Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AFF6
DateThu Jan 5 11:26:07 GMT 2012
Unique Job IDf8574ffcb15887fa

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1l2fA_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
Confidence and coverage
Confidence:100.0% Coverage: 69%
342 residues ( 69% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
477 residues ( 96%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVQIDRKSGDFDTFR
Secondary structure 















SS confidence 



























































Disorder  ??












???























?
















Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  RWLVVDEVTQPTKEITLEAARYEDESLNLGDYVEDQIESVTFDRITTQTAKQVIVQKVRE
Secondary structure 






















SS confidence 



























































Disorder 





















??????































Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  AERAMVVDQFREHEGEIITGVVKKVNRDNISLDLGNNAEAVILREDMLPRENFRPGDRVR
Secondary structure 















SS confidence 



























































Disorder 













































???????






Disorder confidence 



























































 
   .........190.........200.........210.........220.........230.........240
Sequence  GVLYSVRPEARGAQLFVTRSKPEMLIELFRIEVPEIGEEVIEIKAAARDPGSRAKIAVKT
Secondary structure 













SS confidence 



























































Disorder 






????
























?






















Disorder confidence 



























































 
   .........250.........260.........270.........280.........290.........300
Sequence  NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDE
Secondary structure 





















SS confidence 



























































Disorder 












?

?










































Disorder confidence 



























































 
   .........310.........320.........330.........340.........350.........360
Sequence  DKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFT
Secondary structure 














SS confidence 



























































Disorder 










































??????



????


Disorder confidence 



























































 
   .........370.........380.........390.........400.........410.........420
Sequence  KYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNALATIAQA
Secondary structure 














SS confidence 



























































Disorder  ???
?




















?







?
??



















?
Disorder confidence 



























































 
   .........430.........440.........450.........460.........470.........480
Sequence  QEESLGDNKPADDLLNLEGVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGA
Secondary structure 























SS confidence 



























































Disorder  ?
?????????



??????


























?

???





Disorder confidence 



























































 
   .........490.....
Sequence  LIMAARNICWFGDEA
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 1l2f chain A

3D model

Region: 1 - 343
Aligned: 342
Modelled: 340
Confidence: 100.0%
Identity: 35%
PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain

Phyre2

PDB 1hh2 chain P

3D model

Region: 1 - 343
Aligned: 342
Modelled: 343
Confidence: 100.0%
Identity: 35%
PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima

Phyre2

PDB 1k0r chain B

3D model

Region: 1 - 342
Aligned: 311
Modelled: 322
Confidence: 100.0%
Identity: 38%
PDB header:transcription
Chain: B: PDB Molecule:nusa;
PDBTitle: crystal structure of mycobacterium tuberculosis nusa

Phyre2

PDB 2asb chain A

3D model

Region: 131 - 347
Aligned: 217
Modelled: 217
Confidence: 100.0%
Identity: 39%
PDB header:transcription/rna
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex

Phyre2

PDB 2asb chain A domain 2

3D model

Region: 200 - 278
Aligned: 79
Modelled: 79
Confidence: 100.0%
Identity: 47%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

Phyre2

PDB 2kwp chain A

3D model

Region: 1 - 129
Aligned: 129
Modelled: 129
Confidence: 100.0%
Identity: 98%
PDB header:transcription
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: solution structure of the aminoterminal domain of e. coli nusa

Phyre2

PDB 1hh2 chain P domain 2

3D model

Region: 201 - 277
Aligned: 77
Modelled: 77
Confidence: 100.0%
Identity: 47%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

Phyre2

PDB 1hh2 chain P domain 4

3D model

Region: 1 - 125
Aligned: 125
Modelled: 125
Confidence: 100.0%
Identity: 34%
Fold: Transcription factor NusA, N-terminal domain
Superfamily: Transcription factor NusA, N-terminal domain
Family: Transcription factor NusA, N-terminal domain

Phyre2

PDB 1hh2 chain P domain 3

3D model

Region: 278 - 343
Aligned: 66
Modelled: 66
Confidence: 99.9%
Identity: 36%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

Phyre2

PDB 2owo chain A

3D model

Region: 345 - 494
Aligned: 133
Modelled: 150
Confidence: 99.9%
Identity: 20%
PDB header:ligase/dna
Chain: A: PDB Molecule:dna ligase;
PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate

Phyre2

PDB 2asb chain A domain 3

3D model

Region: 279 - 342
Aligned: 64
Modelled: 64
Confidence: 99.9%
Identity: 41%
Fold: Alpha-lytic protease prodomain-like
Superfamily: Prokaryotic type KH domain (KH-domain type II)
Family: Prokaryotic type KH domain (KH-domain type II)

Phyre2

PDB 1dgs chain B

3D model

Region: 345 - 494
Aligned: 133
Modelled: 150
Confidence: 99.9%
Identity: 26%
PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis

Phyre2

PDB 1v9p chain B

3D model

Region: 345 - 494
Aligned: 133
Modelled: 150
Confidence: 99.9%
Identity: 26%
PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase

Phyre2

PDB 1dgs chain A domain 1

3D model

Region: 345 - 494
Aligned: 133
Modelled: 150
Confidence: 99.9%
Identity: 26%
Fold: SAM domain-like
Superfamily: RuvA domain 2-like
Family: NAD+-dependent DNA ligase, domain 3

Phyre2

PDB 1k0r chain A domain 4

3D model

Region: 1 - 122
Aligned: 99
Modelled: 102
Confidence: 99.8%
Identity: 35%
Fold: Transcription factor NusA, N-terminal domain
Superfamily: Transcription factor NusA, N-terminal domain
Family: Transcription factor NusA, N-terminal domain

Phyre2

PDB 2asb chain A domain 1

3D model

Region: 131 - 199
Aligned: 69
Modelled: 69
Confidence: 99.8%
Identity: 30%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1hh2 chain P domain 1

3D model

Region: 127 - 199
Aligned: 72
Modelled: 73
Confidence: 99.8%
Identity: 22%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2cy1 chain A

3D model

Region: 205 - 340
Aligned: 130
Modelled: 136
Confidence: 99.7%
Identity: 23%
PDB header:transcription
Chain: A: PDB Molecule:nusa protein homolog;
PDBTitle: crystal structure of ape1850

Phyre2

PDB 1wcn chain A

3D model

Region: 430 - 495
Aligned: 66
Modelled: 66
Confidence: 99.5%
Identity: 100%
PDB header:rna-binding protein
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: nmr structure of the carboxyterminal domains of escherichia2 coli nusa

Phyre2

PDB 1u9l chain A

3D model

Region: 353 - 419
Aligned: 67
Modelled: 67
Confidence: 99.1%
Identity: 100%
Fold: SAM domain-like
Superfamily: Rad51 N-terminal domain-like
Family: NusA extra C-terminal domains

Phyre2
1

c1l2fA_
2

c1hh2P_
3

c1k0rB_
4

c2asbA_
5

d2asba2
6

c2kwpA_
7

d1hh2p2
8

d1hh2p4
9

d1hh2p3
10

c2owoA_
11

d2asba3
12

c1dgsB_
13

c1v9pB_
14

d1dgsa1
15

d1k0ra4
16

d2asba1
17

d1hh2p1
18

c2cy1A_
19

c1wcnA_
20

d1u9la_
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



61



62



63



64



65



66



67



68



69



70



71



72



73



74



75



76



77



78



79



80



81



82



83



84



85



86



87



88



89



90



91



92



93



94



95



96



97



98



99



100



101



102



103



104



105



106



107



108



109



110



111



112



113



114



115



116



117



118



119



120



121



122



123



124



125



126



127



128



129



130



131



132



133



134



135



136



137



138



139



140



141



142



143



144



145



146



147



148



149



150



151



152



153



154



155



156



157



158



159



160



161



162



163



164



165



166



167



168



169



170



171



172



173



174



175



176



177



178



179



180



181



182



183



184



185



186



187



188



189



190



191



192



193



194



195



196



197



198



199



200



201



202



203



204



205



206



207



208



209



210



211



212



213



214



215



216



217



218



219



220



221



222



223



224



225



226



227



228



229



230



231



232



233



234



235



236



237



238



239



240



241



242



243



244



245



246



247



248



249



250



251



252



253



254



255



256



257



258



259



260



261



262



263



264



265



266



267



268



269



270



271



272



273



274



275



276



277



278



279



280



281



282



283



284



285



286



287



288



289



290



291



292



293



294



295



296



297



298



299



300



301



302






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1l2fA_



100.0 35 PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
2c1hh2P_



100.0 35 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
3c1k0rB_



100.0 38 PDB header:transcription
Chain: B: PDB Molecule:nusa;
PDBTitle: crystal structure of mycobacterium tuberculosis nusa
4c2asbA_



100.0 39 PDB header:transcription/rna
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex
5d2asba2



100.0 47 Fold:Alpha-lytic protease prodomain-like
Superfamily:Prokaryotic type KH domain (KH-domain type II)
Family:Prokaryotic type KH domain (KH-domain type II)
6c2kwpA_



100.0 98 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: solution structure of the aminoterminal domain of e. coli nusa
7d1hh2p2



100.0 47 Fold:Alpha-lytic protease prodomain-like
Superfamily:Prokaryotic type KH domain (KH-domain type II)
Family:Prokaryotic type KH domain (KH-domain type II)
8d1hh2p4



100.0 34 Fold:Transcription factor NusA, N-terminal domain
Superfamily:Transcription factor NusA, N-terminal domain
Family:Transcription factor NusA, N-terminal domain
9d1hh2p3



99.9 36 Fold:Alpha-lytic protease prodomain-like
Superfamily:Prokaryotic type KH domain (KH-domain type II)
Family:Prokaryotic type KH domain (KH-domain type II)
10c2owoA_



99.9 20 PDB header:ligase/dna
Chain: A: PDB Molecule:dna ligase;
PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate
11d2asba3



99.9 41 Fold:Alpha-lytic protease prodomain-like
Superfamily:Prokaryotic type KH domain (KH-domain type II)
Family:Prokaryotic type KH domain (KH-domain type II)
12c1dgsB_



99.9 26 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis
13c1v9pB_



99.9 26 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase
14d1dgsa1



99.9 26 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:NAD+-dependent DNA ligase, domain 3
15d1k0ra4



99.8 35 Fold:Transcription factor NusA, N-terminal domain
Superfamily:Transcription factor NusA, N-terminal domain
Family:Transcription factor NusA, N-terminal domain
16d2asba1



99.8 30 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
17d1hh2p1



99.8 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
18c2cy1A_



99.7 23 PDB header:transcription
Chain: A: PDB Molecule:nusa protein homolog;
PDBTitle: crystal structure of ape1850
19c1wcnA_



99.5 100 PDB header:rna-binding protein
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: nmr structure of the carboxyterminal domains of escherichia2 coli nusa
20d1u9la_



99.1 100 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:NusA extra C-terminal domains
21c3go5A_



not modelled 98.9 19 PDB header:gene regulation
Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains;
PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution
22d1q46a2



not modelled 98.8 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
23c1q46A_



not modelled 98.8 20 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
24c2khjA_



not modelled 98.8 19 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1
25c1yz6A_



not modelled 98.8 20 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 alpha
PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi
26c2k4kA_



not modelled 98.8 18 PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis
27c2khiA_



not modelled 98.8 18 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1
28d2ba0a1



not modelled 98.8 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
29d1go3e1



not modelled 98.8 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
30c2z0sA_



not modelled 98.8 17 PDB header:rna binding protein
Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1;
PDBTitle: crystal structure of putative exosome complex rna-binding2 protein
31c1q8kA_



not modelled 98.8 19 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2
32d2z0sa1



not modelled 98.7 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
33c2k52A_



not modelled 98.7 27 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mj1198;
PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b
34d1wi5a_



not modelled 98.7 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
35d2je6i1



not modelled 98.7 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
36d1kl9a2



not modelled 98.7 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
37d2i1qa1



not modelled 98.7 35 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:DNA repair protein Rad51, N-terminal domain
38d1y14b1



not modelled 98.7 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
39d1pzna1



not modelled 98.7 32 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:DNA repair protein Rad51, N-terminal domain
40d2a1jb1



not modelled 98.7 20 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Hef domain-like
41c2cqoA_



not modelled 98.6 18 PDB header:ribosome
Chain: A: PDB Molecule:nucleolar protein of 40 kda;
PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067
42d2nn6h1



not modelled 98.6 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
43d1szpa1



not modelled 98.6 29 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:DNA repair protein Rad51, N-terminal domain
44c2ahoB_



not modelled 98.6 15 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: structure of the archaeal initiation factor eif2 alpha-2 gamma heterodimer from sulfolobus solfataricus complexed3 with gdpnp
45d3bzka4



not modelled 98.5 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
46d1sroa_



not modelled 98.5 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
47d1x2ia1



not modelled 98.5 18 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Hef domain-like
48c2je6I_



not modelled 98.5 15 PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome
49c1go3E_



not modelled 98.4 22 PDB header:transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex
50d2ahob2



not modelled 98.4 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
51c1kl9A_



not modelled 98.4 24 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 subunit 1;
PDBTitle: crystal structure of the n-terminal segment of human eukaryotic2 initiation factor 2alpha
52c2ba0A_



not modelled 98.4 14 PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core
53d2bgwa1



not modelled 98.4 18 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Hef domain-like
54c2b8kG_



not modelled 98.4 12 PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii
55d1kfta_



not modelled 98.4 18 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Excinuclease UvrC C-terminal domain
56c1kftA_



not modelled 98.4 18 PDB header:dna binding protein
Chain: A: PDB Molecule:excinuclease abc subunit c;
PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli
57c2eqsA_



not modelled 98.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dhx8;
PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8
58c2oceA_



not modelled 98.3 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
59c1b22A_



not modelled 98.3 25 PDB header:dna binding protein
Chain: A: PDB Molecule:dna repair protein rad51;
PDBTitle: rad51 (n-terminal domain)
60d1b22a_



not modelled 98.3 25 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:DNA repair protein Rad51, N-terminal domain
61c3psiA_



not modelled 98.3 16 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt6;
PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(239-1451)
62c2c35F_



not modelled 98.3 22 PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii
63d2c35b1



not modelled 98.2 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
64d2nn6i1



not modelled 98.1 30 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
65d1szpb1



not modelled 98.1 30 Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:DNA repair protein Rad51, N-terminal domain
66c1nt9G_



not modelled 98.0 12 PDB header:transcription, transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide;
PDBTitle: complete 12-subunit rna polymerase ii
67d1smxa_



not modelled 98.0 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
68c2w9mB_



not modelled 98.0 21 PDB header:dna replication
Chain: B: PDB Molecule:polymerase x;
PDBTitle: structure of family x dna polymerase from deinococcus2 radiodurans
69c3h0gS_



not modelled 97.9 22 PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
70c2nn6I_



not modelled 97.9 27 PDB header:hydrolase/transferase
Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
71c2nrzB_



not modelled 97.9 20 PDB header:hydrolase
Chain: B: PDB Molecule:uvrabc system protein c;
PDBTitle: crystal structure of the c-terminal half of uvrc bound to2 its catalytic divalent cation
72c2pmzE_



not modelled 97.9 21 PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
73c2ba1B_



not modelled 97.7 15 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
74c2bhnD_



not modelled 97.7 18 PDB header:hydrolase
Chain: D: PDB Molecule:xpf endonuclease;
PDBTitle: xpf from aeropyrum pernix
75c2ckzB_



not modelled 97.5 23 PDB header:transferase
Chain: B: PDB Molecule:dna-directed rna polymerase iii 25 kd
PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25.
76c2ihmA_



not modelled 97.4 18 PDB header:transferase/dna
Chain: A: PDB Molecule:dna polymerase mu;
PDBTitle: polymerase mu in ternary complex with gapped 11mer dna2 duplex and bound incoming nucleotide
77d2aq0a1



not modelled 97.4 26 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Hef domain-like
78c3ayhB_



not modelled 97.4 17 PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc8;
PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii
79c2ja9A_



not modelled 97.4 20 PDB header:rna-binding protein
Chain: A: PDB Molecule:exosome complex exonuclease rrp40;
PDBTitle: structure of the n-terminal deletion of yeast exosome2 component rrp40
80c1kdhA_



not modelled 97.4 13 PDB header:transferase/dna
Chain: A: PDB Molecule:terminal deoxynucleotidyltransferase short
PDBTitle: binary complex of murine terminal deoxynucleotidyl2 transferase with a primer single stranded dna
81c2bcuA_



not modelled 97.2 16 PDB header:transferase, lyase/dna
Chain: A: PDB Molecule:dna polymerase lambda;
PDBTitle: dna polymerase lambda in complex with a dna duplex2 containing an unpaired damp and a t:t mismatch
82c3c1zA_



not modelled 97.2 17 PDB header:dna binding protein
Chain: A: PDB Molecule:dna integrity scanning protein disa;
PDBTitle: structure of the ligand-free form of a bacterial dna damage2 sensor protein
83d2p6ra2



not modelled 97.1 16 Fold:Sec63 N-terminal domain-like
Superfamily:Sec63 N-terminal domain-like
Family:Achaeal helicase C-terminal domain
84c1ixrA_



not modelled 97.1 20 PDB header:hydrolase
Chain: A: PDB Molecule:holliday junction dna helicase ruva;
PDBTitle: ruva-ruvb complex
85d2nn6g1



not modelled 97.0 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
86d1doqa_



not modelled 97.0 25 Fold:SAM domain-like
Superfamily:C-terminal domain of RNA polymerase alpha subunit
Family:C-terminal domain of RNA polymerase alpha subunit
87d1lb2b_



not modelled 97.0 17 Fold:SAM domain-like
Superfamily:C-terminal domain of RNA polymerase alpha subunit
Family:C-terminal domain of RNA polymerase alpha subunit
88d1cuka2



not modelled 96.9 20 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:DNA helicase RuvA subunit, middle domain
89c8iczA_



not modelled 96.9 21 PDB header:transferase/dna
Chain: A: PDB Molecule:protein (dna polymerase beta (e.c.2.7.7.7));
PDBTitle: dna polymerase beta (pol b) (e.c.2.7.7.7) complexed with2 seven base pairs of dna; soaked in the presence of of datp3 (1 millimolar), mncl2 (5 millimolar), and lithium sulfate4 (75 millimolar)
90c2nn6G_



not modelled 96.9 18 PDB header:hydrolase/transferase
Chain: G: PDB Molecule:exosome complex exonuclease rrp40;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
91c2jvzA_



not modelled 96.9 16 PDB header:splicing
Chain: A: PDB Molecule:far upstream element-binding protein 2;
PDBTitle: solution nmr structure of the second and third kh domains2 of ksrp
92d1z3eb1



not modelled 96.9 19 Fold:SAM domain-like
Superfamily:C-terminal domain of RNA polymerase alpha subunit
Family:C-terminal domain of RNA polymerase alpha subunit
93c2jzxA_



not modelled 96.8 22 PDB header:rna binding protein
Chain: A: PDB Molecule:poly(rc)-binding protein 2;
PDBTitle: pcbp2 kh1-kh2 domains
94d1cooa_



not modelled 96.8 17 Fold:SAM domain-like
Superfamily:C-terminal domain of RNA polymerase alpha subunit
Family:C-terminal domain of RNA polymerase alpha subunit
95d1ixra1



not modelled 96.8 21 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:DNA helicase RuvA subunit, middle domain
96d2ja9a1



not modelled 96.7 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
97c2bh8B_



not modelled 96.7 15 PDB header:transcription
Chain: B: PDB Molecule:1b11;
PDBTitle: combinatorial protein 1b11
98c2va8A_



not modelled 96.6 23 PDB header:hydrolase
Chain: A: PDB Molecule:ski2-type helicase;
PDBTitle: dna repair helicase hel308
99c2wp8J_



not modelled 96.5 22 PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease
100c2csdB_



not modelled 96.5 21 PDB header:isomerase
Chain: B: PDB Molecule:topoisomerase v;
PDBTitle: crystal structure of topoisomerase v (61 kda fragment)
101c2nn6H_



not modelled 96.4 18 PDB header:hydrolase/transferase
Chain: H: PDB Molecule:exosome complex exonuclease rrp4;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
102c2ix1A_



not modelled 96.4 16 PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
103d1pu6a_



not modelled 96.4 22 Fold:DNA-glycosylase
Superfamily:DNA-glycosylase
Family:3-Methyladenine DNA glycosylase III (MagIII)
104c1hjpA_



not modelled 96.3 21 PDB header:dna recombination
Chain: A: PDB Molecule:ruva;
PDBTitle: holliday junction binding protein ruva from e. coli
105c1d8lA_



not modelled 96.3 20 PDB header:gene regulation
Chain: A: PDB Molecule:protein (holliday junction dna helicase ruva);
PDBTitle: e. coli holliday junction binding protein ruva nh2 region2 lacking domain iii
106d1bvsa2



not modelled 96.2 23 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:DNA helicase RuvA subunit, middle domain
107c2h5xA_



not modelled 96.1 24 PDB header:dna binding protein
Chain: A: PDB Molecule:holliday junction atp-dependent dna helicase ruva;
PDBTitle: ruva from mycobacterium tuberculosis
108c2rf4A_



not modelled 96.0 14 PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4;
PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43
109c2p6uA_



not modelled 95.8 16 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
110c1j4wA_



not modelled 95.8 26 PDB header:transcription/dna
Chain: A: PDB Molecule:fuse binding protein;
PDBTitle: complex of the kh3 and kh4 domains of fbp with a2 single_stranded 29mer dna oligonucleotide from the fuse3 element of the c-myc oncogene
111c3krmB_



not modelled 95.7 22 PDB header:rna binding protein
Chain: B: PDB Molecule:insulin-like growth factor 2 mrna-binding protein
PDBTitle: imp1 kh34
112c2anrA_



not modelled 95.4 20 PDB header:rna-binding protein/rna
Chain: A: PDB Molecule:neuro-oncological ventral antigen 1;
PDBTitle: crystal structure (ii) of nova-1 kh1/kh2 domain tandem with 25nt rna2 hairpin
113c2c4rL_



not modelled 95.3 16 PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e
114c1t4gA_



not modelled 95.1 25 PDB header:recombination
Chain: A: PDB Molecule:dna repair and recombination protein rada;
PDBTitle: atpase in complex with amp-pnp
115d1keaa_



not modelled 95.0 17 Fold:DNA-glycosylase
Superfamily:DNA-glycosylase
Family:Mismatch glycosylase
116c1s5lu_



not modelled 95.0 30 PDB header:photosynthesis
Chain: U: PDB Molecule:photosystem ii 12 kda extrinsic protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center
117c2qndA_



not modelled 94.8 19 PDB header:rna binding protein
Chain: A: PDB Molecule:fmr1 protein;
PDBTitle: crystal structure of the kh1-kh2 domains from human fragile x mental2 retardation protein
118d2ba0a3



not modelled 94.6 15 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)
119d1x4ma1



not modelled 94.5 15 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)
120d2axtu1



not modelled 94.5 26 Fold:SAM domain-like
Superfamily:PsbU/PolX domain-like
Family:PsbU-like

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

Transmembrane helix prediction 

Transmembrane helices have been predicted in your sequence to adopt the topology shown below



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