Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2587c_(secD)_2914025_2915746
DateWed Aug 7 12:50:22 BST 2019
Unique Job ID9df7a617771e712b
SequenceVASSSAPVHP ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:87.982 Y:91.585 Z:55.494
Model (left) based on template c3aqpB_
Top template information
PDB header:membrane protein
Chain: B: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
Confidence and coverage
Confidence:100.0% Coverage: 77%
444 residues ( 77% 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.
563 residues ( 98%) 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
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Sequence analysis 

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Secondary structure and disorder prediction [Show] 

Domain analysis [Show] 

Detailed template information [Hide] 

 

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Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3aqpB_



100.0 28
PDB header:membrane protein
Chain: B: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus
2c5xamA_



100.0 30
PDB header:membrane protein
Chain: A: PDB Molecule:protein translocase subunit secd;
PDBTitle: crystal structure of secdf in i form at 4 a resolution
3c5lq3F_



100.0 13
PDB header:transport protein
Chain: F: PDB Molecule:cmeb;
PDBTitle: structures and transport dynamics of the campylobacter jejuni2 multidrug efflux pump cmeb
4c2v50A_



100.0 14
PDB header:membrane protein
Chain: A: PDB Molecule:multidrug resistance protein mexb;
PDBTitle: the missing part of the bacterial mexab-oprm system: structural2 determination of the multidrug exporter mexb
5c6owsB_



100.0 13
PDB header:membrane protein
Chain: B: PDB Molecule:efflux pump membrane transporter;
PDBTitle: cryo-em structure of an acinetobacter baumannii multidrug efflux pump
6c3k07A_



100.0 10
PDB header:transport protein
Chain: A: PDB Molecule:cation efflux system protein cusa;
PDBTitle: crystal structure of cusa
7c4mt1A_



100.0 13
PDB header:membrane protein, tranport protein
Chain: A: PDB Molecule:drug efflux protein;
PDBTitle: crystal structure of the neisseria gonorrhoeae mtrd inner membrane2 multidrug efflux pump
8c1oy8A_



100.0 15
PDB header:membrane protein
Chain: A: PDB Molecule:acriflavine resistance protein b;
PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump
9c6csxA_



100.0 16
PDB header:transport protein
Chain: A: PDB Molecule:multidrug efflux pump subunit acrb;
PDBTitle: single particles cryo-em structure of acrb d407a associated with lipid2 bilayer at 3.0 angstrom
10c4k0eA_



100.0 14
PDB header:transport protein
Chain: A: PDB Molecule:heavy metal cation tricomponent efflux pump znea(czca-
PDBTitle: x-ray crystal structure of a heavy metal efflux pump, crystal form ii
11c4k0eC_



100.0 15
PDB header:transport protein
Chain: C: PDB Molecule:heavy metal cation tricomponent efflux pump znea(czca-
PDBTitle: x-ray crystal structure of a heavy metal efflux pump, crystal form ii
12c5mg3D_



100.0 24
PDB header:chaperone
Chain: D: PDB Molecule:protein translocase subunit secd;
PDBTitle: em fitted model of bacterial holo-translocon
13c5mg3F_



100.0 18
PDB header:chaperone
Chain: F: PDB Molecule:protein translocase subunit secf;
PDBTitle: em fitted model of bacterial holo-translocon
14c6ajjA_



100.0 15
PDB header:membrane protein, hydrolase
Chain: A: PDB Molecule:drug exporters of the rnd superfamily-like protein,
PDBTitle: crystal structure of mycolic acid transporter mmpl3 from mycobacterium2 smegmatis complexed with ica38
15c6dmoA_



100.0 11
PDB header:protein binding
Chain: A: PDB Molecule:protein patched homolog 1;
PDBTitle: cryo-em structure of human ptch1 with three mutations2 l282q/t500f/p504l
16c5khnB_



100.0 15
PDB header:membrane protein
Chain: B: PDB Molecule:rnd transporter;
PDBTitle: crystal structures of the burkholderia multivorans hopanoid2 transporter hpnn
17d1iwga8



100.0 12
Fold:Multidrug efflux transporter AcrB transmembrane domain
Superfamily:Multidrug efflux transporter AcrB transmembrane domain
Family:Multidrug efflux transporter AcrB transmembrane domain
18d1iwga7



99.9 17
Fold:Multidrug efflux transporter AcrB transmembrane domain
Superfamily:Multidrug efflux transporter AcrB transmembrane domain
Family:Multidrug efflux transporter AcrB transmembrane domain
19c3jd8A_



99.9 12
PDB header:membrane protein
Chain: A: PDB Molecule:niemann-pick c1 protein;
PDBTitle: cryo-em structure of the full-length human npc1 at 4.4 angstrom
20c3aqoD_



99.9 31
PDB header:membrane protein
Chain: D: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: structure and function of a membrane component secdf that enhances2 protein export
21c5ensA_



not modelled 99.7 15
PDB header:transport protein
Chain: A: PDB Molecule:multidrug efflux pump subunit acrb,multidrug efflux pump
PDBTitle: rhodamine bound structure of bacterial efflux pump.
22c4r86B_



not modelled 99.1 11
PDB header:protein transport
Chain: B: PDB Molecule:rnd family aminoglycoside/multidrug efflux pump;
PDBTitle: crystal structure of aminoglycoside/multidrug efflux system acrd from2 salmonella typhimurium
23d1iwga1



not modelled 98.1 18
Fold:Ferredoxin-like
Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
24c1ciiA_



not modelled 51.8 13
PDB header:transmembrane protein
Chain: A: PDB Molecule:colicin ia;
PDBTitle: colicin ia
25c2yvxD_



not modelled 40.7 14
PDB header:transport protein
Chain: D: PDB Molecule:mg2+ transporter mgte;
PDBTitle: crystal structure of magnesium transporter mgte
26c2rrnA_



not modelled 33.6 18
PDB header:protein transport
Chain: A: PDB Molecule:probable secdf protein-export membrane protein;
PDBTitle: solution structure of secdf periplasmic domain p4
27d1iwga3



not modelled 29.4 9
Fold:Ferredoxin-like
Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
28d1vq3a_



not modelled 26.8 11
Fold:PurS-like
Superfamily:PurS-like
Family:PurS subunit of FGAM synthetase
29d1iwga5



not modelled 26.3 9
Fold:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Superfamily:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
Family:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
30d1iwga2



not modelled 24.6 19
Fold:Ferredoxin-like
Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
31c2xznC_



not modelled 23.4 9
PDB header:ribosome
Chain: C: PDB Molecule:kh domain containing protein;
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 2
32c2zw2B_



not modelled 18.7 19
PDB header:ligase
Chain: B: PDB Molecule:putative uncharacterized protein sts178;
PDBTitle: crystal structure of formylglycinamide ribonucleotide amidotransferase2 iii from sulfolobus tokodaii (stpurs)
33c5udtD_



not modelled 14.3 16
PDB header:transferase
Chain: D: PDB Molecule:lactate racemization operon protein lare;
PDBTitle: lare, a sulfur transferase involved in synthesis of the cofactor for2 lactate racemase, in complex with amp
34c3zeyX_



not modelled 14.1 12
PDB header:ribosome
Chain: X: PDB Molecule:40s ribosomal protein s3, putative;
PDBTitle: high-resolution cryo-electron microscopy structure of the trypanosoma2 brucei ribosome
35c5xyiD_



not modelled 12.9 12
PDB header:ribosome
Chain: D: PDB Molecule:ribosomal protein s3, putative;
PDBTitle: small subunit of trichomonas vaginalis ribosome
36c5oonA_



not modelled 10.5 21
PDB header:membrane protein
Chain: A: PDB Molecule:undecaprenyl-diphosphatase;
PDBTitle: structure of undecaprenyl-pyrophosphate phosphatase, baca
37c4p6vE_



not modelled 10.4 17
PDB header:oxidoreductase
Chain: E: PDB Molecule:na(+)-translocating nadh-quinone reductase subunit e;
PDBTitle: crystal structure of the na+-translocating nadh: ubiquinone2 oxidoreductase from vibrio cholerae
38c4ky0B_



not modelled 10.1 18
PDB header:transport protein, membrane protein
Chain: B: PDB Molecule:proton/glutamate symporter, sdf family;
PDBTitle: crystal structure of a substrate-free glutamate transporter homologue2 from thermococcus kodakarensis
39c3izbB_



not modelled 9.8 21
PDB header:ribosome
Chain: B: PDB Molecule:40s ribosomal protein rps3 (s3p);
PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
40c5lj7B_



not modelled 9.7 17
PDB header:transport protein
Chain: B: PDB Molecule:macrolide export atp-binding/permease protein macb;
PDBTitle: structure of aggregatibacter actinomycetemcomitans macb bound to atp2 (p21)
41c3fewX_



not modelled 9.2 15
PDB header:immune system
Chain: X: PDB Molecule:colicin s4;
PDBTitle: structure and function of colicin s4, a colicin with a duplicated2 receptor binding domain
42c1s1hC_



not modelled 9.1 22
PDB header:ribosome
Chain: C: PDB Molecule:40s ribosomal protein s3;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from yeast2 obtained by docking atomic models for rna and protein components into3 a 11.7 a cryo-em map. this file, 1s1h, contains 40s subunit. the 60s4 ribosomal subunit is in file 1s1i.
43c2jvfA_



not modelled 9.0 27
PDB header:de novo protein
Chain: A: PDB Molecule:de novo protein m7;
PDBTitle: solution structure of m7, a computationally-designed2 artificial protein
44d1gtda_



not modelled 8.6 13
Fold:PurS-like
Superfamily:PurS-like
Family:PurS subunit of FGAM synthetase
45c5n9yB_



not modelled 8.4 9
PDB header:membrane protein
Chain: B: PDB Molecule:zinc transport protein zntb;
PDBTitle: the full-length structure of zntb
46c3j20C_



not modelled 8.3 18
PDB header:ribosome
Chain: C: PDB Molecule:30s ribosomal protein s3p;
PDBTitle: promiscuous behavior of proteins in archaeal ribosomes revealed by2 cryo-em: implications for evolution of eukaryotic ribosomes (30s3 ribosomal subunit)
47c4a01B_



not modelled 7.9 11
PDB header:hydrolase
Chain: B: PDB Molecule:proton pyrophosphatase;
PDBTitle: crystal structure of the h-translocating pyrophosphatase
48c4o9uB_



not modelled 7.9 17
PDB header:membrane protein
Chain: B: PDB Molecule:nad(p) transhydrogenase subunit beta;
PDBTitle: mechanism of transhydrogenase coupling proton translocation and2 hydride transfer
49c2bbjB_



not modelled 7.3 11
PDB header:metal transport/membrane protein
Chain: B: PDB Molecule:divalent cation transport-related protein;
PDBTitle: crystal structure of the cora mg2+ transporter
50c1rh1A_



not modelled 7.2 12
PDB header:antibiotic
Chain: A: PDB Molecule:colicin b;
PDBTitle: crystal structure of the cytotoxic bacterial protein2 colicin b at 2.5 a resolution
51c5nikK_



not modelled 7.1 16
PDB header:transport protein
Chain: K: PDB Molecule:macrolide export atp-binding/permease protein macb;
PDBTitle: structure of the macab-tolc abc-type tripartite multidrug efflux pump
52c2zkqc_



not modelled 7.0 13
PDB header:ribosomal protein/rna
Chain: C: PDB Molecule:rna expansion segment es4;
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
53d1cola_



not modelled 6.7 18
Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
54c2yx5A_



not modelled 6.7 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0062 protein mj1593;
PDBTitle: crystal structure of methanocaldococcus jannaschii purs, one of the2 subunits of formylglycinamide ribonucleotide amidotransferase in the3 purine biosynthetic pathway
55d1t4aa_



not modelled 6.6 11
Fold:PurS-like
Superfamily:PurS-like
Family:PurS subunit of FGAM synthetase
56c4od5C_



not modelled 6.6 15
PDB header:transferase
Chain: C: PDB Molecule:4-hydroxybenzoate octaprenyltransferase;
PDBTitle: substrate-bound structure of a ubia homolog from aeropyrum pernix k1
57d1ciia1



not modelled 6.5 13
Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
58c2kyzA_



not modelled 6.3 21
PDB header:metal binding protein
Chain: A: PDB Molecule:heavy metal binding protein;
PDBTitle: nmr structure of heavy metal binding protein tm0320 from thermotoga2 maritima
59c4ev6E_



not modelled 6.1 12
PDB header:metal transport
Chain: E: PDB Molecule:magnesium transport protein cora;
PDBTitle: the complete structure of cora magnesium transporter from2 methanocaldococcus jannaschii
60c2i88A_



not modelled 6.0 18
PDB header:membrane protein
Chain: A: PDB Molecule:colicin-e1;
PDBTitle: crystal structure of the channel-forming domain of colicin e1
61c4kppA_



not modelled 6.0 10
PDB header:membrane protein
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of h+/ca2+ exchanger cax
62c4djiA_



not modelled 5.6 12
PDB header:transport protein
Chain: A: PDB Molecule:probable glutamate/gamma-aminobutyrate antiporter;
PDBTitle: structure of glutamate-gaba antiporter gadc
63c1qysA_



not modelled 5.4 27
PDB header:de novo protein
Chain: A: PDB Molecule:top7;
PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold
64c6fvqE_



not modelled 5.4 10
PDB header:membrane protein
Chain: E: PDB Molecule:cys-loop ligand-gated ion channel;
PDBTitle: the active form of a pentameric ion channel (stelic) gated by alkaline2 ph - r86a
65c5vwxD_



not modelled 5.3 42
PDB header:apoptosis
Chain: D: PDB Molecule:bcl-2-like protein 11;
PDBTitle: bak core latch dimer in complex with bim-h0-h3glt
66c5vwxB_



not modelled 5.3 42
PDB header:apoptosis
Chain: B: PDB Molecule:bcl-2-like protein 11;
PDBTitle: bak core latch dimer in complex with bim-h0-h3glt
67d1a87a_



not modelled 5.3 12
Fold:Toxins' membrane translocation domains
Superfamily:Colicin
Family:Colicin
68c1a87A_



not modelled 5.3 12
PDB header:bacteriocin
Chain: A: PDB Molecule:colicin n;
PDBTitle: colicin n
69d2uubc2



not modelled 5.1 20
Fold:Ribosomal protein S3 C-terminal domain
Superfamily:Ribosomal protein S3 C-terminal domain
Family:Ribosomal protein S3 C-terminal domain

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Transmembrane helix prediction 

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