Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionC6Y4B2
DateSun Jul 8 11:45:06 BST 2012
Unique Job IDb74d4ef677be47cc

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2y9mB_
Top template information
PDB header:ligase/transport protein
Chain: B: PDB Molecule:peroxisome assembly protein 22;
PDBTitle: pex4p-pex22p structure
Confidence and coverage
Confidence: 55.6% Coverage: 37%
51 residues ( 37% of your sequence) have been modelled with 55.6% 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  MFYSTTSWFQKATLAIGIGTTLYVLFKDLVRDQEAKSESKSRKKVMILVDETTSEEDIKK
Secondary structure 
SS confidence 
Disorder  ???????
?????????
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  WSDYDLFLASRSTLLSKHTSRLESYVSHPSKALRCDDPDSILTFLKHLDINILVWNAHWS
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.......
Sequence  SERLKTQCENLVYILVE
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 2y9m chain B

3D model

Region: 87 - 137
Aligned: 51
Modelled: 51
Confidence: 55.6%
Identity: 16%
PDB header:ligase/transport protein
Chain: B: PDB Molecule:peroxisome assembly protein 22;
PDBTitle: pex4p-pex22p structure

Phyre2

PDB 2i5n chain H domain 2

3D model

Region: 106 - 119
Aligned: 14
Modelled: 14
Confidence: 44.1%
Identity: 64%
Fold: Single transmembrane helix
Superfamily: Photosystem II reaction centre subunit H, transmembrane region
Family: Photosystem II reaction centre subunit H, transmembrane region

Phyre2

PDB 1jdq chain A

3D model

Region: 29 - 61
Aligned: 33
Modelled: 33
Confidence: 21.4%
Identity: 21%
Fold: IF3-like
Superfamily: SirA-like
Family: SirA-like

Phyre2

PDB 1col chain A

3D model

Region: 81 - 113
Aligned: 33
Modelled: 33
Confidence: 21.4%
Identity: 21%
Fold: Toxins' membrane translocation domains
Superfamily: Colicin
Family: Colicin

Phyre2

PDB 1gjw chain A domain 1

3D model

Region: 114 - 123
Aligned: 10
Modelled: 10
Confidence: 21.2%
Identity: 60%
Fold: Glycosyl hydrolase domain
Superfamily: Glycosyl hydrolase domain
Family: alpha-Amylases, C-terminal beta-sheet domain

Phyre2

PDB 3qqc chain A

3D model

Region: 18 - 62
Aligned: 45
Modelled: 45
Confidence: 20.0%
Identity: 18%
PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit b, dna-directed rna
PDBTitle: crystal structure of archaeal spt4/5 bound to the rnap clamp domain

Phyre2

PDB 2etd chain A domain 1

3D model

Region: 55 - 93
Aligned: 37
Modelled: 39
Confidence: 19.5%
Identity: 22%
Fold: Bromodomain-like
Superfamily: LemA-like
Family: LemA-like

Phyre2

PDB 1cii chain A domain 1

3D model

Region: 81 - 113
Aligned: 33
Modelled: 33
Confidence: 17.5%
Identity: 18%
Fold: Toxins' membrane translocation domains
Superfamily: Colicin
Family: Colicin

Phyre2

PDB 1fkm chain A domain 2

3D model

Region: 64 - 114
Aligned: 51
Modelled: 48
Confidence: 17.5%
Identity: 27%
Fold: Left-handed superhelix
Superfamily: Ypt/Rab-GAP domain of gyp1p
Family: Ypt/Rab-GAP domain of gyp1p

Phyre2

PDB 1je3 chain A

3D model

Region: 29 - 61
Aligned: 33
Modelled: 33
Confidence: 17.4%
Identity: 21%
Fold: IF3-like
Superfamily: SirA-like
Family: SirA-like

Phyre2

PDB 1rh1 chain A domain 2

3D model

Region: 75 - 113
Aligned: 39
Modelled: 39
Confidence: 14.9%
Identity: 15%
Fold: Toxins' membrane translocation domains
Superfamily: Colicin
Family: Colicin

Phyre2

PDB 1gj8 chain A

3D model

Region: 121 - 128
Aligned: 8
Modelled: 8
Confidence: 10.6%
Identity: 63%
PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets

Phyre2

PDB 1gja chain A

3D model

Region: 121 - 128
Aligned: 8
Modelled: 8
Confidence: 10.6%
Identity: 63%
PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets

Phyre2

PDB 1gjd chain A

3D model

Region: 121 - 128
Aligned: 8
Modelled: 8
Confidence: 10.6%
Identity: 63%
PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets

Phyre2

PDB 1a87 chain A

3D model

Region: 23 - 113
Aligned: 91
Modelled: 91
Confidence: 10.2%
Identity: 13%
Fold: Toxins' membrane translocation domains
Superfamily: Colicin
Family: Colicin

Phyre2

PDB 1a87 chain A

3D model

Region: 23 - 113
Aligned: 91
Modelled: 91
Confidence: 10.2%
Identity: 13%
PDB header:bacteriocin
Chain: A: PDB Molecule:colicin n;
PDBTitle: colicin n

Phyre2

PDB 1pav chain A

3D model

Region: 29 - 61
Aligned: 33
Modelled: 33
Confidence: 9.5%
Identity: 15%
Fold: IF3-like
Superfamily: SirA-like
Family: SirA-like

Phyre2

PDB 3few chain X

3D model

Region: 82 - 113
Aligned: 32
Modelled: 32
Confidence: 9.4%
Identity: 19%
PDB header:immune system
Chain: X: PDB Molecule:colicin s4;
PDBTitle: structure and function of colicin s4, a colicin with a2 duplicated receptor binding domain

Phyre2

PDB 1p9g chain A

3D model

Region: 92 - 98
Aligned: 7
Modelled: 7
Confidence: 9.2%
Identity: 57%
Fold: Knottins (small inhibitors, toxins, lectins)
Superfamily: Plant lectins/antimicrobial peptides
Family: Hevein-like agglutinin (lectin) domain

Phyre2

PDB 1dcj chain A

3D model

Region: 29 - 61
Aligned: 33
Modelled: 33
Confidence: 8.9%
Identity: 12%
Fold: IF3-like
Superfamily: SirA-like
Family: SirA-like

Phyre2
1
c2y9mB_
2
d2i5nh2
3
d1jdqa_
4
d1cola_
5
d1gjwa1
6
c3qqcA_
7
d2etda1
8
d1ciia1
9
d1fkma2
10
d1je3a_
11
d1rh1a2
12
c1gj8A_
13
c1gjaA_
14
c1gjdA_
15
d1a87a_
16
c1a87A_
17
d1pava_
18
c3fewX_
19
d1p9ga_
20
d1dcja_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2y9mB_
55.6 16 PDB header:ligase/transport protein
Chain: B: PDB Molecule:peroxisome assembly protein 22;
PDBTitle: pex4p-pex22p structure
2d2i5nh2
44.1 64 Fold:Single transmembrane helix
Superfamily:Photosystem II reaction centre subunit H, transmembrane region
Family:Photosystem II reaction centre subunit H, transmembrane region
3d1jdqa_
21.4 21 Fold:IF3-like
Superfamily:SirA-like
Family:SirA-like
4d1cola_
21.4 21 Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
5d1gjwa1
21.2 60 Fold:Glycosyl hydrolase domain
Superfamily:Glycosyl hydrolase domain
Family:alpha-Amylases, C-terminal beta-sheet domain
6c3qqcA_
20.0 18 PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit b, dna-directed rna
PDBTitle: crystal structure of archaeal spt4/5 bound to the rnap clamp domain
7d2etda1
19.5 22 Fold:Bromodomain-like
Superfamily:LemA-like
Family:LemA-like
8d1ciia1
17.5 18 Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
9d1fkma2
17.5 27 Fold:Left-handed superhelix
Superfamily:Ypt/Rab-GAP domain of gyp1p
Family:Ypt/Rab-GAP domain of gyp1p
10d1je3a_
17.4 21 Fold:IF3-like
Superfamily:SirA-like
Family:SirA-like
11d1rh1a2
14.9 15 Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
12c1gj8A_
10.6 63 PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets
13c1gjaA_
10.6 63 PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets
14c1gjdA_
10.6 63 PDB header:blood clotting, hydrolase
Chain: A: PDB Molecule:urokinase-type plasminogen activator;
PDBTitle: engineering inhibitors highly selective for the s1 sites of ser1902 trypsin-like serine protease drug targets
15d1a87a_
10.2 13 Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
16c1a87A_
10.2 13 PDB header:bacteriocin
Chain: A: PDB Molecule:colicin n;
PDBTitle: colicin n
17d1pava_
9.5 15 Fold:IF3-like
Superfamily:SirA-like
Family:SirA-like
18c3fewX_
9.4 19 PDB header:immune system
Chain: X: PDB Molecule:colicin s4;
PDBTitle: structure and function of colicin s4, a colicin with a2 duplicated receptor binding domain
19d1p9ga_
9.2 57 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Plant lectins/antimicrobial peptides
Family:Hevein-like agglutinin (lectin) domain
20d1dcja_
8.9 12 Fold:IF3-like
Superfamily:SirA-like
Family:SirA-like
21c2kmcA_
not modelled 8.0 30 PDB header:cell adhesion
Chain: A: PDB Molecule:fermitin family homolog 1;
PDBTitle: solution structure of the n-terminal domain of kindlin-1
22c1rh1A_
not modelled 8.0 16 PDB header:antibiotic
Chain: A: PDB Molecule:colicin b;
PDBTitle: crystal structure of the cytotoxic bacterial protein2 colicin b at 2.5 a resolution
23c3oq0D_
not modelled 8.0 33 PDB header:cell cycle
Chain: D: PDB Molecule:dbf4;
PDBTitle: crystal structure of motif n of saccharomyces cerevisiae dbf4
24c2lgxA_
not modelled 8.0 37 PDB header:cell adhesion
Chain: A: PDB Molecule:fermitin family homolog 2;
PDBTitle: nmr structure for kindle-2 n-terminus
25c3mlrP_
not modelled 7.6 62 PDB header:immune system
Chain: P: PDB Molecule:hiv-1 gp120 third variable region (v3) crown;
PDBTitle: crystal structure of anti-hiv-1 v3 fab 2557 in complex with a ny5 v32 peptide
26c3nohA_
not modelled 7.3 16 PDB header:peptide binding protein
Chain: A: PDB Molecule:putative peptide binding protein;
PDBTitle: crystal structure of a putative peptide binding protein (rumgna_00914)2 from ruminococcus gnavus atcc 29149 at 1.60 a resolution
27c3qwlA_
not modelled 7.2 17 PDB header:hydrolase activator
Chain: A: PDB Molecule:tbc1 domain family member 7;
PDBTitle: crystal structure of human tbc1 domain family member 7
28c3lnoA_
not modelled 7.1 54 PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of domain of unknown function duf59 from2 bacillus anthracis
29c1agqB_
not modelled 6.9 29 PDB header:growth factor
Chain: B: PDB Molecule:glial cell-derived neurotrophic factor;
PDBTitle: glial cell-derived neurotrophic factor from rat
30c2i88A_
not modelled 6.8 22 PDB header:membrane protein
Chain: A: PDB Molecule:colicin-e1;
PDBTitle: crystal structure of the channel-forming domain of colicin2 e1
31c2pijB_
not modelled 6.6 25 PDB header:transcription
Chain: B: PDB Molecule:prophage pfl 6 cro;
PDBTitle: structure of the cro protein from prophage pfl 6 in pseudomonas2 fluorescens pf-5
32d1u3da2
not modelled 6.4 21 Fold:Cryptochrome/photolyase, N-terminal domain
Superfamily:Cryptochrome/photolyase, N-terminal domain
Family:Cryptochrome/photolyase, N-terminal domain
33d1d1la_
not modelled 6.2 25 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
34c2diiA_
not modelled 6.1 47 PDB header:transcription
Chain: A: PDB Molecule:tfiih basal transcription factor complex p62
PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit
35d1uwda_
not modelled 6.0 27 Fold:Alpha-lytic protease prodomain-like
Superfamily:Fe-S cluster assembly (FSCA) domain-like
Family:PaaD-like
36d2ha2a1
not modelled 5.6 17 Fold:alpha/beta-Hydrolases
Superfamily:alpha/beta-Hydrolases
Family:Acetylcholinesterase-like
37d2diia1
not modelled 5.6 47 Fold:BSD domain-like
Superfamily:BSD domain-like
Family:BSD domain
38d4croa_
not modelled 5.6 25 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
39d2cu6a1
not modelled 5.2 23 Fold:Alpha-lytic protease prodomain-like
Superfamily:Fe-S cluster assembly (FSCA) domain-like
Family:PaaD-like
40c2yy8B_
not modelled 5.2 24 PDB header:transferase
Chain: B: PDB Molecule:upf0106 protein ph0461;
PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine
41d1dwua_
not modelled 5.1 20 Fold:Ribosomal protein L1
Superfamily:Ribosomal protein L1
Family:Ribosomal protein L1

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