Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3614c_(-)_4054321_4054875
DateFri Aug 9 18:20:30 BST 2019
Unique Job ID1bb420e28d9a018b
SequenceVDLPGNDFDS ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:32.318 Y:30.378 Z:55.202
Model (left) based on template d1puga_
Top template information
Fold:YbaB-like
Superfamily:YbaB-like
Family:YbaB-like
Confidence and coverage
Confidence: 97.5% Coverage: 38%
70 residues ( 38% of your sequence) have been modelled with 97.5% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in JSmol
For other options to view your downloaded structure offline see the FAQ

Sequence analysis 

Download FASTA version

Secondary structure and disorder prediction [Show] 

Domain analysis [Show] 

Detailed template information [Hide] 

 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1puga_



97.5 13
Fold:YbaB-like
Superfamily:YbaB-like
Family:YbaB-like
2d1j8ba_



96.7 11
Fold:YbaB-like
Superfamily:YbaB-like
Family:YbaB-like
3c1ybxA_



96.4 20
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: conserved hypothetical protein cth-383 from clostridium thermocellum
4d1pugb_



93.2 14
Fold:YbaB-like
Superfamily:YbaB-like
Family:YbaB-like
5c5yrxA_



86.5 13
PDB header:dna binding protein
Chain: A: PDB Molecule:nucleoid-associated protein rv3716c;
PDBTitle: crystal structure of a hypothetical protein rv3716c from mycobacterium2 tuberculosis
6c3f42A_



72.2 10
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:protein hp0035;
PDBTitle: crystal structure of uncharacterized protein hp0035 from helicobacter2 pylori
7c6bbqA_



48.5 26
PDB header:lipid binding protein
Chain: A: PDB Molecule:cytohesin-3,adp-ribosylation factor 6;
PDBTitle: model for extended volume of truncated monomeric cytohesin-3 (grp1;2 amino acids 63-399) e161a arf6 q67l fusion protein
8c4oiyA_



39.0 19
PDB header:protein transport
Chain: A: PDB Molecule:protein transport protein sec7;
PDBTitle: crystal structure of sec7p catalytic domain
9c3l8nA_



36.0 30
PDB header:nucleotide-binding protein, metal-bindin
Chain: A: PDB Molecule:brefeldin a-inhibited guanine nucleotide-exchange
PDBTitle: crystal structure of a domain of brefeldin a-inhibited2 guanine nucleotide-exchange protein 2 (brefeldina-inhibited3 gep 2) from homo sapiens (human). northeast structural4 genomics consortium target id hr5562a
10d2ivda2



35.9 19
Fold:FAD-linked reductases, C-terminal domain
Superfamily:FAD-linked reductases, C-terminal domain
Family:L-aminoacid/polyamine oxidase
11d1aepa_



33.2 32
Fold:Apolipophorin-III
Superfamily:Apolipophorin-III
Family:Apolipophorin-III
12d1re0b_



33.0 23
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
13d1seza2



31.2 18
Fold:FAD-linked reductases, C-terminal domain
Superfamily:FAD-linked reductases, C-terminal domain
Family:L-aminoacid/polyamine oxidase
14d1pbva_



30.5 22
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
15c4e6zA_



26.5 15
PDB header:transport protein
Chain: A: PDB Molecule:apicoplast tic22, putative;
PDBTitle: tic22 from plasmodium falciparum
16c3rhiB_



26.5 10
PDB header:dna binding protein
Chain: B: PDB Molecule:dna-binding protein hu;
PDBTitle: dna-binding protein hu from bacillus anthracis
17d1xsza1



25.1 20
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
18d2r09a1



25.0 24
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
19d1ku1a_



23.8 11
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
20c4c0aA_



23.5 15
PDB header:protein transport
Chain: A: PDB Molecule:iq motif and sec7 domain-containing protein 1;
PDBTitle: arf1(delta1-17)in complex with brag2 sec7-ph domain
21c3dinB_



not modelled 22.5 30
PDB header:membrane protein, protein transport
Chain: B: PDB Molecule:protein translocase subunit seca;
PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase
22d1bc9a_



not modelled 22.0 24
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
23c3juxA_



not modelled 22.0 30
PDB header:protein transport
Chain: A: PDB Molecule:protein translocase subunit seca;
PDBTitle: structure of the translocation atpase seca from thermotoga2 maritima
24c1ls4A_



not modelled 22.0 30
PDB header:lipid transport
Chain: A: PDB Molecule:apolipophorin-iii;
PDBTitle: nmr structure of apolipophorin-iii from locusta migratoria
25c1xszA_



not modelled 21.9 20
PDB header:signaling protein
Chain: A: PDB Molecule:guanine nucleotide exchange protein;
PDBTitle: the structure of ralf
26d1sf9a_



not modelled 20.4 30
Fold:SH3-like barrel
Superfamily:Hypothetical protein YfhH
Family:Hypothetical protein YfhH
27d1hn0a3



not modelled 20.1 13
Fold:Hyaluronate lyase-like, C-terminal domain
Superfamily:Hyaluronate lyase-like, C-terminal domain
Family:Hyaluronate lyase-like, C-terminal domain
28c4u3qA_



not modelled 18.9 38
PDB header:lipid binding protein
Chain: A: PDB Molecule:17 kda lipoprotein;
PDBTitle: crystal structure of recombinant tp0435 from treponema pallidum
29c2r09A_



not modelled 18.7 24
PDB header:signaling protein
Chain: A: PDB Molecule:cytohesin-3;
PDBTitle: crystal structure of autoinhibited form of grp1 arf gtpase exchange2 factor
30c3no0B_



not modelled 18.7 33
PDB header:isomerase
Chain: B: PDB Molecule:dna gyrase subunit a;
PDBTitle: aquifex aeolicus type iia topoisomerase c-terminal domain
31c1mpgB_



not modelled 18.4 15
PDB header:hydrolase
Chain: B: PDB Molecule:3-methyladenine dna glycosylase ii;
PDBTitle: 3-methyladenine dna glycosylase ii from escherichia coli
32c3bs6B_



not modelled 17.6 18
PDB header:membrane protein, protein transport
Chain: B: PDB Molecule:inner membrane protein oxaa;
PDBTitle: 1.8 angstrom crystal structure of the periplasmic domain of2 the membrane insertase yidc
33d1r8se_



not modelled 17.4 22
Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain
34c3blcB_



not modelled 17.3 18
PDB header:chaperone,protein transport
Chain: B: PDB Molecule:inner membrane protein oxaa;
PDBTitle: crystal structure of the periplasmic domain of the escherichia coli2 yidc
35d2a9da1



not modelled 16.8 33
Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Molybdenum-containing oxidoreductases-like dimerisation domain
36c4ph8B_



not modelled 14.3 39
PDB header:cell adhesion
Chain: B: PDB Molecule:aggregative adherence fimbrial subunit agga;
PDBTitle: crystal structure of agga, the major subunit of aggregative adherence2 fimbriae type i (aaf/i) from the escherichia coli o4h104
37c3dl8B_



not modelled 14.2 26
PDB header:protein transport
Chain: B: PDB Molecule:protein translocase subunit seca;
PDBTitle: structure of the complex of aquifex aeolicus secyeg and bacillus2 subtilis seca
38d1ogpa1



not modelled 13.7 38
Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Molybdenum-containing oxidoreductases-like dimerisation domain
39d1ofcx1



not modelled 13.3 33
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
40c5n76C_



not modelled 13.3 32
PDB header:nickel-binding protein
Chain: C: PDB Molecule:coot;
PDBTitle: crystal structure of the apo-form of the co dehydrogenase accessory2 protein coot from rhodospirillum rubrum
41c6n2lA_



not modelled 13.1 7
PDB header:dna binding protein
Chain: A: PDB Molecule:histone family protein dna-binding protein;
PDBTitle: crystal structure of a histone family protein dna-binding protein from2 burkholderia ambifaria
42c1tf2A_



not modelled 12.5 26
PDB header:protein transport
Chain: A: PDB Molecule:preprotein translocase seca subunit;
PDBTitle: crystal structure of seca:adp in an open conformation from2 bacillus subtilis
43c5hqhA_



not modelled 12.3 19
PDB header:unknown function
Chain: A: PDB Molecule:lmo2119 protein;
PDBTitle: 1.32 angstrom crystal structure of ybbr like domain of lmo2119 protein2 from listeria monocytogenes.
44c5fmfV_



not modelled 11.9 3
PDB header:transcription
Chain: V: PDB Molecule:transcription initiation factor iif subunit beta, tfg2;
PDBTitle: the p-lobe of rna polymerase ii pre-initiation complex
45c2mvnA_



not modelled 11.8 53
PDB header:translation
Chain: A: PDB Molecule:elongation factor 1-delta;
PDBTitle: solution structure of eef1bdelta car domain in tctp-bound state
46c2mvmA_



not modelled 11.8 53
PDB header:translation
Chain: A: PDB Molecule:elongation factor 1-delta;
PDBTitle: solution structure of eef1bdelta car domain
47c2vdaA_



not modelled 11.6 33
PDB header:protein transport
Chain: A: PDB Molecule:translocase subunit seca;
PDBTitle: solution structure of the seca-signal peptide complex
48d1huua_



not modelled 11.1 17
Fold:IHF-like DNA-binding proteins
Superfamily:IHF-like DNA-binding proteins
Family:Prokaryotic DNA-bending protein
49c1junB_



not modelled 11.1 26
PDB header:transcription regulation
Chain: B: PDB Molecule:c-jun homodimer;
PDBTitle: nmr study of c-jun homodimer
50c3bovA_



not modelled 11.0 35
PDB header:immune system
Chain: A: PDB Molecule:programmed cell death 1 ligand 2;
PDBTitle: crystal structure of the receptor binding domain of mouse pd-l2
51d1b33n_



not modelled 10.8 46
Fold:Allophycocyanin linker chain (domain)
Superfamily:Allophycocyanin linker chain (domain)
Family:Allophycocyanin linker chain (domain)
52c2auhB_



not modelled 10.3 27
PDB header:transferase/signaling protein
Chain: B: PDB Molecule:growth factor receptor-bound protein 14;
PDBTitle: crystal structure of the grb14 bps region in complex with2 the insulin receptor tyrosine kinase
53d3bzka3



not modelled 10.3 14
Fold:Tex N-terminal region-like
Superfamily:Tex N-terminal region-like
Family:Tex N-terminal region-like
54c5mq9A_



not modelled 10.3 15
PDB header:translation
Chain: A: PDB Molecule:uncharacterized protein yacp;
PDBTitle: crystal structure of rae1 (yacp) from bacillus subtilis (w164l mutant)
55c2ipcB_



not modelled 10.2 46
PDB header:transport protein
Chain: B: PDB Molecule:preprotein translocase seca subunit;
PDBTitle: crystal structure of the translocation atpase seca from thermus2 thermophilus reveals a parallel, head-to-head dimer
56d2ifta1



not modelled 9.9 19
Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:YhhF-like
57d1cz5a2



not modelled 9.6 21
Fold:Cdc48 domain 2-like
Superfamily:Cdc48 domain 2-like
Family:Cdc48 domain 2-like
58d1owfa_



not modelled 9.5 7
Fold:IHF-like DNA-binding proteins
Superfamily:IHF-like DNA-binding proteins
Family:Prokaryotic DNA-bending protein
59c4bpyA_



not modelled 9.4 12
PDB header:chaperone
Chain: A: PDB Molecule:sco protein;
PDBTitle: crystal structure of the c90a mutant of the sco copper chaperone2 protein from streptomyces lividans
60c1nl3B_



not modelled 9.3 27
PDB header:protein transport
Chain: B: PDB Molecule:preprotein translocase seca 1 subunit;
PDBTitle: crystal structure of the seca protein translocation atpase2 from mycobacterium tuberculosis in apo form
61d1py9a_



not modelled 9.2 21
Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:V set domains (antibody variable domain-like)
62c5ekaA_



not modelled 9.0 7
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein hu;
PDBTitle: hu dna-binding protein from thermus thermophilus
63c3c4iA_



not modelled 8.3 15
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein hu homolog;
PDBTitle: crystal structure analysis of n terminal region containing the2 dimerization domain and dna binding domain of hu protein(histone like3 protein-dna binding) from mycobacterium tuberculosis [h37rv]
64c1ygaA_



not modelled 8.3 3
PDB header:isomerase
Chain: A: PDB Molecule:hypothetical 37.9 kda protein in bio3-hxt17
PDBTitle: crystal structure of saccharomyces cerevisiae yn9a protein,2 new york structural genomics consortium
65c4ev1A_



not modelled 8.2 21
PDB header:chaperone
Chain: A: PDB Molecule:anabena tic22;
PDBTitle: anabaena tic22 (protein transport)
66d1nsza_



not modelled 8.2 27
Fold:Supersandwich
Superfamily:Galactose mutarotase-like
Family:Aldose 1-epimerase (mutarotase)
67c2yxyA_



not modelled 8.0 20
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical conserved protein, gk0453;
PDBTitle: crystarl structure of hypothetical conserved protein, gk0453
68d1exea_



not modelled 7.9 15
Fold:IHF-like DNA-binding proteins
Superfamily:IHF-like DNA-binding proteins
Family:Prokaryotic DNA-bending protein
69c5bncB_



not modelled 7.8 25
PDB header:heme binding protein
Chain: B: PDB Molecule:heme binding protein msmeg_6519;
PDBTitle: structure of heme binding protein msmeg_6519 from mycobacterium2 smegmatis
70d1h0ha1



not modelled 7.8 8
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
71d1ndba2



not modelled 7.8 18
Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
72c3ogiC_



not modelled 7.6 33
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:putative esat-6-like protein 6;
PDBTitle: crystal structure of the mycobacterium tuberculosis h37rv esxop2 complex (rv2346c-rv2347c)
73c1s5rA_



not modelled 7.5 36
PDB header:transcription
Chain: A: PDB Molecule:high mobility group box transcription factor 1;
PDBTitle: solution structure of hbp1 sid-msin3a pah2 complex
74c4gzrA_



not modelled 7.5 33
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:esat-6-like protein 6;
PDBTitle: crystal structure of the mycobacterium tuberculosis h37rv esxop2 (rv2346c-rv2347c) complex in space group c2221
75c4uaqA_



not modelled 7.5 33
PDB header:protein transport
Chain: A: PDB Molecule:protein translocase subunit seca 2;
PDBTitle: crystal structure of the accessory translocation atpase, seca2, from2 mycobacterium tuberculosis
76d1jmta_



not modelled 7.5 38
Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Splicing factor U2AF subunits
77d1jmxa1



not modelled 7.4 18
Fold:Cytochrome c
Superfamily:Cytochrome c
Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
78c2lf6A_



not modelled 7.4 24
PDB header:signaling protein
Chain: A: PDB Molecule:effector protein hopab1;
PDBTitle: solution nmr structure of hopabpph1448_220_320 from pseudomonas2 syringae pv. phaseolicola str. 1448a, midwest center for structural3 genomics target apc40132.4 and northeast structural genomics4 consortium target pst3a
79c3v8vB_



not modelled 7.3 19
PDB header:transferase
Chain: B: PDB Molecule:ribosomal rna large subunit methyltransferase l;
PDBTitle: crystal structure of bifunctional methyltransferase ycby (rlmlk) from2 escherichia coli, sam binding
80c4qjuB_



not modelled 7.1 22
PDB header:dna binding protein/dna
Chain: B: PDB Molecule:dna-binding protein hu;
PDBTitle: crystal structure of dna-bound nucleoid associated protein, sav1473
81c3na2C_



not modelled 7.0 38
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of protein of unknown function from mine drainage2 metagenome leptospirillum rubarum
82c6raoH_



not modelled 7.0 38
PDB header:virus like particle
Chain: H: PDB Molecule:afp9;
PDBTitle: cryo-em structure of the anti-feeding prophage (afp) baseplate, 6-fold2 symmetrised
83d1b8za_



not modelled 6.6 8
Fold:IHF-like DNA-binding proteins
Superfamily:IHF-like DNA-binding proteins
Family:Prokaryotic DNA-bending protein
84c4il7A_



not modelled 6.4 21
PDB header:viral protein
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of a223 c-terminal domain, a structural protein from2 sulfolobus turreted icosahedral virus (stiv)
85d1ntca_



not modelled 6.4 50
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
86d1pkoa_



not modelled 6.2 21
Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:V set domains (antibody variable domain-like)
87d1kqfa1



not modelled 6.1 12
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
88c4rs7R_



not modelled 6.1 18
PDB header:dna binding protein
Chain: R: PDB Molecule:parb-c;
PDBTitle: structure of pnob8 parb-c
89c3b1sB_



not modelled 6.1 24
PDB header:protein transport
Chain: B: PDB Molecule:flagellar biosynthetic protein flhb;
PDBTitle: crystal structure of the cytoplasmic domain of flhb from aquifex2 aeolicus
90d1we6a_



not modelled 6.0 26
Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
91c5lvtC_



not modelled 6.0 15
PDB header:dna binding protein
Chain: C: PDB Molecule:dna-binding protein hu;
PDBTitle: structure of hu protein from lactococcus lactis
92c3bvsA_



not modelled 5.9 8
PDB header:hydrolase
Chain: A: PDB Molecule:alkylpurine dna glycosylase alkd;
PDBTitle: crystal structure of bacillus cereus alkylpurine dna glycosylase alkd
93c2vt1B_



not modelled 5.9 14
PDB header:membrane protein
Chain: B: PDB Molecule:surface presentation of antigens protein spas;
PDBTitle: crystal structure of the cytoplasmic domain of spa40, the specificity2 switch for the shigella flexneri type iii secretion system
94c3k2kA_



not modelled 5.7 16
PDB header:hydrolase
Chain: A: PDB Molecule:putative carboxypeptidase;
PDBTitle: crystal structure of putative carboxypeptidase (yp_103406.1) from2 burkholderia mallei atcc 23344 at 2.49 a resolution
95c4b24A_



not modelled 5.6 17
PDB header:hydrolase/dna
Chain: A: PDB Molecule:probable dna-3-methyladenine glycosylase 2;
PDBTitle: unprecedented sculpting of dna at abasic sites by dna glycoslase2 homolog mag2
96c2n51A_



not modelled 5.6 53
PDB header:translation
Chain: A: PDB Molecule:elongation factor 1-delta;
PDBTitle: nmr structure of the c-terminal region of human eukaryotic elongation2 factor 1b
97d1pbya1



not modelled 5.4 21
Fold:Cytochrome c
Superfamily:Cytochrome c
Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
98c2n5lA_



not modelled 5.3 46
PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease zc3h12a;
PDBTitle: regnase-1 c-terminal domain
99c2f1mA_



not modelled 5.3 17
PDB header:transport protein
Chain: A: PDB Molecule:acriflavine resistance protein a;
PDBTitle: conformational flexibility in the multidrug efflux system protein acra

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