Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76071
DateThu Jan 5 12:18:09 GMT 2012
Unique Job IDf7a224221019c692

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1musa_
Top template information
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Transposase inhibitor (Tn5 transposase)
Confidence and coverage
Confidence: 98.3% Coverage: 60%
194 residues ( 60% of your sequence) have been modelled with 98.3% 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MSHQLTFADSEFSTKRRQTRKEIFLSRMEQILPWQNMTAVIEPFYPKAGNGRRPYPLETM
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   .........70.........80.........90.........100.........110.........120
Sequence  LRIHCMQHWYNLSDGAMEDALYEIASMRLFARLSLDSALPDRTTIMNFRHLLEQHQLARQ
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   .........130.........140.........150.........160.........170.........180
Sequence  LFKTINRWLAEAGVMMTQGTLVDATIIEAPSSTKNKEQQRDPEMHQTKKGNQWHFGMKAH
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   .........190.........200.........210.........220.........230.........240
Sequence  IGVDAKSGLTHSLVTTAANEHDLNQLGNLLHGEEQFVSADAGYQGAPQREELAEVDVDWL
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   .........250.........260.........270.........280.........290.........300
Sequence  IAERPGKVKTLKQNPRKNKTAINIEYMKASIRARVEHPFRIIKRQFGFVKARYKGLLKND
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   .........310.........320......
Sequence  NQLAMLFTLANLFRVDQMIRQWERSQ
Secondary structure 

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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 1mus chain A

3D model

Region: 106 - 309
Aligned: 194
Modelled: 204
Confidence: 98.3%
Identity: 13%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Transposase inhibitor (Tn5 transposase)

Phyre2

PDB 1b7e chain A

3D model

Region: 216 - 320
Aligned: 104
Modelled: 105
Confidence: 96.9%
Identity: 13%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Transposase inhibitor (Tn5 transposase)

Phyre2

PDB 1asu chain A

3D model

Region: 179 - 311
Aligned: 111
Modelled: 111
Confidence: 87.3%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1cxq chain A

3D model

Region: 132 - 311
Aligned: 130
Modelled: 132
Confidence: 84.1%
Identity: 22%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3nf9 chain A

3D model

Region: 179 - 311
Aligned: 108
Modelled: 111
Confidence: 69.3%
Identity: 14%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design

Phyre2

PDB 1a9x chain A domain 1

3D model

Region: 24 - 86
Aligned: 50
Modelled: 63
Confidence: 47.7%
Identity: 14%
Fold: Carbamoyl phosphate synthetase, large subunit connection domain
Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain
Family: Carbamoyl phosphate synthetase, large subunit connection domain

Phyre2

PDB 1c0m chain A domain 2

3D model

Region: 179 - 311
Aligned: 111
Modelled: 111
Confidence: 43.7%
Identity: 17%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 3f9k chain V

3D model

Region: 179 - 311
Aligned: 108
Modelled: 111
Confidence: 43.6%
Identity: 13%
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd

Phyre2

PDB 1bco chain A

3D model

Region: 132 - 285
Aligned: 114
Modelled: 116
Confidence: 35.9%
Identity: 15%
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain

Phyre2

PDB 1k6y chain B

3D model

Region: 179 - 311
Aligned: 99
Modelled: 102
Confidence: 24.1%
Identity: 15%
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase

Phyre2

PDB 3hef chain B

3D model

Region: 75 - 111
Aligned: 34
Modelled: 37
Confidence: 23.1%
Identity: 15%
PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit

Phyre2

PDB 1hyv chain A

3D model

Region: 179 - 314
Aligned: 103
Modelled: 107
Confidence: 21.4%
Identity: 15%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1c0m chain A

3D model

Region: 179 - 311
Aligned: 110
Modelled: 111
Confidence: 16.1%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase

Phyre2

PDB 1exq chain A

3D model

Region: 181 - 311
Aligned: 99
Modelled: 102
Confidence: 15.6%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1slm chain A domain 1

3D model

Region: 65 - 117
Aligned: 49
Modelled: 53
Confidence: 15.6%
Identity: 22%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2

PDB 3nzq chain B

3D model

Region: 60 - 105
Aligned: 46
Modelled: 46
Confidence: 13.4%
Identity: 17%
PDB header:lyase
Chain: B: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600

Phyre2

PDB 3n2o chain A

3D model

Region: 75 - 105
Aligned: 31
Modelled: 31
Confidence: 10.7%
Identity: 32%
PDB header:lyase
Chain: A: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: x-ray crystal structure of arginine decarboxylase complexed with2 arginine from vibrio vulnificus

Phyre2

PDB 1c6v chain A

3D model

Region: 176 - 311
Aligned: 100
Modelled: 103
Confidence: 10.0%
Identity: 16%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Retroviral integrase, catalytic domain

Phyre2

PDB 1k78 chain A domain 1

3D model

Region: 50 - 116
Aligned: 48
Modelled: 50
Confidence: 8.7%
Identity: 27%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 1bco chain A domain 2

3D model

Region: 132 - 250
Aligned: 102
Modelled: 103
Confidence: 8.1%
Identity: 14%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: mu transposase, core domain

Phyre2
1

d1musa_
2

d1b7ea_
3

d1asua_
4

d1cxqa_
5

c3nf9A_
6

d1a9xa1
7

d1c0ma2
8

c3f9kV_
9

c1bcoA_
10

c1k6yB_
11

c3hefB_
12

d1hyva_
13

c1c0mA_
14

d1exqa_
15

d1slma1
16

c3nzqB_
17

c3n2oA_
18

d1c6va_
19

d1k78a1
20

d1bcoa2
21



22



23



24



25



26



27



28



29



30



31






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1musa_



98.3 13 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Transposase inhibitor (Tn5 transposase)
2d1b7ea_



96.9 13 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Transposase inhibitor (Tn5 transposase)
3d1asua_



87.3 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
4d1cxqa_



84.1 22 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
5c3nf9A_



69.3 14 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
6d1a9xa1



47.7 14 Fold:Carbamoyl phosphate synthetase, large subunit connection domain
Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain
Family:Carbamoyl phosphate synthetase, large subunit connection domain
7d1c0ma2



43.7 17 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
8c3f9kV_



43.6 13 PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
9c1bcoA_



35.9 15 PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
10c1k6yB_



24.1 15 PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
11c3hefB_



23.1 15 PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit
12d1hyva_



21.4 15 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
13c1c0mA_



16.1 20 PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
14d1exqa_



15.6 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
15d1slma1



15.6 22 Fold:PGBD-like
Superfamily:PGBD-like
Family:MMP N-terminal domain
16c3nzqB_



13.4 17 PDB header:lyase
Chain: B: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: crystal structure of biosynthetic arginine decarboxylase adc (spea)2 from escherichia coli, northeast structural genomics consortium3 target er600
17c3n2oA_



10.7 32 PDB header:lyase
Chain: A: PDB Molecule:biosynthetic arginine decarboxylase;
PDBTitle: x-ray crystal structure of arginine decarboxylase complexed with2 arginine from vibrio vulnificus
18d1c6va_



10.0 16 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
19d1k78a1



8.7 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
20d1bcoa2



8.1 14 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
21d1sfka_



not modelled 7.7 13 Fold:Flavivirus capsid protein C
Superfamily:Flavivirus capsid protein C
Family:Flavivirus capsid protein C
22c1bg1A_



not modelled 7.5 15 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (transcription factor stat3b);
PDBTitle: transcription factor stat3b/dna complex
23c3pvpA_



not modelled 7.0 16 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa;
PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna
24d2vo1a1



not modelled 6.6 18 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
25d1s1ma2



not modelled 6.4 24 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
26d2fm9a1



not modelled 6.4 6 Fold:SipA N-terminal domain-like
Superfamily:SipA N-terminal domain-like
Family:SipA N-terminal domain-like
27d6paxa1



not modelled 6.3 29 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
28c3ostA_



not modelled 6.1 18 PDB header:lipid binding protein
Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4;
PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p
29d2ve8a1



not modelled 5.9 36 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FtsK C-terminal domain-like
30c1ex4A_



not modelled 5.9 17 PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
31c3nzpA_



not modelled 5.8 25 PDB header:lyase
Chain: A: PDB Molecule:arginine decarboxylase;
PDBTitle: crystal structure of the biosynthetic arginine decarboxylase spea from2 campylobacter jejuni, northeast structural genomics consortium target3 br53

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