Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77779
DateThu Jan 5 12:32:45 GMT 2012
Unique Job IDf3c6b0c7d5189d78

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3mswA_
Top template information
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a protein with unknown function (bf3112) from2 bacteroides fragilis nctc 9343 at 1.90 a resolution
Confidence and coverage
Confidence: 70.3% Coverage: 7%
34 residues ( 7% of your sequence) have been modelled with 70.3% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MWPDNRIARDAHYLYRYDRHGRLTEKTDLIPEGVIRTDDERTHRYHYDSQHRLVHYTRTQ
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Disorder  ?????
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?????????





















?
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   .........70.........80.........90.........100.........110.........120
Sequence  YAEPLVESRYLYDPLGRRVAKRVWRRERDLTGWMSLSRKPQVTWYGWDGDRLTTIQNDRT
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   .........130.........140.........150.........160.........170.........180
Sequence  RIQTIYQPGSFTPLIRVETATGELAKTQRRSLADTLQQSGGEDGGSVVFPPVLVQMLDRL
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   .........190.........200.........210.........220.........230.........240
Sequence  ESEILADRVSEESRRWLASCGLTVEQMQNQMDPVYTPARKIHLYHCDHRGLPLALVSTEG
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   .........250.........260.........270.........280.........290.........300
Sequence  ATEWCAEYDEWGNLLNEENPHQLQQLIRLPGQQYDEESGLYYNRHRYYDPLQGRYITQDP
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   .........310.........320.........330.........340.........350.........360
Sequence  IGLKGGWNFYQYPLNPVQYIDSMGLASKYGHLNNGGYGARPNKPPTPDPSKLPDIAKQLR
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?

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??
????
??????
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   .........370.........380.........390.........400.........410.........420
Sequence  LPYPIDQASSAPNVFKTFFRALSPYDYTLYCRKWVKPNLTCTPQDDSQYPGMDTKTASDY
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Disorder 
?????
??
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?????????????

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   .........430.........440.........450.........460.........470.......
Sequence  LPQTNWPTTQLPPGYTCAEPYLFPDINKPDGPATAGIDDLGEILAKMKQRTSRGIRK
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????????
















?????
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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 3msw chain A

3D model

Region: 4 - 53
Aligned: 34
Modelled: 34
Confidence: 70.3%
Identity: 26%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a protein with unknown function (bf3112) from2 bacteroides fragilis nctc 9343 at 1.90 a resolution

Phyre2

PDB 2zxe chain B

3D model

Region: 336 - 448
Aligned: 98
Modelled: 113
Confidence: 53.9%
Identity: 16%
PDB header:hydrolase/transport protein
Chain: B: PDB Molecule:na+,k+-atpase beta subunit;
PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state

Phyre2

PDB 1bds chain A

3D model

Region: 385 - 404
Aligned: 18
Modelled: 17
Confidence: 40.2%
Identity: 56%
Fold: Defensin-like
Superfamily: Defensin-like
Family: Defensin

Phyre2

PDB 1x3z chain A domain 1

3D model

Region: 287 - 320
Aligned: 32
Modelled: 34
Confidence: 36.1%
Identity: 22%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Transglutaminase core

Phyre2

PDB 2yy0 chain D

3D model

Region: 451 - 473
Aligned: 23
Modelled: 23
Confidence: 19.9%
Identity: 30%
PDB header:transcription
Chain: D: PDB Molecule:c-myc-binding protein;
PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens

Phyre2

PDB 2b5i chain D domain 2

3D model

Region: 379 - 402
Aligned: 24
Modelled: 24
Confidence: 19.4%
Identity: 38%
Fold: Complement control module/SCR domain
Superfamily: Complement control module/SCR domain
Family: Complement control module/SCR domain

Phyre2

PDB 3ga2 chain A

3D model

Region: 348 - 380
Aligned: 33
Modelled: 33
Confidence: 17.2%
Identity: 33%
PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease_v (bsu36170) from2 bacillus subtilis, northeast structural genomics3 consortium target sr624

Phyre2

PDB 2p0s chain A domain 1

3D model

Region: 453 - 468
Aligned: 16
Modelled: 16
Confidence: 16.2%
Identity: 44%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: PG0945 N-terminal domain-like

Phyre2

PDB 1f00 chain I domain 2

3D model

Region: 305 - 331
Aligned: 27
Modelled: 27
Confidence: 14.1%
Identity: 30%
Fold: Immunoglobulin-like beta-sandwich
Superfamily: Invasin/intimin cell-adhesion fragments
Family: Invasin/intimin cell-adhesion fragments

Phyre2

PDB 3esw chain A

3D model

Region: 287 - 320
Aligned: 32
Modelled: 34
Confidence: 13.6%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.

Phyre2

PDB 3bi7 chain A domain 1

3D model

Region: 45 - 72
Aligned: 28
Modelled: 28
Confidence: 10.8%
Identity: 25%
Fold: PUA domain-like
Superfamily: PUA domain-like
Family: SRA domain-like

Phyre2

PDB 2pb7 chain A

3D model

Region: 45 - 71
Aligned: 27
Modelled: 27
Confidence: 10.5%
Identity: 26%
PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1;
PDBTitle: crystal structure of the sra domain of the human uhrf12 protein

Phyre2

PDB 3swy chain B

3D model

Region: 465 - 473
Aligned: 9
Modelled: 9
Confidence: 10.3%
Identity: 67%
PDB header:transport protein
Chain: B: PDB Molecule:cyclic nucleotide-gated cation channel alpha-3;
PDBTitle: cnga3 626-672 containing clz domain

Phyre2

PDB 2f4m chain A domain 1

3D model

Region: 287 - 320
Aligned: 34
Modelled: 34
Confidence: 9.9%
Identity: 24%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Transglutaminase core

Phyre2

PDB 2zkd chain A domain 1

3D model

Region: 45 - 72
Aligned: 28
Modelled: 28
Confidence: 9.7%
Identity: 25%
Fold: PUA domain-like
Superfamily: PUA domain-like
Family: SRA domain-like

Phyre2

PDB 1bco chain A domain 1

3D model

Region: 279 - 296
Aligned: 18
Modelled: 18
Confidence: 9.7%
Identity: 17%
Fold: mu transposase, C-terminal domain
Superfamily: mu transposase, C-terminal domain
Family: mu transposase, C-terminal domain

Phyre2

PDB 1nln chain A

3D model

Region: 303 - 326
Aligned: 24
Modelled: 24
Confidence: 9.5%
Identity: 21%
Fold: Cysteine proteinases
Superfamily: Cysteine proteinases
Family: Adenain-like

Phyre2

PDB 3nfv chain A

3D model

Region: 422 - 451
Aligned: 30
Modelled: 30
Confidence: 9.3%
Identity: 40%
PDB header:lyase
Chain: A: PDB Molecule:alginate lyase;
PDBTitle: crystal structure of an alginate lyase (bacova_01668) from bacteroides2 ovatus at 1.95 a resolution

Phyre2

PDB 3q0b chain X

3D model

Region: 45 - 72
Aligned: 28
Modelled: 28
Confidence: 9.2%
Identity: 14%
PDB header:transferase/dna
Chain: X: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-9 specific
PDBTitle: crystal structure of suvh5 sra- fully methylated cg dna complex in2 space group p42212

Phyre2

PDB 3lhr chain A

3D model

Region: 369 - 399
Aligned: 31
Modelled: 31
Confidence: 9.1%
Identity: 32%
PDB header:transcription regulator
Chain: A: PDB Molecule:zinc finger protein 24;
PDBTitle: crystal structure of the scan domain from human znf24

Phyre2
1

c3mswA_
2

c2zxeB_
3

d1bdsa_
4

d1x3za1
5

c2yy0D_
6

d2b5id2
7

c3ga2A_
8

d2p0sa1
9

d1f00i2
10

c3eswA_
11

d3bi7a1
12

c2pb7A_
13

c3swyB_
14

d2f4ma1
15

d2zkda1
16

d1bcoa1
17

d1nlna_
18

c3nfvA_
19

c3q0bX_
20

c3lhrA_
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






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3mswA_



70.3 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a protein with unknown function (bf3112) from2 bacteroides fragilis nctc 9343 at 1.90 a resolution
2c2zxeB_



53.9 16 PDB header:hydrolase/transport protein
Chain: B: PDB Molecule:na+,k+-atpase beta subunit;
PDBTitle: crystal structure of the sodium - potassium pump in the e2.2k+.pi2 state
3d1bdsa_



40.2 56 Fold:Defensin-like
Superfamily:Defensin-like
Family:Defensin
4d1x3za1



36.1 22 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:Transglutaminase core
5c2yy0D_



19.9 30 PDB header:transcription
Chain: D: PDB Molecule:c-myc-binding protein;
PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens
6d2b5id2



19.4 38 Fold:Complement control module/SCR domain
Superfamily:Complement control module/SCR domain
Family:Complement control module/SCR domain
7c3ga2A_



17.2 33 PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease v;
PDBTitle: crystal structure of the endonuclease_v (bsu36170) from2 bacillus subtilis, northeast structural genomics3 consortium target sr624
8d2p0sa1



16.2 44 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:PG0945 N-terminal domain-like
9d1f00i2



14.1 30 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Invasin/intimin cell-adhesion fragments
Family:Invasin/intimin cell-adhesion fragments
10c3eswA_



13.6 22 PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.
11d3bi7a1



10.8 25 Fold:PUA domain-like
Superfamily:PUA domain-like
Family:SRA domain-like
12c2pb7A_



10.5 26 PDB header:ligase
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1;
PDBTitle: crystal structure of the sra domain of the human uhrf12 protein
13c3swyB_



10.3 67 PDB header:transport protein
Chain: B: PDB Molecule:cyclic nucleotide-gated cation channel alpha-3;
PDBTitle: cnga3 626-672 containing clz domain
14d2f4ma1



9.9 24 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:Transglutaminase core
15d2zkda1



9.7 25 Fold:PUA domain-like
Superfamily:PUA domain-like
Family:SRA domain-like
16d1bcoa1



9.7 17 Fold:mu transposase, C-terminal domain
Superfamily:mu transposase, C-terminal domain
Family:mu transposase, C-terminal domain
17d1nlna_



9.5 21 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:Adenain-like
18c3nfvA_



9.3 40 PDB header:lyase
Chain: A: PDB Molecule:alginate lyase;
PDBTitle: crystal structure of an alginate lyase (bacova_01668) from bacteroides2 ovatus at 1.95 a resolution
19c3q0bX_



9.2 14 PDB header:transferase/dna
Chain: X: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-9 specific
PDBTitle: crystal structure of suvh5 sra- fully methylated cg dna complex in2 space group p42212
20c3lhrA_



9.1 32 PDB header:transcription regulator
Chain: A: PDB Molecule:zinc finger protein 24;
PDBTitle: crystal structure of the scan domain from human znf24
21c3e21A_



not modelled 8.7 29 PDB header:apoptosis
Chain: A: PDB Molecule:fas-associated factor 1;
PDBTitle: crystal structure of faf-1 uba domain
22d1brwa3



not modelled 8.3 26 Fold:alpha/beta-Hammerhead
Superfamily:Pyrimidine nucleoside phosphorylase C-terminal domain
Family:Pyrimidine nucleoside phosphorylase C-terminal domain
23d2zo1b1



not modelled 8.2 26 Fold:PUA domain-like
Superfamily:PUA domain-like
Family:SRA domain-like
24d2fi2a1



not modelled 8.1 40 Fold:Acyl carrier protein-like
Superfamily:Retrovirus capsid dimerization domain-like
Family:SCAN domain
25d2tpta3



not modelled 7.5 19 Fold:alpha/beta-Hammerhead
Superfamily:Pyrimidine nucleoside phosphorylase C-terminal domain
Family:Pyrimidine nucleoside phosphorylase C-terminal domain
26c3osvC_



not modelled 7.4 17 PDB header:structural protein
Chain: C: PDB Molecule:flagellar basal-body rod modification protein flgd;
PDBTitle: the crytsal structure of flgd from p. aeruginosa
27d1y7qa1



not modelled 6.9 56 Fold:Acyl carrier protein-like
Superfamily:Retrovirus capsid dimerization domain-like
Family:SCAN domain
28c3i08D_



not modelled 6.8 28 PDB header:signaling protein
Chain: D: PDB Molecule:neurogenic locus notch homolog protein 1;
PDBTitle: crystal structure of the s1-cleaved notch1 negative2 regulatory region (nrr)
29d1pk6c_



not modelled 6.8 27 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
30c2wbmA_



not modelled 6.7 26 PDB header:rna-binding protein
Chain: A: PDB Molecule:ribosome maturation protein sdo1 homolog;
PDBTitle: crystal structure of mthsbds, the homologue of the2 shwachman-bodian-diamond syndrome protein in the3 euriarchaeon methanothermobacter thermautotrophicus
31c2ka3C_



not modelled 6.5 36 PDB header:structural protein
Chain: C: PDB Molecule:emilin-1;
PDBTitle: structure of emilin-1 c1q-like domain
32c1t95A_



not modelled 6.5 22 PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein af0491;
PDBTitle: crystal structure of the shwachman-bodian-diamond syndrome2 protein orthologue from archaeoglobus fulgidus
33c1v7fA_



not modelled 6.4 67 PDB header:toxin
Chain: A: PDB Molecule:phrixotoxin 1;
PDBTitle: solution structure of phrixotoxin 1
34d1v7fa_



not modelled 6.4 67 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:omega toxin-like
Family:Spider toxins
35c2ketA_



not modelled 6.4 60 PDB header:antibiotic
Chain: A: PDB Molecule:cathelicidin-6;
PDBTitle: solution structure of bmap-27
36d2doaa1



not modelled 6.3 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ELL N2 domain-like
37c1hcwA_



not modelled 6.3 42 PDB header:growth response protein
Chain: A: PDB Molecule:bba1;
PDBTitle: 23-residue designed metal-free peptide based on the zinc2 finger domains, nmr, 35 structures
38d1pk6b_



not modelled 6.2 27 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
39d1zud21



not modelled 6.0 18 Fold:beta-Grasp (ubiquitin-like)
Superfamily:MoaD/ThiS
Family:ThiS
40d1pk6a_



not modelled 6.0 27 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
41c2kdoA_



not modelled 5.9 27 PDB header:rna binding protein
Chain: A: PDB Molecule:ribosome maturation protein sbds;
PDBTitle: structure of the human shwachman-bodian-diamond syndrome protein, sbds
42d1f1sa3



not modelled 5.8 27 Fold:Hyaluronate lyase-like, C-terminal domain
Superfamily:Hyaluronate lyase-like, C-terminal domain
Family:Hyaluronate lyase-like, C-terminal domain
43c2l16A_



not modelled 5.8 55 PDB header:protein transport
Chain: A: PDB Molecule:sec-independent protein translocase protein tatad;
PDBTitle: solution structure of bacillus subtilits tatad protein in dpc micelles
44c2x12A_



not modelled 5.6 27 PDB header:cell adhesion
Chain: A: PDB Molecule:fimbriae-associated protein fap1;
PDBTitle: ph-induced modulation of streptococcus parasanguinis2 adhesion by fap1 fimbriae
45d1w9pa2



not modelled 5.6 18 Fold:FKBP-like
Superfamily:Chitinase insertion domain
Family:Chitinase insertion domain
46d1ei5a1



not modelled 5.6 38 Fold:Streptavidin-like
Superfamily:D-aminopeptidase, middle and C-terminal domains
Family:D-aminopeptidase, middle and C-terminal domains
47d1s6la1



not modelled 5.6 33 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MerB N-terminal domain-like
48c3vg8F_



not modelled 5.5 38 PDB header:unknown function
Chain: F: PDB Molecule:hypothetical protein tthb210;
PDBTitle: crystal structure of hypothetical protein tthb210 from thermus2 thermophilus hb8
49d1zaka2



not modelled 5.4 33 Fold:Rubredoxin-like
Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain
Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
50d1wiba_



not modelled 5.4 24 Fold:Ribosomal L11/L12e N-terminal domain
Superfamily:Ribosomal L11/L12e N-terminal domain
Family:Ribosomal L11/L12e N-terminal domain
51c1gr3A_



not modelled 5.3 45 PDB header:collagen
Chain: A: PDB Molecule:collagen x;
PDBTitle: structure of the human collagen x nc1 trimer
52d1gr3a_



not modelled 5.3 45 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
53c1o91B_



not modelled 5.3 27 PDB header:collagen
Chain: B: PDB Molecule:collagen alpha 1(viii) chain;
PDBTitle: crystal structure of a collagen viii nc1 domain trimer
54d1o91a_



not modelled 5.3 27 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
55d1c3ha_



not modelled 5.2 31 Fold:TNF-like
Superfamily:TNF-like
Family:TNF-like
56d2vl8a1



not modelled 5.2 74 Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Glycosylating toxin catalytic domain-like
57d2pfxa1



not modelled 5.1 19 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
58c1jjoE_



not modelled 5.1 22 PDB header:signaling protein
Chain: E: PDB Molecule:neuroserpin;
PDBTitle: crystal structure of mouse neuroserpin (cleaved form)
59c7apiB_



not modelled 5.0 6 PDB header:proteinase inhibitor
Chain: B: PDB Molecule:alpha 1-antitrypsin;
PDBTitle: the s variant of human alpha1-antitrypsin, structure and implications2 for function and metabolism
60d2cr5a1



not modelled 5.0 27 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:UBX 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