTitle: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase bifunctional2 enzyme complexed with atp-g-s and phosphate Phyre2 1 d2ae9a1 2 d2idob1 3 d1se7a_ 4 d2eyqa6 5 c2qsrA_ 6 c1zxhA_ 7 d1mvka_ 8 c1urqA_ 9 d1em7a_ 10 c3gxqB_ 11 d1x9fc_ 12 d1x9fa_ 13 c1gl2A_ 14 c2eyqA_ 15 c1k6mA_ 16 d2ieaa1 17 d1q3ma_ 18 c2i1vB_ 19 c3qf7D_ 20 c1bifA_ 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 66

Detailed template information

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

1 d2ae9a1 82.0 26 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 2 d2idob1 79.6 28 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 3 d1se7a_ 79.0 28 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 4 d2eyqa6 52.5 39 Fold:TRCF domain-like Superfamily:TRCF domain-like Family:TRCF domain 5 c2qsrA_ 44.3 22 PDB header:transcription Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of c-terminal domain of transcription-repair2 coupling factor 6 c1zxhA_ 18.3 44 PDB header:immune system/protein binding Chain: A: PDB Molecule:immunoglobulin g binding protein g; PDBTitle: g311 mutant protein 7 d1mvka_ 17.5 14 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 8 c1urqA_ 17.4 18 PDB header:transport protein Chain: A: PDB Molecule:m-tomosyn isoform; PDBTitle: crystal structure of neuronal q-snares in complex with2 r-snare motif of tomosyn 9 d1em7a_ 17.3 44 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 10 c3gxqB_ 16.3 67 PDB header:dna binding protein/dna Chain: B: PDB Molecule:putative regulator of transfer genes arta; PDBTitle: structure of arta and dna complex 11 d1x9fc_ 16.0 15 Fold:Globin-like Superfamily:Globin-like Family:Globins 12 d1x9fa_ 15.2 9 Fold:Globin-like Superfamily:Globin-like Family:Globins 13 c1gl2A_ 13.7 36 PDB header:membrane protein Chain: A: PDB Molecule:endobrevin; PDBTitle: crystal structure of an endosomal snare core complex 14 c2eyqA_ 13.5 39 PDB header:hydrolase Chain: A: PDB Molecule:transcription-repair coupling factor; PDBTitle: crystal structure of escherichia coli transcription-repair2 coupling factor 15 c1k6mA_ 12.4 29 PDB header:transferase, hydrolase Chain: A: PDB Molecule:6-phosphofructo-2-kinase/fructose-2,6- PDBTitle: crystal structure of human liver 6-phosphofructo-2-2 kinase/fructose-2,6-bisphosphatase 16 d2ieaa1 12.2 24 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:TK-like Pyr module 17 d1q3ma_ 11.2 67 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 18 c2i1vB_ 11.2 24 PDB header:transferase, hydrolase Chain: B: PDB Molecule:6-phosphofructo-2-kinase/fructose-2,6- PDBTitle: crystal structure of pfkfb3 in complex with adp and2 fructose-2,6-bisphosphate 19 c3qf7D_ 10.5 86 PDB header:hydrolase Chain: D: PDB Molecule:mre11; PDBTitle: the mre11:rad50 complex forms an atp dependent molecular clamp in dna2 double-strand break repair 20 c1bifA_ 9.6 29 PDB header:bifunctional enzyme Chain: A: PDB Molecule:6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase; PDBTitle: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase bifunctional2 enzyme complexed with atp-g-s and phosphate 21 d1p7ea_ not modelled 9.5 39 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 22 d1pgaa_ not modelled 9.4 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 23 d2es9a1 not modelled 9.4 63 Fold:YoaC-like Superfamily:YoaC-like Family:YoaC-like 24 c1bm4A_ not modelled 9.3 43 PDB header:viral protein Chain: A: PDB Molecule:protein (moloney murine leukemia virus capsid); PDBTitle: momlv capsid protein major homology region peptide analog 25 d3nlaa_ not modelled 9.3 60 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 26 c3b5nE_ not modelled 9.1 29 PDB header:membrane protein Chain: E: PDB Molecule:synaptobrevin homolog 1; PDBTitle: structure of the yeast plasma membrane snare complex 27 c2zs0A_ not modelled 9.0 7 PDB header:oxygen storage, oxygen transport Chain: A: PDB Molecule:extracellular giant hemoglobin major globin subunit a1; PDBTitle: structural basis for the heterotropic and homotropic interactions of2 invertebrate giant hemoglobin 28 c1yhuW_ not modelled 8.9 15 PDB header:oxygen storage/transport Chain: W: PDB Molecule:hemoglobin b1a chain; PDBTitle: crystal structure of riftia pachyptila c1 hemoglobin reveals novel2 assembly of 24 subunits. 29 c1f02T_ not modelled 8.5 100 PDB header:cell adhesion Chain: T: PDB Molecule:translocated intimin receptor; PDBTitle: crystal structure of c-terminal 282-residue fragment of2 intimin in complex with translocated intimin receptor3 (tir) intimin-binding domain 30 c3hg9B_ not modelled 8.3 45 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:pilm; PDBTitle: crystal structure of putative pilm protein from pseudomonas aeruginosa2 2192 31 d1opsa_ not modelled 8.3 40 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 32 c3kyqA_ not modelled 8.3 29 PDB header:transferase Chain: A: PDB Molecule:synaptobrevin homolog ykt6; PDBTitle: lipid-induced conformational switch controls fusion activity of longin2 domain snare ykt6 33 c2bn5A_ not modelled 8.2 35 PDB header:nuclear protein Chain: A: PDB Molecule:psi; PDBTitle: p-element somatic inhibitor protein complex with u1-70k2 proline-rich peptide 34 d1pgxa_ not modelled 8.0 39 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 35 d1c8aa2 not modelled 8.0 50 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 36 d2dy1a3 not modelled 7.8 31 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 37 c2d2mC_ not modelled 7.7 13 PDB header:oxygen storage/transport Chain: C: PDB Molecule:giant hemoglobin, b2(c) globin chain; PDBTitle: structure of an extracellular giant hemoglobin of the2 gutless beard worm oligobrachia mashikoi 38 c1n7sA_ not modelled 7.6 25 PDB header:transport protein Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: high resolution structure of a truncated neuronal snare2 complex 39 c1wvoA_ not modelled 7.5 40 PDB header:transferase Chain: A: PDB Molecule:sialic acid synthase; PDBTitle: solution structure of rsgi ruh-029, an antifreeze protein2 like domain in human n-acetylneuraminic acid phosphate3 synthase gene. 40 d1fcla_ not modelled 7.4 22 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 41 c2ckcA_ not modelled 7.2 29 PDB header:hydrolase Chain: A: PDB Molecule:chromodomain-helicase-dna-binding protein 7; PDBTitle: solution structures of the brk domains of the human chromo2 helicase domain 7 and 8, reveals structural similarity3 with gyf domain suggesting a role in protein interaction 42 d2ckca1 not modelled 7.2 29 Fold:GYF/BRK domain-like Superfamily:BRK domain-like Family:BRK domain-like 43 d1qkza_ not modelled 7.0 33 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 44 c3hd7A_ not modelled 7.0 25 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 45 d1irqa_ not modelled 6.8 50 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Omega transcriptional repressor 46 d1fd6a_ not modelled 6.8 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 47 c3e0dA_ not modelled 6.7 13 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase iii subunit alpha; PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit 48 c1irqB_ not modelled 6.5 50 PDB header:gene regulation Chain: B: PDB Molecule:omega transcriptional repressor; PDBTitle: crystal structure of omega transcriptional repressor at2 1.5a resolution 49 d1gb4a_ not modelled 6.3 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 50 d2qfka1 not modelled 6.1 15 Fold:Globin-like Superfamily:Globin-like Family:Globins 51 d1mi0a_ not modelled 5.9 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 52 d1urva_ not modelled 5.9 6 Fold:Globin-like Superfamily:Globin-like Family:Globins 53 c1ut0A_ not modelled 5.9 6 PDB header:oxygen transport Chain: A: PDB Molecule:cytoglobin; PDBTitle: crystal structure of cytoglobin: the fourth globin type2 discovered in man displays heme hexa-coordination 54 c2ebzA_ not modelled 5.8 22 PDB header:signaling protein Chain: A: PDB Molecule:regulator of g-protein signaling 12; PDBTitle: solution structure of the rgs domain from human regulator2 of g-protein signaling 12 (rgs12) 55 d1mhxa_ not modelled 5.8 28 Fold:beta-Grasp (ubiquitin-like) Superfamily:Immunoglobulin-binding domains Family:Immunoglobulin-binding domains 56 c1c8aA_ not modelled 5.8 60 PDB header:antifreeze protein Chain: A: PDB Molecule:protein (antifreeze protein type iii); PDBTitle: nmr structure of intramolecular dimer antifreeze protein2 rd3, 40 sa structures 57 c3ideD_ not modelled 5.7 33 PDB header:virus like particle Chain: D: PDB Molecule:capsid protein vp2; PDBTitle: structure of ipnv subviral particle 58 c3h9pB_ not modelled 5.5 20 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative triphosphoribosyl-dephospho-coa synthase; PDBTitle: crystal structure of putative triphosphoribosyl-dephospho-coa synthase2 from archaeoglobus fulgidus 59 c2okrF_ not modelled 5.4 47 PDB header:transferase Chain: F: PDB Molecule:map kinase-activated protein kinase 2; PDBTitle: crystal structure of the p38a-mapkap kinase 2 heterodimer 60 c2zs1D_ not modelled 5.4 15 PDB header:oxygen storage, oxygen transport Chain: D: PDB Molecule:extracellular giant hemoglobin major globin subunit b1; PDBTitle: structural basis for the heterotropic and homotropic interactions of2 invertebrate giant hemoglobin 61 c1pznG_ not modelled 5.4 41 PDB header:recombination Chain: G: PDB Molecule:dna repair and recombination protein rad51; PDBTitle: rad51 (rada) 62 d1hg7a_ not modelled 5.3 60 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like domain 63 d1bifa1 not modelled 5.3 29 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain 64 d2bv3a3 not modelled 5.2 38 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Translational machinery components 65 d2e50a1 not modelled 5.2 23 Fold:NAP-like Superfamily:NAP-like Family:NAP-like 66 d1ucsa_ not modelled 5.1 60 Fold:beta-clip Superfamily:AFP III-like domain Family:AFP III-like 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

---

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