Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP41441
DateThu Jan 5 12:01:31 GMT 2012
Unique Job IDa792d5c43a913f5b

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3c1qA_
Top template information
PDB header:transport protein
Chain: A: PDB Molecule:general secretion pathway protein f;
PDBTitle: the three-dimensional structure of the cytoplasmic domains of epsf2 from the type 2 secretion system of vibrio cholerae
Confidence and coverage
Confidence: 99.9% Coverage: 29%
114 residues ( 29% of your sequence) have been modelled with 99.9% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
220 residues ( 55%) 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  MNYRYRAMTQDGQKLQGIIDANDERQARLRLREEGLFLLDIRPQKSSGVKTRRPRISHSE
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   .........70.........80.........90.........100.........110.........120
Sequence  LTLFTRQLATLSAAALPLEESLAVIGQQSSNKRLGDVLNQVRSAILEGHPLSDALQHFPT
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   .........130.........140.........150.........160.........170.........180
Sequence  LFDSLYRTLVKAGEKSGLLAPVLEKLADYNENRQKIRSKLIQSLIYPCMLTTVAIGVVII
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   .........190.........200.........210.........220.........230.........240
Sequence  LLTAVVPKITEQFVHMKQQLPLSTRILLGLSDTLQRTGPTLLATVFIVAVGFWLWLKRGN
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   .........250.........260.........270.........280.........290.........300
Sequence  NRHRFHAMLLRVALIGPLICAINSARYLRTLSILQSSGVPLLDGMNLSTESLNNLEIRQR
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   .........310.........320.........330.........340.........350.........360
Sequence  LANAAENVRQGNSIHLSLEQTAIFPPMMLYMVASGEKSGQLGTLMVRAADNQETLQQNRI
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   .........370.........380.........390........
Sequence  ALTLSIFEPALIITMALIVLFIVVSVLQPLLQLNSMIN
Secondary structure 

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????
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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 3c1q chain A

3D model

Region: 50 - 163
Aligned: 114
Modelled: 114
Confidence: 99.9%
Identity: 51%
PDB header:transport protein
Chain: A: PDB Molecule:general secretion pathway protein f;
PDBTitle: the three-dimensional structure of the cytoplasmic domains of epsf2 from the type 2 secretion system of vibrio cholerae

Phyre2

PDB 2whn chain A

3D model

Region: 250 - 359
Aligned: 110
Modelled: 110
Confidence: 99.9%
Identity: 23%
PDB header:protein transport
Chain: A: PDB Molecule:pilus assembly protein pilc;
PDBTitle: n-terminal domain from the pilc type iv pilus biogenesis2 protein

Phyre2

PDB 3c8m chain A

3D model

Region: 74 - 117
Aligned: 44
Modelled: 44
Confidence: 42.1%
Identity: 18%
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of homoserine dehydrogenase from thermoplasma2 volcanium

Phyre2

PDB 3cum chain A domain 1

3D model

Region: 254 - 355
Aligned: 102
Modelled: 102
Confidence: 38.1%
Identity: 8%
Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like
Family: Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain

Phyre2

PDB 3i3a chain C

3D model

Region: 42 - 103
Aligned: 62
Modelled: 62
Confidence: 36.5%
Identity: 8%
PDB header:transferase
Chain: C: PDB Molecule:acyl-[acyl-carrier-protein]--udp-n-
PDBTitle: structural basis for the sugar nucleotide and acyl chain2 selectivity of leptospira interrogans lpxa

Phyre2

PDB 3ing chain A

3D model

Region: 74 - 117
Aligned: 44
Modelled: 44
Confidence: 34.4%
Identity: 27%
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of homoserine dehydrogenase (np_394635.1) from2 thermoplasma acidophilum at 1.95 a resolution

Phyre2

PDB 2ejw chain B

3D model

Region: 74 - 117
Aligned: 44
Modelled: 44
Confidence: 34.2%
Identity: 16%
PDB header:oxidoreductase
Chain: B: PDB Molecule:homoserine dehydrogenase;
PDBTitle: homoserine dehydrogenase from thermus thermophilus hb8

Phyre2

PDB 2d1l chain A

3D model

Region: 80 - 164
Aligned: 84
Modelled: 85
Confidence: 33.4%
Identity: 10%
PDB header:protein binding
Chain: A: PDB Molecule:metastasis suppressor protein 1;
PDBTitle: structure of f-actin binding domain imd of mim (missing in metastasis)

Phyre2

PDB 3ok8 chain A

3D model

Region: 91 - 164
Aligned: 73
Modelled: 74
Confidence: 31.0%
Identity: 15%
PDB header:protein binding
Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein
PDBTitle: i-bar of pinkbar

Phyre2

PDB 1y2o chain A domain 1

3D model

Region: 78 - 164
Aligned: 85
Modelled: 83
Confidence: 29.7%
Identity: 15%
Fold: BAR/IMD domain-like
Superfamily: BAR/IMD domain-like
Family: IMD domain

Phyre2

PDB 3iug chain A

3D model

Region: 108 - 160
Aligned: 52
Modelled: 53
Confidence: 20.0%
Identity: 17%
PDB header:splicing
Chain: A: PDB Molecule:rho/cdc42/rac gtpase-activating protein rics;
PDBTitle: crystal structure of the rhogap domain of rics

Phyre2

PDB 2jf2 chain A domain 1

3D model

Region: 42 - 103
Aligned: 62
Modelled: 62
Confidence: 17.0%
Identity: 11%
Fold: Single-stranded left-handed beta-helix
Superfamily: Trimeric LpxA-like enzymes
Family: UDP N-acetylglucosamine acyltransferase

Phyre2

PDB 3k4i chain C

3D model

Region: 99 - 118
Aligned: 20
Modelled: 20
Confidence: 15.1%
Identity: 25%
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of uncharacterized protein pspto_3204 from2 pseudomonas syringae pv. tomato str. dc3000

Phyre2

PDB 3r1f chain O

3D model

Region: 111 - 150
Aligned: 40
Modelled: 40
Confidence: 14.5%
Identity: 15%
PDB header:transcription
Chain: O: PDB Molecule:esx-1 secretion-associated regulator espr;
PDBTitle: crystal structure of a key regulator of virulence in mycobacterium2 tuberculosis

Phyre2

PDB 2c5q chain E

3D model

Region: 92 - 122
Aligned: 31
Modelled: 31
Confidence: 14.1%
Identity: 19%
PDB header:structural genomics,unknown function
Chain: E: PDB Molecule:rraa-like protein yer010c;
PDBTitle: crystal structure of yeast yer010cp

Phyre2

PDB 2bbj chain B

3D model

Region: 59 - 240
Aligned: 134
Modelled: 147
Confidence: 13.0%
Identity: 17%
PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter

Phyre2

PDB 1xa6 chain A domain 1

3D model

Region: 108 - 160
Aligned: 53
Modelled: 53
Confidence: 12.8%
Identity: 13%
Fold: GTPase activation domain, GAP
Superfamily: GTPase activation domain, GAP
Family: BCR-homology GTPase activation domain (BH-domain)

Phyre2

PDB 3kuq chain A

3D model

Region: 108 - 160
Aligned: 53
Modelled: 53
Confidence: 12.8%
Identity: 15%
PDB header:hydrolase activator
Chain: A: PDB Molecule:rho gtpase-activating protein 7;
PDBTitle: crystal structure of the dlc1 rhogap domain

Phyre2

PDB 3byi chain A

3D model

Region: 108 - 160
Aligned: 53
Modelled: 53
Confidence: 12.7%
Identity: 19%
PDB header:signaling protein
Chain: A: PDB Molecule:rho gtpase activating protein 15;
PDBTitle: crystal structure of human rho gtpase activating protein 15 (arhgap15)

Phyre2

PDB 1vq3 chain A

3D model

Region: 10 - 33
Aligned: 24
Modelled: 24
Confidence: 11.9%
Identity: 13%
Fold: PurS-like
Superfamily: PurS-like
Family: PurS subunit of FGAM synthetase

Phyre2
1

c3c1qA_
2

c2whnA_
3

c3c8mA_
4

d3cuma1
5

c3i3aC_
6

c3ingA_
7

c2ejwB_
8

c2d1lA_
9

c3ok8A_
10

d1y2oa1
11

c3iugA_
12

d2jf2a1
13

c3k4iC_
14

c3r1fO_
15

c2c5qE_
16

c2bbjB_
17

d1xa6a1
18

c3kuqA_
19

c3byiA_
20

d1vq3a_
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






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3c1qA_



99.9 51 PDB header:transport protein
Chain: A: PDB Molecule:general secretion pathway protein f;
PDBTitle: the three-dimensional structure of the cytoplasmic domains of epsf2 from the type 2 secretion system of vibrio cholerae
2c2whnA_



99.9 23 PDB header:protein transport
Chain: A: PDB Molecule:pilus assembly protein pilc;
PDBTitle: n-terminal domain from the pilc type iv pilus biogenesis2 protein
3c3c8mA_



42.1 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of homoserine dehydrogenase from thermoplasma2 volcanium
4d3cuma1



38.1 8 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain
5c3i3aC_



36.5 8 PDB header:transferase
Chain: C: PDB Molecule:acyl-[acyl-carrier-protein]--udp-n-
PDBTitle: structural basis for the sugar nucleotide and acyl chain2 selectivity of leptospira interrogans lpxa
6c3ingA_



34.4 27 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of homoserine dehydrogenase (np_394635.1) from2 thermoplasma acidophilum at 1.95 a resolution
7c2ejwB_



34.2 16 PDB header:oxidoreductase
Chain: B: PDB Molecule:homoserine dehydrogenase;
PDBTitle: homoserine dehydrogenase from thermus thermophilus hb8
8c2d1lA_



33.4 10 PDB header:protein binding
Chain: A: PDB Molecule:metastasis suppressor protein 1;
PDBTitle: structure of f-actin binding domain imd of mim (missing in metastasis)
9c3ok8A_



31.0 15 PDB header:protein binding
Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein
PDBTitle: i-bar of pinkbar
10d1y2oa1



29.7 15 Fold:BAR/IMD domain-like
Superfamily:BAR/IMD domain-like
Family:IMD domain
11c3iugA_



20.0 17 PDB header:splicing
Chain: A: PDB Molecule:rho/cdc42/rac gtpase-activating protein rics;
PDBTitle: crystal structure of the rhogap domain of rics
12d2jf2a1



17.0 11 Fold:Single-stranded left-handed beta-helix
Superfamily:Trimeric LpxA-like enzymes
Family:UDP N-acetylglucosamine acyltransferase
13c3k4iC_



15.1 25 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of uncharacterized protein pspto_3204 from2 pseudomonas syringae pv. tomato str. dc3000
14c3r1fO_



14.5 15 PDB header:transcription
Chain: O: PDB Molecule:esx-1 secretion-associated regulator espr;
PDBTitle: crystal structure of a key regulator of virulence in mycobacterium2 tuberculosis
15c2c5qE_



14.1 19 PDB header:structural genomics,unknown function
Chain: E: PDB Molecule:rraa-like protein yer010c;
PDBTitle: crystal structure of yeast yer010cp
16c2bbjB_



13.0 17 PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter
17d1xa6a1



12.8 13 Fold:GTPase activation domain, GAP
Superfamily:GTPase activation domain, GAP
Family:BCR-homology GTPase activation domain (BH-domain)
18c3kuqA_



12.8 15 PDB header:hydrolase activator
Chain: A: PDB Molecule:rho gtpase-activating protein 7;
PDBTitle: crystal structure of the dlc1 rhogap domain
19c3byiA_



12.7 19 PDB header:signaling protein
Chain: A: PDB Molecule:rho gtpase activating protein 15;
PDBTitle: crystal structure of human rho gtpase activating protein 15 (arhgap15)
20d1vq3a_



11.9 13 Fold:PurS-like
Superfamily:PurS-like
Family:PurS subunit of FGAM synthetase
21d2ezla_



not modelled 11.4 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
22c2f4qA_



not modelled 10.7 18 PDB header:isomerase
Chain: A: PDB Molecule:type i topoisomerase, putative;
PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib
23c3ibqA_



not modelled 10.7 22 PDB header:transferase
Chain: A: PDB Molecule:pyridoxal kinase;
PDBTitle: crystal structure of pyridoxal kinase from lactobacillus2 plantarum in complex with atp
24c3r0sA_



not modelled 10.5 16 PDB header:transferase
Chain: A: PDB Molecule:acyl-[acyl-carrier-protein]--udp-n-acetylglucosamine o-
PDBTitle: udp-n-acetylglucosamine acyltransferase from campylobacter jejuni
25c3do5A_



not modelled 10.5 18 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of putative homoserine dehydrogenase (np_069768.1)2 from archaeoglobus fulgidus at 2.20 a resolution
26c2hx1D_



not modelled 10.4 11 PDB header:hydrolase
Chain: D: PDB Molecule:predicted sugar phosphatases of the had
PDBTitle: crystal structure of possible sugar phosphatase, had2 superfamily (zp_00311070.1) from cytophaga hutchinsonii3 atcc 33406 at 2.10 a resolution
27d1j2za_



not modelled 9.3 12 Fold:Single-stranded left-handed beta-helix
Superfamily:Trimeric LpxA-like enzymes
Family:UDP N-acetylglucosamine acyltransferase
28d1gtda_



not modelled 9.3 4 Fold:PurS-like
Superfamily:PurS-like
Family:PurS subunit of FGAM synthetase
29c2zw2B_



not modelled 9.2 13 PDB header:ligase
Chain: B: PDB Molecule:putative uncharacterized protein sts178;
PDBTitle: crystal structure of formylglycinamide ribonucleotide amidotransferase2 iii from sulfolobus tokodaii (stpurs)
30c1xa6A_



not modelled 8.9 13 PDB header:signaling protein
Chain: A: PDB Molecule:beta2-chimaerin;
PDBTitle: crystal structure of the human beta2-chimaerin
31c3neuA_



not modelled 8.8 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
32c2pmzN_



not modelled 8.4 13 PDB header:translation, transferase
Chain: N: PDB Molecule:dna-directed rna polymerase subunit n;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
33d1hara_



not modelled 8.3 5 Fold:DNA/RNA polymerases
Superfamily:DNA/RNA polymerases
Family:Reverse transcriptase
34d2f06a1



not modelled 7.8 19 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:BT0572-like
35d1e8ob_



not modelled 7.6 23 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14
Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14
Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14
36c3mtjA_



not modelled 7.5 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: the crystal structure of a homoserine dehydrogenase from thiobacillus2 denitrificans to 2.15a
37d2c4na1



not modelled 6.8 14 Fold:HAD-like
Superfamily:HAD-like
Family:NagD-like
38d2gyqa1



not modelled 6.3 18 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:YciF-like
39c3gdeA_



not modelled 5.7 10 PDB header:ligase
Chain: A: PDB Molecule:dna ligase;
PDBTitle: the closed conformation of atp-dependent dna ligase from2 archaeoglobus fulgidus
40d1ijwc_



not modelled 5.7 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
41c1n54A_



not modelled 5.6 21 PDB header:rna binding protein
Chain: A: PDB Molecule:80 kda nuclear cap binding protein;
PDBTitle: cap binding complex m7gpppg free
42c1zk6A_



not modelled 5.6 13 PDB header:isomerase
Chain: A: PDB Molecule:foldase protein prsa;
PDBTitle: nmr solution structure of b. subtilis prsa ppiase
43d1jnsa_



not modelled 5.6 8 Fold:FKBP-like
Superfamily:FKBP-like
Family:FKBP immunophilin/proline isomerase
44d1zhva2



not modelled 5.5 29 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Atu0741-like
45c2i7aA_



not modelled 5.4 14 PDB header:hydrolase
Chain: A: PDB Molecule:calpain 13;
PDBTitle: domain iv of human calpain 13
46c2kk6A_



not modelled 5.4 24 PDB header:transferase
Chain: A: PDB Molecule:proto-oncogene tyrosine-protein kinase fer;
PDBTitle: solution structure of sh2 domain of proto-oncogene tyrosine-2 protein kinase fer from homo sapiens, northeast structural3 genomics consortium (nesg) target hr3461d
47d1914a2



not modelled 5.3 23 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14
Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14
Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14
48d2gs4a1



not modelled 5.1 20 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:YciF-like
49c2kncB_



not modelled 5.1 10 PDB header:cell adhesion
Chain: B: PDB Molecule:integrin beta-3;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
50c1ebuA_



not modelled 5.1 23 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: homoserine dehydrogenase complex with nad analogue and l-2 homoserine
51c2kncA_



not modelled 5.1 9 PDB header:cell adhesion
Chain: A: PDB Molecule:integrin alpha-iib;
PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex
52c1sneB_



not modelled 5.1 31 PDB header:de novo protein
Chain: B: PDB Molecule:tetrameric beta-beta-alpha mini-protein;
PDBTitle: an oligomeric domain-swapped beta-beta-alpha mini-protein
53c1sneA_



not modelled 5.1 31 PDB header:de novo protein
Chain: A: PDB Molecule:tetrameric beta-beta-alpha mini-protein;
PDBTitle: an oligomeric domain-swapped beta-beta-alpha mini-protein
54d1hcra_



not modelled 5.1 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
55c3nmeA_



not modelled 5.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:sex4 glucan phosphatase;
PDBTitle: structure of a plant phosphatase

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