Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionD6VPM8
DateMon Jul 2 19:10:02 BST 2012
Unique Job IDdcb9f5d08c9cc38c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d2cqra1
Top template information
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
Confidence and coverage
Confidence: 46.3% Coverage: 22%
40 residues ( 22% of your sequence) have been modelled with 46.3% 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  MINFLLFVLTILATLTNIWFSGVLSPAMVIRICLGGSMVVLQIWSFSRPISNETFRTKLL
Secondary structure 
SS confidence 
Disorder  ??
???
??
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LEVITHRPSIAGKEWKTITYNMNQYLFKAGLWKTPYHFFCEHQCYEFFKDLIKGKYPDVQ
Secondary structure 
SS confidence 
Disorder 
???
???
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........
Sequence  WDTANTQPFISVPENQAATQNSDVEPTVKWCLFKAAEIQAHAVREYWQSQYPDVGIPAI
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 2cqr chain A domain 1

3D model

Region: 58 - 111
Aligned: 40
Modelled: 40
Confidence: 46.3%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Myb/SANT domain

Phyre2

PDB 2cqq chain A domain 1

3D model

Region: 58 - 111
Aligned: 39
Modelled: 39
Confidence: 33.7%
Identity: 15%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Myb/SANT domain

Phyre2

PDB 2d9a chain A

3D model

Region: 58 - 115
Aligned: 41
Modelled: 44
Confidence: 27.0%
Identity: 15%
PDB header:transcription
Chain: A: PDB Molecule:myb-related protein b;
PDBTitle: solution structure of rsgi ruh-050, a myb dna-binding2 domain in mouse cdna

Phyre2

PDB 2din chain A

3D model

Region: 58 - 124
Aligned: 48
Modelled: 44
Confidence: 25.9%
Identity: 21%
PDB header:dna binding protein
Chain: A: PDB Molecule:cell division cycle 5-like protein;
PDBTitle: solution structure of the myb_dna-binding domain of human2 cell division cycle 5-like protein

Phyre2

PDB 1wgx chain A

3D model

Region: 54 - 120
Aligned: 53
Modelled: 53
Confidence: 25.9%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Myb/SANT domain

Phyre2

PDB 2yus chain A

3D model

Region: 58 - 123
Aligned: 48
Modelled: 52
Confidence: 25.3%
Identity: 19%
PDB header:transcription
Chain: A: PDB Molecule:swi/snf-related matrix-associated actin-
PDBTitle: solution structure of the sant domain of human swi/snf-2 related matrix-associated actin-dependent regulator of3 chromatin subfamily c member 1

Phyre2

PDB 3fov chain A

3D model

Region: 62 - 100
Aligned: 39
Modelled: 52
Confidence: 22.1%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0102 protein rpa0323;
PDBTitle: crystal structure of protein rpa0323 of unknown function from2 rhodopseudomonas palustris

Phyre2

PDB 4eef chain I

3D model

Region: 58 - 82
Aligned: 25
Modelled: 25
Confidence: 20.4%
Identity: 8%
PDB header:immune system/inhibitor
Chain: I: PDB Molecule:f-hb80.4, designed hemagglutinin binding protein;
PDBTitle: crystal structure of the designed inhibitor protein f-hb80.4 in2 complex with the 1918 influenza virus hemagglutinin.

Phyre2

PDB 1un2 chain A

3D model

Region: 60 - 102
Aligned: 42
Modelled: 43
Confidence: 19.6%
Identity: 17%
Fold: Thioredoxin fold
Superfamily: Thioredoxin-like
Family: DsbA-like

Phyre2

PDB 3l9v chain E

3D model

Region: 70 - 102
Aligned: 33
Modelled: 33
Confidence: 16.7%
Identity: 12%
PDB header:oxidoreductase
Chain: E: PDB Molecule:putative thiol-disulfide isomerase or thioredoxin;
PDBTitle: crystal structure of salmonella enterica serovar typhimurium srga

Phyre2

PDB 2f76 chain X domain 1

3D model

Region: 36 - 90
Aligned: 55
Modelled: 33
Confidence: 15.6%
Identity: 20%
Fold: Retroviral matrix proteins
Superfamily: Retroviral matrix proteins
Family: Mason-Pfizer monkey virus matrix protein

Phyre2

PDB 2ebi chain A

3D model

Region: 68 - 111
Aligned: 34
Modelled: 44
Confidence: 15.6%
Identity: 21%
PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding protein gt-1;
PDBTitle: arabidopsis gt-1 dna-binding domain with t133d phosphomimetic mutation

Phyre2

PDB 3c7m chain B

3D model

Region: 50 - 102
Aligned: 52
Modelled: 53
Confidence: 15.4%
Identity: 10%
PDB header:oxidoreductase
Chain: B: PDB Molecule:thiol:disulfide interchange protein dsba-like;
PDBTitle: crystal structure of reduced dsbl

Phyre2

PDB 2kdt chain A

3D model

Region: 41 - 67
Aligned: 27
Modelled: 53
Confidence: 14.7%
Identity: 11%
PDB header:protein transport
Chain: A: PDB Molecule:neuroendocrine convertase 1;
PDBTitle: pc1/3 dcsg sorting domain structure in dpc

Phyre2

PDB 1q5z chain A

3D model

Region: 56 - 68
Aligned: 13
Modelled: 13
Confidence: 14.6%
Identity: 54%
Fold: Invasion protein A (SipA) , C-terminal actin binding domain
Superfamily: Invasion protein A (SipA) , C-terminal actin binding domain
Family: Invasion protein A (SipA) , C-terminal actin binding domain

Phyre2

PDB 1q5z chain A

3D model

Region: 56 - 68
Aligned: 13
Modelled: 13
Confidence: 14.6%
Identity: 54%
PDB header:cell invasion
Chain: A: PDB Molecule:sipa;
PDBTitle: crystal structure of the c-terminal actin binding domain of2 salmonella invasion protein a (sipa)

Phyre2

PDB 1kkx chain A

3D model

Region: 55 - 83
Aligned: 28
Modelled: 29
Confidence: 13.5%
Identity: 11%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: ARID-like
Family: ARID domain

Phyre2

PDB 3gyk chain C

3D model

Region: 64 - 102
Aligned: 39
Modelled: 29
Confidence: 12.9%
Identity: 13%
PDB header:oxidoreductase
Chain: C: PDB Molecule:27kda outer membrane protein;
PDBTitle: the crystal structure of a thioredoxin-like oxidoreductase from2 silicibacter pomeroyi dss-3

Phyre2

PDB 3gn3 chain B

3D model

Region: 70 - 102
Aligned: 33
Modelled: 33
Confidence: 12.6%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative protein-disulfide isomerase;
PDBTitle: crystal structure of a putative protein-disulfide isomerase from2 pseudomonas syringae to 2.5a resolution.

Phyre2

PDB 1ig6 chain A

3D model

Region: 55 - 83
Aligned: 28
Modelled: 29
Confidence: 12.2%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: ARID-like
Family: ARID domain

Phyre2
1
d2cqra1
2
d2cqqa1
3
c2d9aA_
4
c2dinA_
5
d1wgxa_
6
c2yusA_
7
c3fovA_
8
c4eefI_
9
d1un2a_
10
c3l9vE_
11
d2f76x1
12
c2ebiA_
13
c3c7mB_
14
c2kdtA_
15
d1q5za_
16
c1q5zA_
17
d1kkxa_
18
c3gykC_
19
c3gn3B_
20
d1ig6a_
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
1d2cqra1
46.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
2d2cqqa1
33.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
3c2d9aA_
27.0 15 PDB header:transcription
Chain: A: PDB Molecule:myb-related protein b;
PDBTitle: solution structure of rsgi ruh-050, a myb dna-binding2 domain in mouse cdna
4c2dinA_
25.9 21 PDB header:dna binding protein
Chain: A: PDB Molecule:cell division cycle 5-like protein;
PDBTitle: solution structure of the myb_dna-binding domain of human2 cell division cycle 5-like protein
5d1wgxa_
25.9 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
6c2yusA_
25.3 19 PDB header:transcription
Chain: A: PDB Molecule:swi/snf-related matrix-associated actin-
PDBTitle: solution structure of the sant domain of human swi/snf-2 related matrix-associated actin-dependent regulator of3 chromatin subfamily c member 1
7c3fovA_
22.1 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0102 protein rpa0323;
PDBTitle: crystal structure of protein rpa0323 of unknown function from2 rhodopseudomonas palustris
8c4eefI_
20.4 8 PDB header:immune system/inhibitor
Chain: I: PDB Molecule:f-hb80.4, designed hemagglutinin binding protein;
PDBTitle: crystal structure of the designed inhibitor protein f-hb80.4 in2 complex with the 1918 influenza virus hemagglutinin.
9d1un2a_
19.6 17 Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:DsbA-like
10c3l9vE_
16.7 12 PDB header:oxidoreductase
Chain: E: PDB Molecule:putative thiol-disulfide isomerase or thioredoxin;
PDBTitle: crystal structure of salmonella enterica serovar typhimurium srga
11d2f76x1
15.6 20 Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:Mason-Pfizer monkey virus matrix protein
12c2ebiA_
15.6 21 PDB header:dna binding protein
Chain: A: PDB Molecule:dna binding protein gt-1;
PDBTitle: arabidopsis gt-1 dna-binding domain with t133d phosphomimetic mutation
13c3c7mB_
15.4 10 PDB header:oxidoreductase
Chain: B: PDB Molecule:thiol:disulfide interchange protein dsba-like;
PDBTitle: crystal structure of reduced dsbl
14c2kdtA_
14.7 11 PDB header:protein transport
Chain: A: PDB Molecule:neuroendocrine convertase 1;
PDBTitle: pc1/3 dcsg sorting domain structure in dpc
15d1q5za_
14.6 54 Fold:Invasion protein A (SipA) , C-terminal actin binding domain
Superfamily:Invasion protein A (SipA) , C-terminal actin binding domain
Family:Invasion protein A (SipA) , C-terminal actin binding domain
16c1q5zA_
14.6 54 PDB header:cell invasion
Chain: A: PDB Molecule:sipa;
PDBTitle: crystal structure of the c-terminal actin binding domain of2 salmonella invasion protein a (sipa)
17d1kkxa_
13.5 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:ARID-like
Family:ARID domain
18c3gykC_
12.9 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:27kda outer membrane protein;
PDBTitle: the crystal structure of a thioredoxin-like oxidoreductase from2 silicibacter pomeroyi dss-3
19c3gn3B_
12.6 15 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative protein-disulfide isomerase;
PDBTitle: crystal structure of a putative protein-disulfide isomerase from2 pseudomonas syringae to 2.5a resolution.
20d1ig6a_
12.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:ARID-like
Family:ARID domain
21c2cjjA_
not modelled 11.0 8 PDB header:dna-binding protein
Chain: A: PDB Molecule:radialis;
PDBTitle: crystal structure of the myb domain of the rad2 transcription factor from antirrhinum majus
22d2cjja1
not modelled 11.0 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
23d1mwpa_
not modelled 10.7 25 Fold:SRCR-like
Superfamily:A heparin-binding domain
Family:A heparin-binding domain
24d1c20a_
not modelled 10.1 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:ARID-like
Family:ARID domain
25c3kzqE_
not modelled 10.0 9 PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:putative uncharacterized protein vp2116;
PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633
26c3hd5A_
not modelled 10.0 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:thiol:disulfide interchange protein dsba;
PDBTitle: crystal structure of a thiol:disulfide interchange protein2 dsba from bordetella parapertussis
27d2g3ra1
not modelled 9.8 18 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
28c2eqyA_
not modelled 9.6 18 PDB header:dna binding protein
Chain: A: PDB Molecule:jumonji, at rich interactive domain 1b;
PDBTitle: solution structure of the arid domain of jarid1b protein
29c2lm1A_
not modelled 9.2 14 PDB header:dna binding protein
Chain: A: PDB Molecule:lysine-specific demethylase lid;
PDBTitle: solution nmr structure of lysine-specific demethylase lid from2 drosophila melanogaster, northeast structural genomics consortium3 target fr824d
30c4ffeX_
not modelled 9.2 21 PDB header:viral protein
Chain: X: PDB Molecule:cpxv018 protein;
PDBTitle: the structure of cowpox virus cpxv018 (omcp)
31c2jxjA_
not modelled 8.8 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:histone demethylase jarid1a;
PDBTitle: nmr structure of the arid domain from the histone h3k42 demethylase rbp2
32c3mopC_
not modelled 8.2 14 PDB header:signaling protein, immune system
Chain: C: PDB Molecule:myeloid differentiation primary response protein myd88;
PDBTitle: the ternary death domain complex of myd88, irak4, and irak2
33d2eiaa2
not modelled 7.6 29 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
34d2hwna1
not modelled 7.6 18 Fold:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
35c2dimA_
not modelled 7.5 11 PDB header:dna binding protein
Chain: A: PDB Molecule:cell division cycle 5-like protein;
PDBTitle: solution structure of the myb_dna-binding domain of human2 cell division cycle 5-like protein
36c2yqeA_
not modelled 7.4 14 PDB header:dna binding protein
Chain: A: PDB Molecule:jumonji/arid domain-containing protein 1d;
PDBTitle: solution structure of the arid domain of jarid1d protein
37d1m9dc_
not modelled 7.4 29 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
38c1x41A_
not modelled 7.1 17 PDB header:transcription
Chain: A: PDB Molecule:transcriptional adaptor 2-like, isoform b;
PDBTitle: solution structure of the myb-like dna binding domain of2 human transcriptional adaptor 2-like, isoform b
39c3n7nE_
not modelled 7.1 35 PDB header:replication
Chain: E: PDB Molecule:monopolin complex subunit lrs4;
PDBTitle: structure of csm1/lrs4 complex
40d1h8ac1
not modelled 7.1 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
41d1z6ma1
not modelled 7.1 9 Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:DsbA-like
42c3bciA_
not modelled 7.0 9 PDB header:oxidoreductase
Chain: A: PDB Molecule:disulfide bond protein a;
PDBTitle: crystal structure of staphylococcus aureus dsba
43d1r2aa_
not modelled 6.2 18 Fold:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Superfamily:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
Family:Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit
44c2rh0B_
not modelled 6.1 21 PDB header:nuclear protein
Chain: B: PDB Molecule:nudc domain-containing protein 2;
PDBTitle: crystal structure of nudc domain-containing protein 22 (13542905) from mus musculus at 1.95 a resolution
45d1gvda_
not modelled 5.9 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
46c3ktmB_
not modelled 5.7 25 PDB header:cell adhesion, signaling protein
Chain: B: PDB Molecule:amyloid beta a4 protein;
PDBTitle: structure of the heparin-induced e1-dimer of the amyloid precursor2 protein (app)
47c2l6wB_
not modelled 5.7 21 PDB header:membrane protein
Chain: B: PDB Molecule:beta-type platelet-derived growth factor receptor;
PDBTitle: pdgfr beta-tm
48c2l6wA_
not modelled 5.7 21 PDB header:membrane protein
Chain: A: PDB Molecule:beta-type platelet-derived growth factor receptor;
PDBTitle: pdgfr beta-tm
49d1r5la1
not modelled 5.6 17 Fold:RuvA C-terminal domain-like
Superfamily:CRAL/TRIO N-terminal domain
Family:CRAL/TRIO N-terminal domain
50c2wlvA_
not modelled 5.5 24 PDB header:virus protein
Chain: A: PDB Molecule:gag polyprotein;
PDBTitle: structure of the n-terminal capsid domain of hiv-2
51c2xgvA_
not modelled 5.5 24 PDB header:viral protein
Chain: A: PDB Molecule:psiv capsid n-terminal domain;
PDBTitle: structure of the n-terminal domain of capsid protein from2 rabbit endogenous lentivirus (relik)
52d1beda_
not modelled 5.4 10 Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:DsbA-like
53d1tuaa2
not modelled 5.3 16 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
54c2rq5A_
not modelled 5.3 7 PDB header:transcription
Chain: A: PDB Molecule:protein jumonji;
PDBTitle: solution structure of the at-rich interaction domain (arid)2 of jumonji/jarid2
55d2pxrc1
not modelled 5.3 29 Fold:Retrovirus capsid protein, N-terminal core domain
Superfamily:Retrovirus capsid protein, N-terminal core domain
Family:Retrovirus capsid protein, N-terminal core domain
56d1k1fa_
not modelled 5.3 46 Fold:Bcr-Abl oncoprotein oligomerization domain
Superfamily:Bcr-Abl oncoprotein oligomerization domain
Family:Bcr-Abl oncoprotein oligomerization domain
57d1wmga_
not modelled 5.2 12 Fold:DEATH domain
Superfamily:DEATH domain
Family:DEATH domain, DD
58c2xgyA_
not modelled 5.1 18 PDB header:viral protein/isomerase
Chain: A: PDB Molecule:relik capsid n-terminal domain;
PDBTitle: complex of rabbit endogenous lentivirus (relik)capsid with2 cyclophilin a
59c2pfcA_
not modelled 5.1 27 PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein rv0098/mt0107;
PDBTitle: structure of mycobacterium tuberculosis rv0098
60c2ib1A_
not modelled 5.1 13 PDB header:apoptosis
Chain: A: PDB Molecule:death domain containing membrane protein nradd;
PDBTitle: solution structure of p45 death domain

Binding site prediction 

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If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite