Secondary structure and disorder prediction

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Sequence		M	K	K	D	I	H	P	K	Y	E	E	I	T	A	S	C	S	C	G	N	V	M	K	I	R	S	T	V	G	H	D	L	N	L	D	V	C	S	K	C	H	P	F	F	T	G	K	Q	R	D	V	A	T	G	G	R	V	D	R	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																															?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70
Sequence		N	K	R	F	N	I	P	G	S	K
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 1vs6 chain Z domain 1 Region: 1 - 70 Aligned: 70 Modelled: 70 Confidence: 100.0% Identity: 100% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L31p Phyre2 PDB 2b66 chain 4 Region: 1 - 70 Aligned: 69 Modelled: 69 Confidence: 100.0% Identity: 42% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf1,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400 Phyre2 PDB 3bbo chain 1 Region: 2 - 69 Aligned: 67 Modelled: 68 Confidence: 99.9% Identity: 31% PDB header:ribosome Chain: 1: PDB Molecule:ribosomal protein l31; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2j03 chain 4 Region: 1 - 50 Aligned: 49 Modelled: 50 Confidence: 99.9% Identity: 51% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: structure of the thermus thermophilus 70s ribosome2 complexed with mrna, trna and paromomycin (part 4 of 4).3 this file contains the 50s subunit from molecule ii. Phyre2 PDB 2j01 chain 4 domain 1 Region: 1 - 50 Aligned: 49 Modelled: 50 Confidence: 99.9% Identity: 51% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L31p Phyre2 PDB 3f1f chain 4 Region: 11 - 40 Aligned: 29 Modelled: 30 Confidence: 97.4% Identity: 41% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: crystal structure of a translation termination complex2 formed with release factor rf2. this file contains the 50s3 subunit of one 70s ribosome. the entire crystal structure4 contains two 70s ribosomes as described in remark 400. Phyre2 PDB 2wh4 chain 4 Region: 11 - 40 Aligned: 29 Modelled: 30 Confidence: 97.4% Identity: 41% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome Phyre2 PDB 3cng chain C Region: 16 - 57 Aligned: 42 Modelled: 42 Confidence: 38.9% Identity: 26% PDB header:hydrolase Chain: C: PDB Molecule:nudix hydrolase; PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea Phyre2 PDB 1iuf chain A domain 2 Region: 42 - 66 Aligned: 25 Modelled: 25 Confidence: 23.2% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 3cuc chain B Region: 41 - 60 Aligned: 13 Modelled: 20 Confidence: 20.7% Identity: 54% PDB header:signaling protein Chain: B: PDB Molecule:protein of unknown function with a fic domain; PDBTitle: crystal structure of a fic domain containing signaling protein2 (bt_2513) from bacteroides thetaiotaomicron vpi-5482 at 2.71 a3 resolution Phyre2 PDB 1tqz chain A domain 1 Region: 37 - 56 Aligned: 20 Modelled: 20 Confidence: 19.8% Identity: 25% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Necap1 N-terminal domain-like Phyre2 PDB 2ket chain A Region: 55 - 64 Aligned: 10 Modelled: 10 Confidence: 18.6% Identity: 60% PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 Phyre2 PDB 3g66 chain A Region: 40 - 58 Aligned: 19 Modelled: 19 Confidence: 18.1% Identity: 26% PDB header:transferase Chain: A: PDB Molecule:sortase c; PDBTitle: the crystal structure of streptococcus pneumoniae sortase c2 provides novel insights into catalysis as well as pilin3 substrate specificity Phyre2 PDB 3o0p chain A Region: 40 - 58 Aligned: 19 Modelled: 19 Confidence: 16.3% Identity: 26% PDB header:transferase , hydrolase Chain: A: PDB Molecule:sortase family protein; PDBTitle: pilus-related sortase c of group b streptococcus Phyre2 PDB 1x6h chain A domain 1 Region: 11 - 28 Aligned: 18 Modelled: 18 Confidence: 16.1% Identity: 33% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 1iuf chain A Region: 42 - 66 Aligned: 25 Modelled: 25 Confidence: 15.9% Identity: 20% PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein Phyre2 PDB 1eb7 chain A domain 2 Region: 37 - 48 Aligned: 12 Modelled: 12 Confidence: 14.5% Identity: 42% Fold: Cytochrome c Superfamily: Cytochrome c Family: Di-heme cytochrome c peroxidase Phyre2 PDB 4a1e chain T Region: 32 - 57 Aligned: 26 Modelled: 26 Confidence: 13.6% Identity: 35% PDB header:ribosome Chain: T: PDB Molecule:rpl24; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 Phyre2 PDB 2keq chain A Region: 37 - 47 Aligned: 11 Modelled: 11 Confidence: 13.5% Identity: 36% PDB header:splicing Chain: A: PDB Molecule:dna polymerase iii alpha subunit, nucleic acid PDBTitle: solution structure of dnae intein from nostoc punctiforme Phyre2 PDB 3izc chain Z Region: 32 - 57 Aligned: 26 Modelled: 26 Confidence: 13.5% Identity: 12% PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein rpl24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 1 d1vs6z1 2 c2b664_ 3 c3bbo1_ 4 c2j034_ 5 d2j0141 6 c3f1f4_ 7 c2wh44_ 8 c3cngC_ 9 d1iufa2 10 c3cucB_ 11 d1tqza1 12 c2ketA_ 13 c3g66A_ 14 c3o0pA_ 15 d1x6ha1 16 c1iufA_ 17 d1eb7a2 18 c4a1eT_ 19 c2keqA_ 20 c3izcZ_ 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 67 68 69 70

Detailed template information

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

1 d1vs6z1 100.0 100 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L31p 2 c2b664_ 100.0 42 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: 50s ribosomal subunit from a crystal structure of release factor rf1,2 trnas and mrna bound to the ribosome. this file contains the 50s3 subunit from a crystal structure of release factor rf1, trnas and4 mrna bound to the ribosome and is described in remark 400 3 c3bbo1_ 99.9 31 PDB header:ribosome Chain: 1: PDB Molecule:ribosomal protein l31; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 4 c2j034_ 99.9 51 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: structure of the thermus thermophilus 70s ribosome2 complexed with mrna, trna and paromomycin (part 4 of 4).3 this file contains the 50s subunit from molecule ii. 5 d2j0141 99.9 51 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L31p 6 c3f1f4_ 97.4 41 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: crystal structure of a translation termination complex2 formed with release factor rf2. this file contains the 50s3 subunit of one 70s ribosome. the entire crystal structure4 contains two 70s ribosomes as described in remark 400. 7 c2wh44_ 97.4 41 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome 8 c3cngC_ 38.9 26 PDB header:hydrolase Chain: C: PDB Molecule:nudix hydrolase; PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea 9 d1iufa2 23.2 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 10 c3cucB_ 20.7 54 PDB header:signaling protein Chain: B: PDB Molecule:protein of unknown function with a fic domain; PDBTitle: crystal structure of a fic domain containing signaling protein2 (bt_2513) from bacteroides thetaiotaomicron vpi-5482 at 2.71 a3 resolution 11 d1tqza1 19.8 25 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Necap1 N-terminal domain-like 12 c2ketA_ 18.6 60 PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 13 c3g66A_ 18.1 26 PDB header:transferase Chain: A: PDB Molecule:sortase c; PDBTitle: the crystal structure of streptococcus pneumoniae sortase c2 provides novel insights into catalysis as well as pilin3 substrate specificity 14 c3o0pA_ 16.3 26 PDB header:transferase , hydrolase Chain: A: PDB Molecule:sortase family protein; PDBTitle: pilus-related sortase c of group b streptococcus 15 d1x6ha1 16.1 33 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 16 c1iufA_ 15.9 20 PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein 17 d1eb7a2 14.5 42 Fold:Cytochrome c Superfamily:Cytochrome c Family:Di-heme cytochrome c peroxidase 18 c4a1eT_ 13.6 35 PDB header:ribosome Chain: T: PDB Molecule:rpl24; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 19 c2keqA_ 13.5 36 PDB header:splicing Chain: A: PDB Molecule:dna polymerase iii alpha subunit, nucleic acid PDBTitle: solution structure of dnae intein from nostoc punctiforme 20 c3izcZ_ 13.5 12 PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein rpl24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 21 c2kw8A_ not modelled 13.3 26 PDB header:protein binding Chain: A: PDB Molecule:lpxtg-site transpeptidase family protein; PDBTitle: solution structure of bacillus anthracis sortase a (srta)2 transpeptidase 22 c2w1jB_ not modelled 13.1 26 PDB header:transferase Chain: B: PDB Molecule:putative sortase; PDBTitle: crystal structure of sortase c-1 (srtc-1) from2 streptococcus pneumoniae 23 d1nmla2 not modelled 12.5 33 Fold:Cytochrome c Superfamily:Cytochrome c Family:Di-heme cytochrome c peroxidase 24 c3n3vA_ not modelled 11.9 46 PDB header:transferase Chain: A: PDB Molecule:adenosine monophosphate-protein transferase ibpa; PDBTitle: crystal structure of ibpafic2-h3717a in complex with adenylylated2 cdc42 25 c1zd7B_ not modelled 11.8 25 PDB header:transferase Chain: B: PDB Molecule:dna polymerase iii alpha subunit; PDBTitle: 1.7 angstrom crystal structure of post-splicing form of a dnae intein2 from synechocystis sp. pcc 6803 26 d1mi8a_ not modelled 11.7 25 Fold:Hedgehog/intein (Hint) domain Superfamily:Hedgehog/intein (Hint) domain Family:Intein (protein splicing domain) 27 d1oa8a_ not modelled 11.3 31 Fold:AXH domain Superfamily:AXH domain Family:AXH domain 28 c1v0eB_ not modelled 11.0 32 PDB header:hydrolase Chain: B: PDB Molecule:endo-alpha-sialidase; PDBTitle: endosialidase of bacteriophage k1f 29 d1e7la1 not modelled 10.6 60 Fold:LEM/SAP HeH motif Superfamily:Recombination endonuclease VII, C-terminal and dimerization domains Family:Recombination endonuclease VII, C-terminal and dimerization domains 30 c1nmlA_ not modelled 10.5 33 PDB header:oxidoreductase Chain: A: PDB Molecule:di-haem cytochrome c peroxidase; PDBTitle: di-haemic cytochrome c peroxidase from pseudomonas nautica 617, form2 in (ph 4.0) 31 c2yiuE_ not modelled 10.3 63 PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution 32 d1jz8a1 not modelled 10.0 10 Fold:Immunoglobulin-like beta-sandwich Superfamily:beta-Galactosidase/glucuronidase domain Family:beta-Galactosidase/glucuronidase domain 33 c3iz5Z_ not modelled 10.0 23 PDB header:ribosome Chain: Z: PDB Molecule:60s ribosomal protein l24 (l24e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 34 c3cwbQ_ not modelled 9.6 71 PDB header:oxidoreductase Chain: Q: PDB Molecule:mitochondrial cytochrome c1, heme protein; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 35 c2w1kB_ not modelled 9.4 32 PDB header:transferase Chain: B: PDB Molecule:putative sortase; PDBTitle: crystal structure of sortase c-3 (srtc-3) from2 streptococcus pneumoniae 36 c3rbjB_ not modelled 9.3 21 PDB header:hydrolase Chain: B: PDB Molecule:sortase family protein; PDBTitle: crystal structure of the lid-mutant of streptococcus agalactiae2 sortase c1 37 d3cx5d1 not modelled 9.2 57 Fold:Cytochrome c Superfamily:Cytochrome c Family:Cytochrome bc1 domain 38 c2fynH_ not modelled 9.0 57 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c1; PDBTitle: crystal structure analysis of the double mutant rhodobacter2 sphaeroides bc1 complex 39 d1at0a_ not modelled 8.9 10 Fold:Hedgehog/intein (Hint) domain Superfamily:Hedgehog/intein (Hint) domain Family:Hedgehog C-terminal (Hog) autoprocessing domain 40 c3hq7A_ not modelled 8.9 33 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c551 peroxidase; PDBTitle: ccpa from g. sulfurreducens, g94k/k97q/r100i variant 41 d1am2a_ not modelled 8.9 20 Fold:Hedgehog/intein (Hint) domain Superfamily:Hedgehog/intein (Hint) domain Family:Intein (protein splicing domain) 42 c3dd7A_ not modelled 8.7 20 PDB header:ribosome inhibitor Chain: A: PDB Molecule:death on curing protein; PDBTitle: structure of doch66y in complex with the c-terminal domain of phd 43 c2lcjA_ not modelled 8.7 20 PDB header:hydrolase Chain: A: PDB Molecule:pab polc intein; PDBTitle: solution nmr structure of pab polii intein 44 c1p84D_ not modelled 8.5 57 PDB header:oxidoreductase Chain: D: PDB Molecule:cytochrome c1, heme protein; PDBTitle: hdbt inhibited yeast cytochrome bc1 complex 45 c3eqxB_ not modelled 8.4 54 PDB header:dna binding protein Chain: B: PDB Molecule:fic domain containing transcriptional regulator; PDBTitle: crystal structure of a fic family protein (so_4266) from shewanella2 oneidensis at 1.6 a resolution 46 d1ppjd1 not modelled 8.4 71 Fold:Cytochrome c Superfamily:Cytochrome c Family:Cytochrome bc1 domain 47 c2imzA_ not modelled 8.2 17 PDB header:hydrolase Chain: A: PDB Molecule:endonuclease pi-mtui; PDBTitle: crystal structure of mtu reca intein splicing domain 48 c1zrtD_ not modelled 8.2 71 PDB header:oxidoreductase/metal transport Chain: D: PDB Molecule:cytochrome c1; PDBTitle: rhodobacter capsulatus cytochrome bc1 complex with2 stigmatellin bound 49 c3ltiA_ not modelled 8.2 32 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta; PDBTitle: crystal structure of the escherichia coli rna polymerase beta subunit2 beta2-betai4 domains 50 d1wada_ not modelled 7.9 67 Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Cytochrome c3-like 51 d1ltla_ not modelled 7.4 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA replication initiator (cdc21/cdc54) N-terminal domain 52 c2in0A_ not modelled 7.2 15 PDB header:hydrolase Chain: A: PDB Molecule:endonuclease pi-mtui; PDBTitle: crystal structure of mtu reca intein splicing domain 53 d2cbpa_ not modelled 7.2 25 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 54 c2ov7C_ not modelled 6.7 17 PDB header:ribosomal protein Chain: C: PDB Molecule:50s ribosomal protein l1; PDBTitle: the first domain of the ribosomal protein l1 from thermus2 thermophilus 55 c2jmzA_ not modelled 6.6 20 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein mj0781; PDBTitle: solution structure of a klba intein precursor from2 methanococcus jannaschii 56 c3mdnD_ not modelled 6.6 31 PDB header:transferase Chain: D: PDB Molecule:glutamine aminotransferase class-ii domain protein; PDBTitle: structure of glutamine aminotransferase class-ii domain protein2 (spo2029) from silicibacter pomeroyi 57 c3re9A_ not modelled 6.6 26 PDB header:transferase Chain: A: PDB Molecule:sortase-like protein; PDBTitle: crystal structure of sortasec1 from streptococcus suis 58 c2cazB_ not modelled 6.4 30 PDB header:protein transport Chain: B: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: escrt-i core 59 d2cazb1 not modelled 6.4 30 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS28 N-terminal domain 60 c1iqcB_ not modelled 6.2 42 PDB header:oxidoreductase Chain: B: PDB Molecule:di-heme peroxidase; PDBTitle: crystal structure of di-heme peroxidase from nitrosomonas europaea 61 c2zkru_ not modelled 6.1 30 PDB header:ribosomal protein/rna Chain: U: PDB Molecule:rna expansion segment es41; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 62 c2xwgA_ not modelled 6.1 39 PDB header:hydrolase Chain: A: PDB Molecule:sortase; PDBTitle: crystal structure of sortase c-1 from actinomyces oris (formerly2 actinomyces naeslundii) 63 c2wg6L_ not modelled 6.1 9 PDB header:transcription,hydrolase Chain: L: PDB Molecule:general control protein gcn4, PDBTitle: proteasome-activating nucleotidase (pan) n-domain (57-134)2 from archaeoglobus fulgidus fused to gcn4, p61a mutant 64 c3h43F_ not modelled 6.1 12 PDB header:hydrolase Chain: F: PDB Molecule:proteasome-activating nucleotidase; PDBTitle: n-terminal domain of the proteasome-activating nucleotidase2 of methanocaldococcus jannaschii 65 d1i77a_ not modelled 5.9 83 Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Cytochrome c3-like 66 d1up9a_ not modelled 5.3 83 Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Cytochrome c3-like 67 c1x0gA_ not modelled 5.2 23 PDB header:metal binding protein Chain: A: PDB Molecule:isca; PDBTitle: crystal structure of isca with the [2fe-2s] cluster 68 d2f6mb1 not modelled 5.2 30 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS28 N-terminal domain 69 c2wcvI_ not modelled 5.2 36 PDB header:isomerase Chain: I: PDB Molecule:l-fucose mutarotase; PDBTitle: crystal structure of bacterial fucu 70 d1j5ya2 not modelled 5.2 16 Fold:HPr-like Superfamily:Putative transcriptional regulator TM1602, C-terminal domain Family:Putative transcriptional regulator TM1602, 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