Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A0H0
DateTue Jul 17 17:05:06 BST 2012
Unique Job IDc60cf05d72fae754

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1i94l_
Top template information
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
Confidence and coverage
Confidence:100.0% Coverage: 90%
123 residues ( 90% of your sequence) have been modelled with 100.0% 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  MPTINQLVRKPRQSKIKKSDSPALNKGFNSKKKKFTDLNSPQKRGVCTRVGTMTPKKPNS
Secondary structure 
SS confidence 
Disorder  ???????????????????????????????????????
???
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  ALRKYARVRLSNNIEINAYIPGIGHNLQEHSVVLVRGGRVKDLPGVRYHIVRGALDTSGV
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........130.......
Sequence  DGRRQGRSLYGTKKPKN
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 1i94 chain L

3D model

Region: 2 - 137
Aligned: 123
Modelled: 123
Confidence: 100.0%
Identity: 70%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2qal chain L domain 1

3D model

Region: 2 - 137
Aligned: 123
Modelled: 136
Confidence: 100.0%
Identity: 71%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2uub chain L domain 1

3D model

Region: 2 - 132
Aligned: 118
Modelled: 118
Confidence: 100.0%
Identity: 69%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1zn1 chain L

3D model

Region: 41 - 137
Aligned: 97
Modelled: 97
Confidence: 100.0%
Identity: 75%
PDB header:biosynthetic/structural protein/rna
Chain: L: PDB Molecule:30s ribosomal protein s12;
PDBTitle: coordinates of rrf fitted into cryo-em map of the 70s post-2 termination complex

Phyre2

PDB 2xzm chain L

3D model

Region: 1 - 127
Aligned: 124
Modelled: 127
Confidence: 100.0%
Identity: 31%
PDB header:ribosome
Chain: L: PDB Molecule:40s ribosomal protein s12;
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 1

Phyre2

PDB 1s1h chain L

3D model

Region: 25 - 137
Aligned: 105
Modelled: 113
Confidence: 100.0%
Identity: 30%
PDB header:ribosome
Chain: L: PDB Molecule:40s ribosomal protein s23;
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 2zkq chain L

3D model

Region: 25 - 126
Aligned: 102
Modelled: 102
Confidence: 100.0%
Identity: 29%
PDB header:ribosomal protein/rna
Chain: L: PDB Molecule:
PDBTitle: structure of a mammalian ribosomal 40s subunit within an 80s complex2 obtained by docking homology models of the rna and proteins into an3 8.7 a cryo-em map

Phyre2

PDB 1ah9 chain A

3D model

Region: 67 - 96
Aligned: 30
Modelled: 30
Confidence: 85.5%
Identity: 30%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 3i4o chain A

3D model

Region: 67 - 96
Aligned: 30
Modelled: 30
Confidence: 85.4%
Identity: 27%
PDB header:translation
Chain: A: PDB Molecule:translation initiation factor if-1;
PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis

Phyre2

PDB 1hr0 chain W

3D model

Region: 67 - 96
Aligned: 30
Modelled: 30
Confidence: 71.0%
Identity: 37%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1jt8 chain A

3D model

Region: 67 - 82
Aligned: 16
Modelled: 16
Confidence: 46.7%
Identity: 38%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2oqk chain A

3D model

Region: 67 - 82
Aligned: 16
Modelled: 16
Confidence: 38.3%
Identity: 13%
PDB header:translation
Chain: A: PDB Molecule:putative translation initiation factor eif-1a;
PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a

Phyre2

PDB 2d1c chain B

3D model

Region: 70 - 84
Aligned: 15
Modelled: 15
Confidence: 28.5%
Identity: 33%
PDB header:oxidoreductase
Chain: B: PDB Molecule:isocitrate dehydrogenase;
PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8

Phyre2

PDB 2ix0 chain A domain 3

3D model

Region: 67 - 112
Aligned: 44
Modelled: 46
Confidence: 24.3%
Identity: 43%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1y80 chain A

3D model

Region: 71 - 87
Aligned: 17
Modelled: 17
Confidence: 23.3%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica

Phyre2

PDB 1v7w chain A domain 1

3D model

Region: 49 - 97
Aligned: 47
Modelled: 49
Confidence: 21.1%
Identity: 21%
Fold: alpha/alpha toroid
Superfamily: Six-hairpin glycosidases
Family: Glycosyltransferase family 36 C-terminal domain

Phyre2

PDB 1d7q chain A

3D model

Region: 66 - 96
Aligned: 31
Modelled: 31
Confidence: 20.9%
Identity: 13%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1ju2 chain A domain 1

3D model

Region: 71 - 90
Aligned: 20
Modelled: 20
Confidence: 18.0%
Identity: 30%
Fold: FAD/NAD(P)-binding domain
Superfamily: FAD/NAD(P)-binding domain
Family: FAD-linked reductases, N-terminal domain

Phyre2

PDB 1pb1 chain A

3D model

Region: 67 - 84
Aligned: 18
Modelled: 18
Confidence: 16.1%
Identity: 39%
Fold: Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like
Family: Dimeric isocitrate & isopropylmalate dehydrogenases

Phyre2

PDB 3bul chain A domain 2

3D model

Region: 71 - 87
Aligned: 17
Modelled: 17
Confidence: 15.0%
Identity: 24%
Fold: Flavodoxin-like
Superfamily: Cobalamin (vitamin B12)-binding domain
Family: Cobalamin (vitamin B12)-binding domain

Phyre2
1
d1i94l_
2
d2qall1
3
d2uubl1
4
c1zn1L_
5
c2xzmL_
6
c1s1hL_
7
c2zkql_
8
d1ah9a_
9
c3i4oA_
10
d1hr0w_
11
d1jt8a_
12
c2oqkA_
13
c2d1cB_
14
d2ix0a3
15
c1y80A_
16
d1v7wa1
17
d1d7qa_
18
d1ju2a1
19
d1pb1a_
20
d3bula2
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1i94l_
100.0 70 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
2d2qall1
100.0 71 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
3d2uubl1
100.0 69 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
4c1zn1L_
100.0 75 PDB header:biosynthetic/structural protein/rna
Chain: L: PDB Molecule:30s ribosomal protein s12;
PDBTitle: coordinates of rrf fitted into cryo-em map of the 70s post-2 termination complex
5c2xzmL_
100.0 31 PDB header:ribosome
Chain: L: PDB Molecule:40s ribosomal protein s12;
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 1
6c1s1hL_
100.0 30 PDB header:ribosome
Chain: L: PDB Molecule:40s ribosomal protein s23;
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.
7c2zkql_
100.0 29 PDB header:ribosomal protein/rna
Chain: L: PDB Molecule:
PDBTitle: structure of a mammalian ribosomal 40s subunit within an 80s complex2 obtained by docking homology models of the rna and proteins into an3 8.7 a cryo-em map
8d1ah9a_
85.5 30 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
9c3i4oA_
85.4 27 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor if-1;
PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis
10d1hr0w_
71.0 37 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
11d1jt8a_
46.7 38 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
12c2oqkA_
38.3 13 PDB header:translation
Chain: A: PDB Molecule:putative translation initiation factor eif-1a;
PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a
13c2d1cB_
28.5 33 PDB header:oxidoreductase
Chain: B: PDB Molecule:isocitrate dehydrogenase;
PDBTitle: crystal structure of tt0538 protein from thermus thermophilus hb8
14d2ix0a3
24.3 43 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
15c1y80A_
23.3 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from2 moorella thermoacetica
16d1v7wa1
21.1 21 Fold:alpha/alpha toroid
Superfamily:Six-hairpin glycosidases
Family:Glycosyltransferase family 36 C-terminal domain
17d1d7qa_
20.9 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
18d1ju2a1
18.0 30 Fold:FAD/NAD(P)-binding domain
Superfamily:FAD/NAD(P)-binding domain
Family:FAD-linked reductases, N-terminal domain
19d1pb1a_
16.1 39 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Dimeric isocitrate & isopropylmalate dehydrogenases
20d3bula2
15.0 24 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
21d1dwna_
not modelled 13.9 36 Fold:RNA bacteriophage capsid protein
Superfamily:RNA bacteriophage capsid protein
Family:RNA bacteriophage capsid protein
22d1eara1
not modelled 12.0 13 Fold:Urease metallochaperone UreE, N-terminal domain
Superfamily:Urease metallochaperone UreE, N-terminal domain
Family:Urease metallochaperone UreE, N-terminal domain
23d2dipa1
not modelled 11.0 11 Fold:RING/U-box
Superfamily:RING/U-box
Family:ZZ domain
24d1yrra1
not modelled 10.5 21 Fold:Composite domain of metallo-dependent hydrolases
Superfamily:Composite domain of metallo-dependent hydrolases
Family:N-acetylglucosamine-6-phosphate deacetylase, NagA
25d1e32a1
not modelled 10.4 24 Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
26d1o7ia_
not modelled 10.0 7 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
27d2fcta1
not modelled 9.2 18 Fold:Double-stranded beta-helix
Superfamily:Clavaminate synthase-like
Family:PhyH-like
28d1rutx4
not modelled 8.5 29 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
29d1hqsa_
not modelled 8.4 33 Fold:Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like
Family:Dimeric isocitrate & isopropylmalate dehydrogenases
30c2jx5A_
not modelled 8.0 32 PDB header:ribosomal protein
Chain: A: PDB Molecule:glub(s27a);
PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia
31c3swnA_
not modelled 7.9 9 PDB header:rna binding protein
Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5;
PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings
32d1x7fa2
not modelled 7.8 25 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Outer surface protein, N-terminal domain
33d1rxta1
not modelled 7.2 18 Fold:Acyl-CoA N-acyltransferases (Nat)
Superfamily:Acyl-CoA N-acyltransferases (Nat)
Family:N-myristoyl transferase, NMT
34d1w98b1
not modelled 7.1 31 Fold:Cyclin-like
Superfamily:Cyclin-like
Family:Cyclin
35d1ccwa_
not modelled 6.7 11 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
36c3n0vD_
not modelled 6.6 10 PDB header:hydrolase
Chain: D: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pp_0327)2 from pseudomonas putida kt2440 at 2.25 a resolution
37c1x7fA_
not modelled 6.1 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:outer surface protein;
PDBTitle: crystal structure of an uncharacterized b. cereus protein
38d1d3ba_
not modelled 6.0 5 Fold:Sm-like fold
Superfamily:Sm-like ribonucleoproteins
Family:Sm motif of small nuclear ribonucleoproteins, SNRNP
39d2vo1a1
not modelled 6.0 36 Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
40c2e0cA_
not modelled 5.9 28 PDB header:oxidoreductase
Chain: A: PDB Molecule:409aa long hypothetical nadp-dependent isocitrate
PDBTitle: crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii2 strain7 at 2.0 a resolution
41c2r8cB_
not modelled 5.6 13 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative amidohydrolase;
PDBTitle: crystal structure of uncharacterized protein eaj56179
42c3louB_
not modelled 5.5 11 PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of formyltetrahydrofolate deformylase (yp_105254.1)2 from burkholderia mallei atcc 23344 at 1.90 a resolution
43c1xyr6_
not modelled 5.5 45 PDB header:virus
Chain: 6: PDB Molecule:genome polyprotein, coat protein vp3;
PDB Fragment:residues 620-630 PDBTitle: poliovirus 135s cell entry intermediate
44c3bw1A_
not modelled 5.3 9 PDB header:rna binding protein
Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm3;
PDBTitle: crystal structure of homomeric yeast lsm3 exhibiting novel octameric2 ring organisation

Binding site prediction 

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