Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionO08387
DateTue Jul 17 17:05:02 BST 2012
Unique Job ID8394b0217ec82c09

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3j01A_
Top template information
PDB header:ribosome/ribosomal protein
Chain: A: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: structure of the ribosome-secye complex in the membrane environment
Confidence and coverage
Confidence:100.0% Coverage: 96%
413 residues ( 96% 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  MIQTLVNFFRTKEVRNKIFFTLAMLVIFKIGTYIPAPGVNPAAFDNPQGSQGATELLNTF
Secondary structure 
SS confidence 
Disorder  ??
???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GGGALKRFSIFAMGIVPYITASIVMQLLQMDIVPKFSEWAKQGEVGRRKLNNVTRYLAIS
Secondary structure 
SS confidence 
Disorder 
?
??
?
??
???
?????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  LAFIQSIGMAFQFNNYLKGALIINQSIMSYLLIALVLTAGTAFLIWLGDQITQFGVGNGI
Secondary structure 
SS confidence 
Disorder 
?????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  SIIIFAGILSTLPASLIQFGQTAFVGQEDTSLAWLKVLGLLVSLILLTVGAIYVLEAVRK
Secondary structure 
SS confidence 
Disorder 
?????????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  IPIQYAKKQTAQRLGSQATYLPLKVNSAGVIPVIFAMAFFLLPRTLTLFYPDKEWAQNIA
Secondary structure 
SS confidence 
Disorder 
????????????????
?
??
?
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  NAANPSSNVGMVVYIVLIILFTYFYAFVQVNPEKMADNLKKQGSYVPGIRPGEQTKKYIT
Secondary structure 
SS confidence 
Disorder 
?
?????????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  KVLYRLTFVGSIFLAVISILPILATKFMGLPQSIQIGGTSLLIVIGVAIETMKSLEAQVS
Secondary structure 
SS confidence 
Disorder 
???????
?
Disorder confidence 
 
   .........430
Sequence  QKEYKGFGGR
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 3j01 chain A

3D model

Region: 11 - 430
Aligned: 413
Modelled: 419
Confidence: 100.0%
Identity: 41%
PDB header:ribosome/ribosomal protein
Chain: A: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: structure of the ribosome-secye complex in the membrane environment

Phyre2

PDB 2zqp chain Y

3D model

Region: 1 - 422
Aligned: 410
Modelled: 421
Confidence: 100.0%
Identity: 38%
PDB header:protein transport
Chain: Y: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: crystal structure of secye translocon from thermus2 thermophilus

Phyre2

PDB 3dl8 chain H

3D model

Region: 9 - 429
Aligned: 401
Modelled: 401
Confidence: 100.0%
Identity: 42%
PDB header:protein transport
Chain: H: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca

Phyre2

PDB 3din chain F

3D model

Region: 8 - 429
Aligned: 394
Modelled: 422
Confidence: 100.0%
Identity: 39%
PDB header:membrane protein, protein transport
Chain: F: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase

Phyre2

PDB 2wwb chain A

3D model

Region: 10 - 419
Aligned: 379
Modelled: 410
Confidence: 100.0%
Identity: 21%
PDB header:ribosome
Chain: A: PDB Molecule:protein transport protein sec61 subunit alpha isoform 1;
PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome

Phyre2

PDB 2aki chain Y

3D model

Region: 12 - 430
Aligned: 378
Modelled: 385
Confidence: 100.0%
Identity: 42%
PDB header:protein transport
Chain: Y: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli

Phyre2

PDB 2wwa chain A

3D model

Region: 1 - 430
Aligned: 400
Modelled: 422
Confidence: 100.0%
Identity: 19%
PDB header:ribosome
Chain: A: PDB Molecule:sec sixty-one protein homolog;
PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome

Phyre2

PDB 1rh5 chain A

3D model

Region: 9 - 419
Aligned: 367
Modelled: 394
Confidence: 100.0%
Identity: 20%
Fold: Preprotein translocase SecY subunit
Superfamily: Preprotein translocase SecY subunit
Family: Preprotein translocase SecY subunit

Phyre2

PDB 3mp7 chain A

3D model

Region: 14 - 426
Aligned: 353
Modelled: 370
Confidence: 100.0%
Identity: 22%
PDB header:protein transport
Chain: A: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes

Phyre2

PDB 2nsc chain A

3D model

Region: 328 - 363
Aligned: 36
Modelled: 36
Confidence: 71.6%
Identity: 28%
PDB header:chaperone
Chain: A: PDB Molecule:trigger factor;
PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima

Phyre2

PDB 1t11 chain A domain 2

3D model

Region: 334 - 365
Aligned: 32
Modelled: 32
Confidence: 66.4%
Identity: 16%
Fold: Ribosome binding domain-like
Superfamily: Trigger factor ribosome-binding domain
Family: Trigger factor ribosome-binding domain

Phyre2

PDB 1p9y chain A

3D model

Region: 334 - 365
Aligned: 32
Modelled: 32
Confidence: 65.2%
Identity: 13%
Fold: Ribosome binding domain-like
Superfamily: Trigger factor ribosome-binding domain
Family: Trigger factor ribosome-binding domain

Phyre2

PDB 1w26 chain A domain 2

3D model

Region: 334 - 363
Aligned: 30
Modelled: 30
Confidence: 56.7%
Identity: 13%
Fold: Ribosome binding domain-like
Superfamily: Trigger factor ribosome-binding domain
Family: Trigger factor ribosome-binding domain

Phyre2

PDB 2d3o chain 1

3D model

Region: 333 - 362
Aligned: 29
Modelled: 30
Confidence: 48.8%
Identity: 31%
PDB header:ribosome
Chain: 1: PDB Molecule:trigger factor;
PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans

Phyre2

PDB 1w26 chain B

3D model

Region: 333 - 353
Aligned: 20
Modelled: 21
Confidence: 45.3%
Identity: 25%
PDB header:chaperone
Chain: B: PDB Molecule:trigger factor;
PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins

Phyre2

PDB 1t11 chain A

3D model

Region: 334 - 377
Aligned: 43
Modelled: 44
Confidence: 39.4%
Identity: 14%
PDB header:chaperone
Chain: A: PDB Molecule:trigger factor;
PDBTitle: trigger factor

Phyre2

PDB 1zl8 chain A domain 1

3D model

Region: 96 - 117
Aligned: 22
Modelled: 22
Confidence: 19.8%
Identity: 32%
Fold: L27 domain
Superfamily: L27 domain
Family: L27 domain

Phyre2

PDB 1wmx chain B

3D model

Region: 255 - 272
Aligned: 18
Modelled: 18
Confidence: 18.0%
Identity: 33%
Fold: Galactose-binding domain-like
Superfamily: Galactose-binding domain-like
Family: Family 30 carbohydrate binding module, CBM30 (PKD repeat)

Phyre2

PDB 1y74 chain A domain 1

3D model

Region: 96 - 117
Aligned: 22
Modelled: 22
Confidence: 16.3%
Identity: 27%
Fold: L27 domain
Superfamily: L27 domain
Family: L27 domain

Phyre2

PDB 1ebf chain A domain 2

3D model

Region: 168 - 188
Aligned: 21
Modelled: 21
Confidence: 11.5%
Identity: 29%
Fold: FwdE/GAPDH domain-like
Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family: Homoserine dehydrogenase-like

Phyre2
1
c3j01A_
2
c2zqpY_
3
c3dl8H_
4
c3dinF_
5
c2wwbA_
6
c2akiY_
7
c2wwaA_
8
d1rh5a_
9
c3mp7A_
10
c2nscA_
11
d1t11a2
12
d1p9ya_
13
d1w26a2
14
c2d3o1_
15
c1w26B_
16
c1t11A_
17
d1zl8a1
18
d1wmxb_
19
d1y74a1
20
d1ebfa2
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3j01A_
100.0 41 PDB header:ribosome/ribosomal protein
Chain: A: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: structure of the ribosome-secye complex in the membrane environment
2c2zqpY_
100.0 38 PDB header:protein transport
Chain: Y: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: crystal structure of secye translocon from thermus2 thermophilus
3c3dl8H_
100.0 42 PDB header:protein transport
Chain: H: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca
4c3dinF_
100.0 39 PDB header:membrane protein, protein transport
Chain: F: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase
5c2wwbA_
100.0 21 PDB header:ribosome
Chain: A: PDB Molecule:protein transport protein sec61 subunit alpha isoform 1;
PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome
6c2akiY_
100.0 42 PDB header:protein transport
Chain: Y: PDB Molecule:preprotein translocase secy subunit;
PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli
7c2wwaA_
100.0 19 PDB header:ribosome
Chain: A: PDB Molecule:sec sixty-one protein homolog;
PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome
8d1rh5a_
100.0 20 Fold:Preprotein translocase SecY subunit
Superfamily:Preprotein translocase SecY subunit
Family:Preprotein translocase SecY subunit
9c3mp7A_
100.0 22 PDB header:protein transport
Chain: A: PDB Molecule:preprotein translocase subunit secy;
PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes
10c2nscA_
71.6 28 PDB header:chaperone
Chain: A: PDB Molecule:trigger factor;
PDBTitle: structures of and interactions between domains of trigger factor from2 themotoga maritima
11d1t11a2
66.4 16 Fold:Ribosome binding domain-like
Superfamily:Trigger factor ribosome-binding domain
Family:Trigger factor ribosome-binding domain
12d1p9ya_
65.2 13 Fold:Ribosome binding domain-like
Superfamily:Trigger factor ribosome-binding domain
Family:Trigger factor ribosome-binding domain
13d1w26a2
56.7 13 Fold:Ribosome binding domain-like
Superfamily:Trigger factor ribosome-binding domain
Family:Trigger factor ribosome-binding domain
14c2d3o1_
48.8 31 PDB header:ribosome
Chain: 1: PDB Molecule:trigger factor;
PDBTitle: structure of ribosome binding domain of the trigger factor2 on the 50s ribosomal subunit from d. radiodurans
15c1w26B_
45.3 25 PDB header:chaperone
Chain: B: PDB Molecule:trigger factor;
PDBTitle: trigger factor in complex with the ribosome forms a2 molecular cradle for nascent proteins
16c1t11A_
39.4 14 PDB header:chaperone
Chain: A: PDB Molecule:trigger factor;
PDBTitle: trigger factor
17d1zl8a1
19.8 32 Fold:L27 domain
Superfamily:L27 domain
Family:L27 domain
18d1wmxb_
18.0 33 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 30 carbohydrate binding module, CBM30 (PKD repeat)
19d1y74a1
16.3 27 Fold:L27 domain
Superfamily:L27 domain
Family:L27 domain
20d1ebfa2
11.5 29 Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:Homoserine dehydrogenase-like
21d1wpga4
not modelled 10.9 13 Fold:Calcium ATPase, transmembrane domain M
Superfamily:Calcium ATPase, transmembrane domain M
Family:Calcium ATPase, transmembrane domain M
22c3ku7B_
not modelled 10.7 25 PDB header:cell cycle
Chain: B: PDB Molecule:cell division topological specificity factor;
PDBTitle: crystal structure of helicobacter pylori mine, a cell division2 topological specificity factor
23c2l02B_
not modelled 8.0 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: solution nmr structure of protein bt2368 from bacteroides2 thetaiotaomicron, northeast structural genomics consortium target3 btr375
24d1to9a_
not modelled 7.9 19 Fold:Heme oxygenase-like
Superfamily:Heme oxygenase-like
Family:TENA/THI-4
25c1to9A_
not modelled 7.9 19 PDB header:biosynthetic protein
Chain: A: PDB Molecule:thi-4 protein;
PDBTitle: crystal structure of thi-4 protein from bacillus subtilis
26d2jdid1
not modelled 7.5 12 Fold:Left-handed superhelix
Superfamily:C-terminal domain of alpha and beta subunits of F1 ATP synthase
Family:C-terminal domain of alpha and beta subunits of F1 ATP synthase
27c3kpaB_
not modelled 7.5 21 PDB header:ligase
Chain: B: PDB Molecule:probable ubiquitin fold modifier conjugating enzyme;
PDBTitle: ubiquitin fold modifier conjugating enzyme from leishmania major2 (probable)
28c3okqA_
not modelled 7.1 19 PDB header:protein binding
Chain: A: PDB Molecule:bud site selection protein 6;
PDBTitle: crystal structure of a core domain of yeast actin nucleation cofactor2 bud6
29d1qd1a2
not modelled 6.7 21 Fold:Ferredoxin-like
Superfamily:Formiminotransferase domain of formiminotransferase-cyclodeaminase.
Family:Formiminotransferase domain of formiminotransferase-cyclodeaminase.
30c1mhsA_
not modelled 6.6 13 PDB header:membrane protein, proton transport
Chain: A: PDB Molecule:plasma membrane atpase;
PDBTitle: model of neurospora crassa proton atpase
31d1jjcb1
not modelled 6.5 23 Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:Domains B1 and B5 of PheRS-beta, PheT
32d1iqoa_
not modelled 6.4 21 Fold:Hypothetical protein MTH1880
Superfamily:Hypothetical protein MTH1880
Family:Hypothetical protein MTH1880
33d2huec1
not modelled 6.3 29 Fold:Histone-fold
Superfamily:Histone-fold
Family:Nucleosome core histones
34d1zq1c1
not modelled 6.2 37 Fold:GatB/YqeY motif
Superfamily:GatB/YqeY motif
Family:GatB/GatE C-terminal domain-like
35d1uara1
not modelled 6.1 10 Fold:Rhodanese/Cell cycle control phosphatase
Superfamily:Rhodanese/Cell cycle control phosphatase
Family:Multidomain sulfurtransferase (rhodanese)
36d2gycf1
not modelled 5.9 22 Fold:Ribosomal protein L9 C-domain
Superfamily:Ribosomal protein L9 C-domain
Family:Ribosomal protein L9 C-domain
37c3qxlB_
not modelled 5.9 27 PDB header:signaling protein
Chain: B: PDB Molecule:ras-specific guanine nucleotide-releasing factor ralgps1;
PDBTitle: crystal structure of the cdc25 domain from ral-specific guanine-2 nucleotide exchange factor ralgps1a
38c2voyK_
not modelled 5.8 22 PDB header:hydrolase
Chain: K: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium
PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus
39c4a01B_
not modelled 5.8 14 PDB header:hydrolase
Chain: B: PDB Molecule:proton pyrophosphatase;
PDBTitle: crystal structure of the h-translocating pyrophosphatase
40d1zrra1
not modelled 5.7 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
41c3hlsE_
not modelled 5.6 33 PDB header:signaling protein
Chain: E: PDB Molecule:guanylate cyclase soluble subunit beta-1;
PDBTitle: crystal structure of the signaling helix coiled-coil doimain2 of the beta-1 subunit of the soluble guanylyl cyclase
42c3mvuA_
not modelled 5.5 8 PDB header:transcription regulator
Chain: A: PDB Molecule:tena family transcriptional regulator;
PDBTitle: crystal structure of a tena family transcription regulator2 (tm1040_3656) from silicibacter sp. tm1040 at 1.80 a resolution
43c3gxxB_
not modelled 5.5 29 PDB header:transcription
Chain: B: PDB Molecule:transcription elongation factor spt6;
PDBTitle: structure of the sh2 domain of the candida glabrata2 transcription elongation factor spt6, crystal form b
44d2fiqa1
not modelled 5.4 25 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:GatZ-like
45c1uv7A_
not modelled 5.1 21 PDB header:transport
Chain: A: PDB Molecule:general secretion pathway protein m;
PDBTitle: periplasmic domain of epsm from vibrio cholerae
46d1uv7a_
not modelled 5.1 21 Fold:RRF/tRNA synthetase additional domain-like
Superfamily:General secretion pathway protein M, EpsM
Family:General secretion pathway protein M, EpsM

Binding site prediction 

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