Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD0667_(rpoB)_759810_763328
DateFri Jul 26 01:50:23 BST 2019
Unique Job ID45c45dc0742dc1a2
SequenceLADSRQSKTA ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:105.065 Y:100.370 Z:105.529
Model (left) based on template c3lu0C_
Top template information
PDB header:transferase
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: molecular model of escherichia coli core rna polymerase
Confidence and coverage
Confidence:100.0% Coverage: 91%
1072 residues ( 91% 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.
1123 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.
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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
1c3lu0C_
100.0 58
PDB header:transferase
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: molecular model of escherichia coli core rna polymerase
2c6j9eC_
100.0 56
PDB header:transcription
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: cryo-em structure of xanthomonos oryzae transcription elongation2 complex with nusa and the bacteriophage protein p7
3c5tw1C_
100.0 93
PDB header:transcription activator/transferase/dna
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of a mycobacterium smegmatis transcription2 initiation complex with rbpa
4d1smyc_
100.0 52
Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase
Family:RNA-polymerase beta
5d1ynjc1
100.0 51
Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase
Family:RNA-polymerase beta
6c6dcfC_
100.0 95
PDB header:transcription/dna/antibiotic
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of a mycobacterium smegmatis transcription2 initiation complex with rifampicin-resistant rna polymerase and bound3 to kanglemycin a
7c4c2mQ_
100.0 24
PDB header:transcription
Chain: Q: PDB Molecule:dna-directed rna polymerase i subunit rpa135;
PDBTitle: structure of rna polymerase i at 2.8 a resolution
8c3iydC_
100.0 57
PDB header:transcription/dna
Chain: C: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
9c5flmB_
100.0 27
PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase ii subunit rpb2;
PDBTitle: structure of transcribing mammalian rna polymerase ii
10c5fj9B_
100.0 27
PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc2;
PDBTitle: cryo-em structure of yeast apo rna polymerase iii at 4.6 a
11c2pmzB_
100.0 31
PDB header:translation, transferase
Chain: B: PDB Molecule:dna-directed rna polymerase subunit b;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
12c3h0gN_
100.0 27
PDB header:transcription
Chain: N: PDB Molecule:dna-directed rna polymerase ii subunit rpb2;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
13d1twfb_
100.0 27
Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase
Family:RNA-polymerase beta
14c4qiwB_
100.0 31
PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase;
PDBTitle: crystal structure of euryarchaeal rna polymerase from thermococcus2 kodakarensis
15c4kbmA_
100.0 99
PDB header:transferase/transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: structure of the mtb card/rnap beta subunit b1-b2 domains complex
16c3mlqD_
100.0 55
PDB header:transferase/transcription
Chain: D: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain
17c3mlqB_
100.0 44
PDB header:transferase/transcription
Chain: B: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of the thermus thermophilus transcription-repair2 coupling factor rna polymerase interacting domain with the thermus3 aquaticus rna polymerase beta1 domain
18c2ly7A_
100.0 74
PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: b-flap domain of rna polymerase (b. subtilis)
19c3tbiB_
100.0 44
PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of t4 gp33 bound to e. coli rnap beta-flap domain
20c3ltiA_
100.0 50
PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: crystal structure of the escherichia coli rna polymerase beta subunit2 beta2-betai4 domains
21c3qqcA_
not modelled 99.4 22
PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit b, dna-directed rna
PDBTitle: crystal structure of archaeal spt4/5 bound to the rnap clamp domain
22c5j1lA_
not modelled 93.5 26
PDB header:hydrolase
Chain: A: PDB Molecule:toxr-activated gene (tage);
PDBTitle: crystal structure of csd1-csd2 dimer i
23c2lmcB_
not modelled 92.8 27
PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase subunit beta;
PDBTitle: structure of t7 transcription factor gp2-e. coli rnap jaw domain2 complex
24c2gu1A_
not modelled 89.9 28
PDB header:hydrolase
Chain: A: PDB Molecule:zinc peptidase;
PDBTitle: crystal structure of a zinc containing peptidase from2 vibrio cholerae
25c2hsiB_
not modelled 89.3 26
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative peptidase m23;
PDBTitle: crystal structure of putative peptidase m23 from2 pseudomonas aeruginosa, new york structural genomics3 consortium
26c3sluB_
not modelled 84.0 27
PDB header:hydrolase
Chain: B: PDB Molecule:m23 peptidase domain protein;
PDBTitle: crystal structure of nmb0315
27c5j1mD_
not modelled 80.6 23
PDB header:hydrolase
Chain: D: PDB Molecule:toxr-activated gene (tage);
PDBTitle: crystal structure of csd1-csd2 dimer ii
28d1qwya_
not modelled 80.4 31
Fold:Barrel-sandwich hybrid
Superfamily:Duplicated hybrid motif
Family:Peptidoglycan hydrolase LytM
29c4bh5B_
not modelled 79.7 33
PDB header:cell cycle
Chain: B: PDB Molecule:murein hydrolase activator envc;
PDBTitle: lytm domain of envc, an activator of cell wall amidases in2 escherichia coli
30c4rnzA_
not modelled 74.6 24
PDB header:hydrolase
Chain: A: PDB Molecule:conserved hypothetical secreted protein;
PDBTitle: structure of helicobacter pylori csd3 from the hexagonal crystal
31c5gt1A_
not modelled 73.9 24
PDB header:choline-binding protein
Chain: A: PDB Molecule:choline binding protein a;
PDBTitle: crystal structure of cbpa from l. salivarius ren
32c2aujD_
not modelled 73.4 25
PDB header:transferase
Chain: D: PDB Molecule:dna-directed rna polymerase beta' chain;
PDBTitle: structure of thermus aquaticus rna polymerase beta'-subunit2 insert
33c4lxcA_
not modelled 73.1 29
PDB header:hydrolase
Chain: A: PDB Molecule:lysostaphin;
PDBTitle: the antimicrobial peptidase lysostaphin from staphylococcus simulans
34c4qpbB_
not modelled 71.5 32
PDB header:hydrolase
Chain: B: PDB Molecule:lysostaphin;
PDBTitle: catalytic domain of the antimicrobial peptidase lysostaphin from2 staphylococcus simulans crystallized in the absence of phosphate
35c3tufB_
not modelled 71.3 30
PDB header:signaling protein
Chain: B: PDB Molecule:stage ii sporulation protein q;
PDBTitle: structure of the spoiiq-spoiiiah pore forming complex.
36c5kvpA_
not modelled 68.4 22
PDB header:hydrolase
Chain: A: PDB Molecule:zoocin a endopeptidase;
PDBTitle: solution structure of the catalytic domain of zoocin a
37c2b44A_
not modelled 64.3 29
PDB header:hydrolase
Chain: A: PDB Molecule:glycyl-glycine endopeptidase lytm;
PDBTitle: truncated s. aureus lytm, p 32 2 1 crystal form
38c3uz0D_
not modelled 61.5 29
PDB header:transport protein
Chain: D: PDB Molecule:stage ii sporulation protein q;
PDBTitle: crystal structure of spoiiiah and spoiiq complex
39c2aukA_
not modelled 56.6 24
PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase beta' chain;
PDBTitle: structure of e. coli rna polymerase beta' g/g' insert
40d1r46a1
not modelled 54.4 24
Fold:Glycosyl hydrolase domain
Superfamily:Glycosyl hydrolase domain
Family:alpha-Amylases, C-terminal beta-sheet domain
41c6ekaB_
not modelled 47.1 86
PDB header:protein fibril
Chain: B: PDB Molecule:podospora anserina s mat+ genomic dna chromosome 3,
PDBTitle: solid-state mas nmr structure of the hellf prion amyloid fibrils
42c5kqbA_
not modelled 47.0 26
PDB header:hydrolase
Chain: A: PDB Molecule:peptidase m23;
PDBTitle: identification and structural characterization of lytu
43c5b0hB_
not modelled 44.6 11
PDB header:metal binding protein
Chain: B: PDB Molecule:leukocyte cell-derived chemotaxin-2;
PDBTitle: crystal structure of human leukocyte cell-derived chemotaxin 2
44c3nyyA_
not modelled 44.6 28
PDB header:hydrolase
Chain: A: PDB Molecule:putative glycyl-glycine endopeptidase lytm;
PDBTitle: crystal structure of a putative glycyl-glycine endopeptidase lytm2 (rumgna_02482) from ruminococcus gnavus atcc 29149 at 1.60 a3 resolution
45c4yk3B_
not modelled 42.1 30
PDB header:protein binding
Chain: B: PDB Molecule:bepe protein;
PDBTitle: crystal structure of the bid domain of bepe from bartonella henselae
46c4yk2B_
not modelled 42.1 20
PDB header:protein binding
Chain: B: PDB Molecule:bartonella effector protein (bep) substrate of virb t4ss;
PDBTitle: crystal structure of the bid domain of bep9 from bartonella2 clarridgeiae
47d2gpra_
not modelled 42.1 16
Fold:Barrel-sandwich hybrid
Superfamily:Duplicated hybrid motif
Family:Glucose permease-like
48d1glaf_
not modelled 40.3 20
Fold:Barrel-sandwich hybrid
Superfamily:Duplicated hybrid motif
Family:Glucose permease-like
49d2f3ga_
not modelled 36.5 20
Fold:Barrel-sandwich hybrid
Superfamily:Duplicated hybrid motif
Family:Glucose permease-like
50d1gpra_
not modelled 35.9 28
Fold:Barrel-sandwich hybrid
Superfamily:Duplicated hybrid motif
Family:Glucose permease-like
51c2ivfC_
not modelled 35.0 16
PDB header:oxidoreductase
Chain: C: PDB Molecule:ethylbenzene dehydrogenase gamma-subunit;
PDBTitle: ethylbenzene dehydrogenase from aromatoleum aromaticum
52d1uc8a1
not modelled 32.3 18
Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:Lysine biosynthesis enzyme LysX, N-terminal domain
53c2gtiA_
not modelled 32.2 16
PDB header:viral protein
Chain: A: PDB Molecule:replicase polyprotein 1ab;
PDBTitle: mutation of mhv coronavirus non-structural protein nsp15 (f307l)
54c4yk1A_
not modelled 29.7 10
PDB header:protein binding
Chain: A: PDB Molecule:bartonella effector protein (bep) substrate of virb t4ss;
PDBTitle: crystal structure of the bid domain of bep6 from bartonella rochalimae
55c1wcoN_
not modelled 29.1 86
PDB header:peptide/antibiotic
Chain: N: PDB Molecule:nisin z;
PDBTitle: the solution structure of the nisin-lipid ii complex
56d1y4oa1
not modelled 28.8 53
Fold:Profilin-like
Superfamily:Roadblock/LC7 domain
Family:Roadblock/LC7 domain
57c6h5nA_
not modelled 27.8 27
PDB header:cell invasion
Chain: A: PDB Molecule:gametocyte surface protein p45/48;
PDBTitle: plasmodium falciparum pfs48/45 c-terminal domain bound to monoclonal2 antibody 85rf45.1
58d1n26a2
not modelled 26.6 14
Fold:Immunoglobulin-like beta-sandwich
Superfamily:Fibronectin type III
Family:Fibronectin type III
59c4p6vA_
not modelled 25.8 17
PDB header:oxidoreductase
Chain: A: PDB Molecule:na(+)-translocating nadh-quinone reductase subunit a;
PDBTitle: crystal structure of the na+-translocating nadh: ubiquinone2 oxidoreductase from vibrio cholerae
60d1gm5a4
not modelled 25.6 15
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
61c2db3D_
not modelled 24.8 33
PDB header:hydrolase/rna
Chain: D: PDB Molecule:atp-dependent rna helicase vasa;
PDBTitle: structural basis for rna unwinding by the dead-box protein2 drosophila vasa
62c4iqzD_
not modelled 24.2 16
PDB header:unknown function
Chain: D: PDB Molecule:dna-directed rna polymerase subunit beta';
PDBTitle: the crystal structure of a large insert in rna polymerase (rpoc)2 subunit from e. coli
63d1ni7a_
not modelled 23.8 18
Fold:SufE/NifU
Superfamily:SufE/NifU
Family:SufE-like
64c4nhoA_
not modelled 22.5 38
PDB header:hydrolase
Chain: A: PDB Molecule:probable atp-dependent rna helicase ddx23;
PDBTitle: structure of the spliceosomal dead-box protein prp28
65d1lk5a2
not modelled 22.4 17
Fold:Ferredoxin-like
Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain
Family:D-ribose-5-phosphate isomerase (RpiA), lid domain
66d2eyqa5
not modelled 22.3 16
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
67d1mzga_
not modelled 21.8 14
Fold:SufE/NifU
Superfamily:SufE/NifU
Family:SufE-like
68c4meiA_
not modelled 21.2 16
PDB header:protein transport
Chain: A: PDB Molecule:virb8 protein;
PDBTitle: crystal structure of a virb8 type iv secretion system machinery2 soluble domain from bartonella tribocorum
69c5m88A_
not modelled 21.0 23
PDB header:splicing
Chain: A: PDB Molecule:core;
PDBTitle: spliceosome component
70c5c22A_
not modelled 21.0 53
PDB header:protein transport
Chain: A: PDB Molecule:chromosomal hemolysin d;
PDBTitle: crystal structure of zn-bound hlyd from e. coli
71c4bmjC_
not modelled 20.4 50
PDB header:apoptosis
Chain: C: PDB Molecule:tax1-binding protein 1;
PDBTitle: structure of the ubz1and2 tandem of the ubiquitin-binding adaptor2 protein tax1bp1
72c4l0zA_
not modelled 20.4 21
PDB header:transcription/dna
Chain: A: PDB Molecule:runt-related transcription factor 1;
PDBTitle: crystal structure of runx1 and ets1 bound to tcr alpha promoter2 (crystal form 2)
73c1rb8J_
not modelled 20.2 55
PDB header:virus/dna
Chain: J: PDB Molecule:small core protein;
PDBTitle: the phix174 dna binding protein j in two different capsid2 environments.
74c3mjhD_
not modelled 19.9 50
PDB header:protein transport
Chain: D: PDB Molecule:early endosome antigen 1;
PDBTitle: crystal structure of human rab5a in complex with the c2h2 zinc finger2 of eea1
75c3bxzA_
not modelled 19.7 39
PDB header:transport protein
Chain: A: PDB Molecule:preprotein translocase subunit seca;
PDBTitle: crystal structure of the isolated dead motor domains from escherichia2 coli seca
76c4upcA_
not modelled 19.7 20
PDB header:protein binding
Chain: A: PDB Molecule:nicastrin;
PDBTitle: structure of a extracellular domain
77c5xyiT_
not modelled 19.5 20
PDB header:ribosome
Chain: T: PDB Molecule:ribosomal protein s19e, putative;
PDBTitle: small subunit of trichomonas vaginalis ribosome
78c2vb0A_
not modelled 19.2 21
PDB header:hydrolase
Chain: A: PDB Molecule:polyprotein 3bcd;
PDBTitle: crystal structure of coxsackievirus b3 proteinase 3c
79c2nu9E_
not modelled 18.3 21
PDB header:ligase
Chain: E: PDB Molecule:succinyl-coa synthetase beta chain;
PDBTitle: c123at mutant of e. coli succinyl-coa synthetase2 orthorhombic crystal form
80d1cf2o2
not modelled 18.3 29
Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:GAPDH-like
81c5xxuI_
not modelled 17.3 35
PDB header:ribosome
Chain: I: PDB Molecule:ribosomal protein es8;
PDBTitle: small subunit of toxoplasma gondii ribosome
82c5gmkq_
not modelled 17.2 24
PDB header:rna binding protein/rna
Chain: Q: PDB Molecule:pre-mrna-splicing factor slt11;
PDBTitle: cryo-em structure of the catalytic step i spliceosome (c complex) at2 3.4 angstrom resolution
83c3it5B_
not modelled 17.0 22
PDB header:hydrolase
Chain: B: PDB Molecule:protease lasa;
PDBTitle: crystal structure of the lasa virulence factor from pseudomonas2 aeruginosa
84c3cwiA_
not modelled 16.8 18
PDB header:biosynthetic protein
Chain: A: PDB Molecule:thiamine-biosynthesis protein this;
PDBTitle: crystal structure of thiamine biosynthesis protein (this)2 from geobacter metallireducens. northeast structural3 genomics consortium target gmr137
85d1tf5a4
not modelled 15.8 39
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Tandem AAA-ATPase domain
86d1d02a_
not modelled 15.5 17
Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:Restriction endonuclease MunI
87d1px5a1
not modelled 15.3 28
Fold:PAP/OAS1 substrate-binding domain
Superfamily:PAP/OAS1 substrate-binding domain
Family:2'-5'-oligoadenylate synthetase 1, OAS1, second domain
88c6em5b_
not modelled 15.3 25
PDB header:ribosome
Chain: B: PDB Molecule:60s ribosomal protein l3;
PDBTitle: state d architectural model (nsa1-tap flag-ytm1) - visualizing the2 assembly pathway of nucleolar pre-60s ribosomes
89c6g2jY_
not modelled 15.2 38
PDB header:oxidoreductase
Chain: Y: PDB Molecule:mcg5603;
PDBTitle: mouse mitochondrial complex i in the active state
90c4nhfF_
not modelled 15.2 17
PDB header:protein transport
Chain: F: PDB Molecule:trwg protein;
PDBTitle: crystal structure of the soluble domain of trwg type iv secretion2 machinery from bartonella grahamii
91c3izbX_
not modelled 15.2 42
PDB header:ribosome
Chain: X: PDB Molecule:40s ribosomal protein rps27 (s27e);
PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
92c3j20W_
not modelled 15.1 33
PDB header:ribosome
Chain: W: PDB Molecule:30s ribosomal protein s27e;
PDBTitle: promiscuous behavior of proteins in archaeal ribosomes revealed by2 cryo-em: implications for evolution of eukaryotic ribosomes (30s3 ribosomal subunit)
93c1gjjA_
not modelled 15.0 35
PDB header:membrane protein
Chain: A: PDB Molecule:lap2;
PDBTitle: n-terminal constant region of the nuclear envelope protein2 lap2
94c2qhoB_
not modelled 14.9 52
PDB header:protein binding/ligase
Chain: B: PDB Molecule:e3 ubiquitin-protein ligase edd1;
PDBTitle: crystal structure of the uba domain from edd ubiquitin2 ligase in complex with ubiquitin
95c1m1jA_
not modelled 14.9 50
PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha subunit;
PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands
96c2f1mA_
not modelled 14.8 20
PDB header:transport protein
Chain: A: PDB Molecule:acriflavine resistance protein a;
PDBTitle: conformational flexibility in the multidrug efflux system protein acra
97c3wfoB_
not modelled 14.8 34
PDB header:transferase
Chain: B: PDB Molecule:poly a polymerase;
PDBTitle: trna processing enzyme (apo form 1)
98c1bplA_
not modelled 14.6 26
PDB header:glycosyltransferase
Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase;
PDBTitle: glycosyltransferase
99c2bhmE_
not modelled 14.6 8
PDB header:bacterial protein
Chain: E: PDB Molecule:type iv secretion system protein virb8;
PDBTitle: crystal structure of virb8 from brucella suis

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Transmembrane helix prediction 

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