Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AB03
DateThu Jan 5 11:14:16 GMT 2012
Unique Job ID82ecc2b3de4e7e37

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3f7wA_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:putative fructosamine-3-kinase;
PDBTitle: crystal structure of putative fructosamine-3-kinase (yp_290396.1) from2 thermobifida fusca yx-er1 at 1.85 a resolution
Confidence and coverage
Confidence: 98.6% Coverage: 87%
258 residues ( 87% of your sequence) have been modelled with 98.6% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MEQLRAELSHLLGEKLSRIECVNEKADTALWALYDSQGNPMPLMARSFSTPGKARQLAWK
Secondary structure 



















SS confidence 



























































Disorder  ??









































???????
?




?
Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  TTMLARSGTVRMPTIYGVMTHEEHPGPDVLLLERMRGVSVEAPARTPERWEQLKDQIVEA
Secondary structure 




























SS confidence 



























































Disorder  ????????




























???????????











Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  LLAWHRQDSRGCVGAVDNTQENFWPSWYRQHVEVLWTTLNQFNNTGLTMQDKRILFRTRE
Secondary structure 



















SS confidence 



























































Disorder 











???

























?
??


?










Disorder confidence 



























































 
   .........190.........200.........210.........220.........230.........240
Sequence  CLPALFEGFNDNCVLIHGNFCLRSMLKDSRSDQLLAMVGPGLMLWAPREYELFRLMDNSL
Secondary structure 

























SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........250.........260.........270.........280.........290.......
Sequence  AEDLLWSYLQRAPVAESFIWRRWLYVLWDEVAQLVNTGRFSRRNFDLASKSLLPWLA
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

RankAligned region

PDB 3f7w chain A

3D model

Region: 1 - 268
Aligned: 258
Modelled: 268
Confidence: 98.6%
Identity: 18%
PDB header:transferase
Chain: A: PDB Molecule:putative fructosamine-3-kinase;
PDBTitle: crystal structure of putative fructosamine-3-kinase (yp_290396.1) from2 thermobifida fusca yx-er1 at 1.85 a resolution

Phyre2

PDB 3csv chain A

3D model

Region: 31 - 282
Aligned: 234
Modelled: 252
Confidence: 97.6%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:aminoglycoside phosphotransferase;
PDBTitle: crystal structure of a putative aminoglycoside phosphotransferase2 (yp_614837.1) from silicibacter sp. tm1040 at 2.15 a resolution

Phyre2

PDB 1j7l chain A

3D model

Region: 62 - 270
Aligned: 192
Modelled: 209
Confidence: 97.4%
Identity: 18%
Fold: Protein kinase-like (PK-like)
Superfamily: Protein kinase-like (PK-like)
Family: APH phosphotransferases

Phyre2

PDB 3lzh chain A

3D model

Region: 2 - 275
Aligned: 261
Modelled: 266
Confidence: 97.0%
Identity: 12%
PDB header:transferase
Chain: A: PDB Molecule:aph(2")-id/aph(2")-iva;
PDBTitle: crystal structure of aminoglycoside phosphotransferase aph(2")-2 id/aph(2")-iva

Phyre2

PDB 3ovc chain A

3D model

Region: 3 - 275
Aligned: 262
Modelled: 271
Confidence: 97.0%
Identity: 14%
PDB header:transferase/antibiotic
Chain: A: PDB Molecule:hygromycin-b 4-o-kinase;
PDBTitle: crystal structure of aminoglycoside phosphotransferase aph(4)-ia

Phyre2

PDB 3jr1 chain A

3D model

Region: 2 - 268
Aligned: 245
Modelled: 267
Confidence: 97.0%
Identity: 16%
PDB header:transferase
Chain: A: PDB Molecule:putative fructosamine-3-kinase;
PDBTitle: crystal structure of putative fructosamine-3-kinase2 (yp_719053.1) from haemophilus somnus 129pt at 2.32 a3 resolution

Phyre2

PDB 1nd4 chain A

3D model

Region: 18 - 270
Aligned: 230
Modelled: 251
Confidence: 96.9%
Identity: 18%
Fold: Protein kinase-like (PK-like)
Superfamily: Protein kinase-like (PK-like)
Family: APH phosphotransferases

Phyre2

PDB 3ham chain A

3D model

Region: 1 - 293
Aligned: 280
Modelled: 291
Confidence: 96.2%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:aminoglycoside phosphotransferase;
PDBTitle: structure of the gentamicin-aph(2")-iia complex

Phyre2

PDB 3i0o chain A

3D model

Region: 2 - 269
Aligned: 258
Modelled: 262
Confidence: 95.6%
Identity: 15%
PDB header:transferase
Chain: A: PDB Molecule:spectinomycin phosphotransferase;
PDBTitle: crystal structure of spectinomycin phosphotransferase,2 aph(9)-ia, in complex with adp and spectinomcyin

Phyre2

PDB 3att chain A

3D model

Region: 64 - 274
Aligned: 202
Modelled: 209
Confidence: 94.7%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of rv3168 with atp

Phyre2

PDB 3dxp chain A

3D model

Region: 64 - 232
Aligned: 160
Modelled: 165
Confidence: 94.3%
Identity: 18%
PDB header:transferase
Chain: A: PDB Molecule:putative acyl-coa dehydrogenase;
PDBTitle: crystal structure of a putative aminoglycoside phosphotransferase2 (reut_a1007) from ralstonia eutropha jmp134 at 2.32 a resolution

Phyre2

PDB 2pul chain A domain 1

3D model

Region: 2 - 276
Aligned: 261
Modelled: 270
Confidence: 85.2%
Identity: 12%
Fold: Protein kinase-like (PK-like)
Superfamily: Protein kinase-like (PK-like)
Family: APH phosphotransferases

Phyre2

PDB 3r78 chain B

3D model

Region: 67 - 270
Aligned: 189
Modelled: 202
Confidence: 65.0%
Identity: 18%
PDB header:transferase
Chain: B: PDB Molecule:aminoglycoside 3'-phosphotransferase apha1-iab;
PDBTitle: crystal structure of the aminoglycoside phosphotransferase aph(3')-ia,2 atp-bound

Phyre2

PDB 2ply chain B

3D model

Region: 106 - 127
Aligned: 22
Modelled: 22
Confidence: 57.1%
Identity: 23%
PDB header:translation/rna
Chain: B: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna.

Phyre2

PDB 2v9v chain A domain 2

3D model

Region: 108 - 127
Aligned: 20
Modelled: 20
Confidence: 49.9%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: C-terminal fragment of elongation factor SelB

Phyre2

PDB 2xzn chain H

3D model

Region: 16 - 83
Aligned: 68
Modelled: 68
Confidence: 36.3%
Identity: 19%
PDB header:ribosome
Chain: H: PDB Molecule:ribosomal protein s8 containing protein;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2

Phyre2

PDB 1oy0 chain A

3D model

Region: 70 - 126
Aligned: 55
Modelled: 57
Confidence: 27.9%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: Phosphoenolpyruvate/pyruvate domain
Family: Ketopantoate hydroxymethyltransferase PanB

Phyre2

PDB 2fs1 chain A

3D model

Region: 104 - 121
Aligned: 18
Modelled: 18
Confidence: 22.6%
Identity: 50%
PDB header:protein binding
Chain: A: PDB Molecule:psd-1;
PDBTitle: solution structure of psd-1

Phyre2

PDB 1s1h chain H

3D model

Region: 34 - 83
Aligned: 49
Modelled: 50
Confidence: 22.1%
Identity: 18%
PDB header:ribosome
Chain: H: PDB Molecule:40s ribosomal protein s22;
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, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.

Phyre2

PDB 2gy9 chain H domain 1

3D model

Region: 37 - 83
Aligned: 47
Modelled: 47
Confidence: 19.9%
Identity: 26%
Fold: Ribosomal protein S8
Superfamily: Ribosomal protein S8
Family: Ribosomal protein S8

Phyre2
1

c3f7wA_
2

c3csvA_
3

d1j7la_
4

c3lzhA_
5

c3ovcA_
6

c3jr1A_
7

d1nd4a_
8

c3hamA_
9

c3i0oA_
10

c3attA_
11

c3dxpA_
12

d2pula1
13

c3r78B_
14

c2plyB_
15

d2v9va2
16

c2xznH_
17

d1oy0a_
18

c2fs1A_
19

c1s1hH_
20

d2gy9h1
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






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3f7wA_



98.6 18 PDB header:transferase
Chain: A: PDB Molecule:putative fructosamine-3-kinase;
PDBTitle: crystal structure of putative fructosamine-3-kinase (yp_290396.1) from2 thermobifida fusca yx-er1 at 1.85 a resolution
2c3csvA_



97.6 17 PDB header:transferase
Chain: A: PDB Molecule:aminoglycoside phosphotransferase;
PDBTitle: crystal structure of a putative aminoglycoside phosphotransferase2 (yp_614837.1) from silicibacter sp. tm1040 at 2.15 a resolution
3d1j7la_



97.4 18 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:APH phosphotransferases
4c3lzhA_



97.0 12 PDB header:transferase
Chain: A: PDB Molecule:aph(2")-id/aph(2")-iva;
PDBTitle: crystal structure of aminoglycoside phosphotransferase aph(2")-2 id/aph(2")-iva
5c3ovcA_



97.0 14 PDB header:transferase/antibiotic
Chain: A: PDB Molecule:hygromycin-b 4-o-kinase;
PDBTitle: crystal structure of aminoglycoside phosphotransferase aph(4)-ia
6c3jr1A_



97.0 16 PDB header:transferase
Chain: A: PDB Molecule:putative fructosamine-3-kinase;
PDBTitle: crystal structure of putative fructosamine-3-kinase2 (yp_719053.1) from haemophilus somnus 129pt at 2.32 a3 resolution
7d1nd4a_



96.9 18 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:APH phosphotransferases
8c3hamA_



96.2 14 PDB header:transferase
Chain: A: PDB Molecule:aminoglycoside phosphotransferase;
PDBTitle: structure of the gentamicin-aph(2")-iia complex
9c3i0oA_



95.6 15 PDB header:transferase
Chain: A: PDB Molecule:spectinomycin phosphotransferase;
PDBTitle: crystal structure of spectinomycin phosphotransferase,2 aph(9)-ia, in complex with adp and spectinomcyin
10c3attA_



94.7 17 PDB header:transferase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of rv3168 with atp
11c3dxpA_



94.3 18 PDB header:transferase
Chain: A: PDB Molecule:putative acyl-coa dehydrogenase;
PDBTitle: crystal structure of a putative aminoglycoside phosphotransferase2 (reut_a1007) from ralstonia eutropha jmp134 at 2.32 a resolution
12d2pula1



85.2 12 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:APH phosphotransferases
13c3r78B_



65.0 18 PDB header:transferase
Chain: B: PDB Molecule:aminoglycoside 3'-phosphotransferase apha1-iab;
PDBTitle: crystal structure of the aminoglycoside phosphotransferase aph(3')-ia,2 atp-bound
14c2plyB_



57.1 23 PDB header:translation/rna
Chain: B: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna.
15d2v9va2



49.9 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal fragment of elongation factor SelB
16c2xznH_



36.3 19 PDB header:ribosome
Chain: H: PDB Molecule:ribosomal protein s8 containing protein;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2
17d1oy0a_



27.9 20 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Ketopantoate hydroxymethyltransferase PanB
18c2fs1A_



22.6 50 PDB header:protein binding
Chain: A: PDB Molecule:psd-1;
PDBTitle: solution structure of psd-1
19c1s1hH_



22.1 18 PDB header:ribosome
Chain: H: PDB Molecule:40s ribosomal protein s22;
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, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.
20d2gy9h1



19.9 26 Fold:Ribosomal protein S8
Superfamily:Ribosomal protein S8
Family:Ribosomal protein S8
21d1gjsa_



not modelled 19.5 44 Fold:immunoglobulin/albumin-binding domain-like
Superfamily:Bacterial immunoglobulin/albumin-binding domains
Family:GA module, an albumin-binding domain
22c1nyqA_



not modelled 18.2 32 PDB header:ligase
Chain: A: PDB Molecule:threonyl-trna synthetase 1;
PDBTitle: structure of staphylococcus aureus threonyl-trna synthetase2 complexed with an analogue of threonyl adenylate
23d1i94h_



not modelled 17.7 24 Fold:Ribosomal protein S8
Superfamily:Ribosomal protein S8
Family:Ribosomal protein S8
24d1an7a_



not modelled 16.7 24 Fold:Ribosomal protein S8
Superfamily:Ribosomal protein S8
Family:Ribosomal protein S8
25d1seia_



not modelled 16.1 20 Fold:Ribosomal protein S8
Superfamily:Ribosomal protein S8
Family:Ribosomal protein S8
26d1na6a2



not modelled 14.7 25 Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:Type II restriction endonuclease catalytic domain
27c2v9vA_



not modelled 14.4 24 PDB header:transcription
Chain: A: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: crystal structure of moorella thermoacetica selb(377-511)
28c2pywA_



not modelled 13.7 15 PDB header:transferase
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: structure of a. thaliana 5-methylthioribose kinase in complex with adp2 and mtr
29c2q83A_



not modelled 13.0 13 PDB header:transferase
Chain: A: PDB Molecule:ytaa protein;
PDBTitle: crystal structure of ytaa (2635576) from bacillus subtilis at 2.50 a2 resolution
30c1qf6A_



not modelled 12.7 20 PDB header:ligase/rna
Chain: A: PDB Molecule:threonyl-trna synthetase;
PDBTitle: structure of e. coli threonyl-trna synthetase complexed with its2 cognate trna
31c3bbnH_



not modelled 12.2 22 PDB header:ribosome
Chain: H: PDB Molecule:ribosomal protein s8;
PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome.
32c3ez4B_



not modelled 12.1 27 PDB header:transferase
Chain: B: PDB Molecule:3-methyl-2-oxobutanoate hydroxymethyltransferase;
PDBTitle: crystal structure of 3-methyl-2-oxobutanoate2 hydroxymethyltransferase from burkholderia pseudomallei
33d1m9fd_



not modelled 11.8 19 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
34d1zyla1



not modelled 11.0 13 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:APH phosphotransferases
35d1ve2a1



not modelled 10.9 23 Fold:Tetrapyrrole methylase
Superfamily:Tetrapyrrole methylase
Family:Tetrapyrrole methylase
36c2pqrD_



not modelled 10.8 88 PDB header:apoptosis
Chain: D: PDB Molecule:wd repeat protein ykr036c;
PDBTitle: crystal structure of yeast fis1 complexed with a fragment of yeast2 caf4
37d2ppqa1



not modelled 10.8 14 Fold:Protein kinase-like (PK-like)
Superfamily:Protein kinase-like (PK-like)
Family:APH phosphotransferases
38c3dxqB_



not modelled 10.7 13 PDB header:transferase
Chain: B: PDB Molecule:choline/ethanolamine kinase family protein;
PDBTitle: crystal structure of choline/ethanolamine kinase family protein2 (np_106042.1) from mesorhizobium loti at 2.55 a resolution
39c2f3iA_



not modelled 10.4 25 PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerases i, ii, and iii 17.1
PDBTitle: solution structure of a subunit of rna polymerase ii
40d1m9dc_



not modelled 10.2 19 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
41c2kdnA_



not modelled 9.6 36 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c;
PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum.
42c2wlvA_



not modelled 9.6 22 PDB header:virus protein
Chain: A: PDB Molecule:gag polyprotein;
PDBTitle: structure of the n-terminal capsid domain of hiv-2
43d1w0ba_



not modelled 9.0 43 Fold:Spectrin repeat-like
Superfamily:Alpha-hemoglobin stabilizing protein AHSP
Family:Alpha-hemoglobin stabilizing protein AHSP
44d1nyra4



not modelled 9.0 30 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
45c3cf6E_



not modelled 8.9 39 PDB header:signaling protein/gtp-binding protein
Chain: E: PDB Molecule:rap guanine nucleotide exchange factor (gef) 4;
PDBTitle: structure of epac2 in complex with cyclic-amp and rap
46c3tr7A_



not modelled 8.7 32 PDB header:hydrolase
Chain: A: PDB Molecule:uracil-dna glycosylase;
PDBTitle: structure of a uracil-dna glycosylase (ung) from coxiella burnetii
47d1upka_



not modelled 8.6 21 Fold:alpha-alpha superhelix
Superfamily:ARM repeat
Family:Mo25 protein
48c1na6B_



not modelled 8.5 25 PDB header:hydrolase
Chain: B: PDB Molecule:restriction endonuclease ecorii;
PDBTitle: crystal structure of restriction endonuclease ecorii mutant2 r88a
49d1m3ua_



not modelled 7.9 11 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Ketopantoate hydroxymethyltransferase PanB
50d2cqqa1



not modelled 7.6 40 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
51c2f5xC_



not modelled 7.4 21 PDB header:transport protein
Chain: C: PDB Molecule:bugd;
PDBTitle: structure of periplasmic binding protein bugd
52d1z8ua1



not modelled 7.2 43 Fold:Spectrin repeat-like
Superfamily:Alpha-hemoglobin stabilizing protein AHSP
Family:Alpha-hemoglobin stabilizing protein AHSP
53c3lyrA_



not modelled 6.9 47 PDB header:transcription activator
Chain: A: PDB Molecule:transcription factor coe1;
PDBTitle: human early b-cell factor 1 (ebf1) dna-binding domain
54c3cdxB_



not modelled 6.4 28 PDB header:hydrolase
Chain: B: PDB Molecule:succinylglutamatedesuccinylase/aspartoacylase;
PDBTitle: crystal structure of2 succinylglutamatedesuccinylase/aspartoacylase from3 rhodobacter sphaeroides
55d1ouoa_



not modelled 6.4 25 Fold:His-Me finger endonucleases
Superfamily:His-Me finger endonucleases
Family:Endonuclease I
56d1l9bh2



not modelled 5.6 100 Fold:Single transmembrane helix
Superfamily:Photosystem II reaction centre subunit H, transmembrane region
Family:Photosystem II reaction centre subunit H, transmembrane region
57c2owrD_



not modelled 5.2 6 PDB header:hydrolase
Chain: D: PDB Molecule:uracil-dna glycosylase;
PDBTitle: crystal structure of vaccinia virus uracil-dna glycosylase
58d2f1fa1



not modelled 5.1 33 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
59d2fgca2



not modelled 5.1 28 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like

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