Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD0430_(-)_518736_519044
DateTue Jul 23 14:50:50 BST 2019
Unique Job IDafcd674ca09e725a
SequenceMDSAMARAIR ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:27.349 Y:24.387 Z:33.035
Model (left) based on template c3jsoA_
Top template information
PDB header:hydrolase/dna
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: classic protein with a new twist: crystal structure of a lexa2 repressor dna complex
Confidence and coverage
Confidence: 89.1% Coverage: 44%
45 residues ( 44% of your sequence) have been modelled with 89.1% confidence by the single highest scoring template.
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Sequence analysis 

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Secondary structure and disorder prediction [Show] 

Domain analysis [Show] 

Detailed template information [Hide] 

 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3jsoA_
89.1 22
PDB header:hydrolase/dna
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: classic protein with a new twist: crystal structure of a lexa2 repressor dna complex
2d1jhfa1
89.0 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
3c3k2zA_
85.6 24
PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
4c2l4aA_
83.7 13
PDB header:dna binding protein
Chain: A: PDB Molecule:leucine responsive regulatory protein;
PDBTitle: nmr structure of the dna-binding domain of e.coli lrp
5d2cfxa1
77.3 9
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
6d2cg4a1
74.7 9
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
7c1dpuA_
73.3 22
PDB header:dna binding protein
Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain;
PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88)
8d1dpua_
73.3 22
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal domain of RPA32
9d1i1ga1
73.2 19
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
10d1ku7a_
72.7 19
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
11c1zljE_
71.3 17
PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
12d1a04a1
65.1 23
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
13c3sztB_
63.6 17
PDB header:transcription
Chain: B: PDB Molecule:quorum-sensing control repressor;
PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone
14c2q0oA_
62.1 21
PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
15c4czdA_
60.8 6
PDB header:lyase
Chain: A: PDB Molecule:putative transcriptional regulator, asnc family;
PDBTitle: sirohaem decarboxylase ahba/b - an enzyme with structural homology2 to the lrp/asnc transcription factor family that is part of the3 alternative haem biosynthesis pathway.
16c4lfuA_
56.3 14
PDB header:dna binding protein
Chain: A: PDB Molecule:regulatory protein sdia;
PDBTitle: crystal structure of escherichia coli sdia in the space group c2
17d1ku3a_
56.1 19
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
18c4czdD_
55.4 13
PDB header:lyase
Chain: D: PDB Molecule:putative transcriptional regulator, asnc family;
PDBTitle: sirohaem decarboxylase ahba/b - an enzyme with structural homology2 to the lrp/asnc transcription factor family that is part of the3 alternative haem biosynthesis pathway.
19d1l3la1
55.1 19
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
20c6jqsA_
54.0 19
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: structure of transcription factor, gere
21c2krfB_
not modelled 53.8 26
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
22d2cyya1
not modelled 52.7 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Lrp/AsnC-like transcriptional regulator N-terminal domain
23c1i1gA_
not modelled 52.6 19
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
24c2cg4B_
not modelled 52.4 9
PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
25c1h0mD_
not modelled 51.7 25
PDB header:transcription/dna
Chain: D: PDB Molecule:transcriptional activator protein trar;
PDBTitle: three-dimensional structure of the quorum sensing protein trar bound2 to its autoinducer and to its target dna
26c4pcqC_
not modelled 50.7 16
PDB header:transcription
Chain: C: PDB Molecule:possible transcriptional regulatory protein (probably
PDBTitle: crystal structure of mtbaldr (rv2779c)
27c2dbbA_
not modelled 49.0 9
PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
28c2ia0A_
not modelled 48.5 14
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864;
PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
29c2vbzA_
not modelled 47.4 11
PDB header:dna-binding protein
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
30d2p7vb1
not modelled 44.8 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
31d2oyoa1
not modelled 42.7 15
Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
32c6c05F_
not modelled 40.4 15
PDB header:transcription
Chain: F: PDB Molecule:rna polymerase sigma factor siga;
PDBTitle: mycobacterium tuberculosis rnap holo/rbpa in relaxed state
33c3qp5C_
not modelled 39.4 22
PDB header:transcription
Chain: C: PDB Molecule:cvir transcriptional regulator;
PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl)
34c2cfxD_
not modelled 39.0 9
PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
35c2e7xA_
not modelled 38.3 11
PDB header:transcription regulator
Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator;
PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
36d3proc1
not modelled 38.2 22
Fold:Alpha-lytic protease prodomain-like
Superfamily:Alpha-lytic protease prodomain
Family:Alpha-lytic protease prodomain
37c2e1cA_
not modelled 38.1 11
PDB header:transcription/dna
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519;
PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
38d1fsea_
not modelled 36.4 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
39c2p6tH_
not modelled 35.1 19
PDB header:transcription
Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family;
PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
40d1ttya_
not modelled 34.2 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
41c2rnjA_
not modelled 32.4 21
PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
42c1rp3G_
not modelled 32.1 15
PDB header:transcription
Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia);
PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma complex, sigma-2 28/flgm
43c2vn2B_
not modelled 31.2 17
PDB header:replication
Chain: B: PDB Molecule:chromosome replication initiation protein;
PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426
44d2fm8c1
not modelled 29.6 44
Fold:SipA N-terminal domain-like
Superfamily:SipA N-terminal domain-like
Family:SipA N-terminal domain-like
45c1l9uH_
not modelled 29.2 19
PDB header:transcription
Chain: H: PDB Molecule:sigma factor siga;
PDBTitle: thermus aquaticus rna polymerase holoenzyme at 4 a2 resolution
46c3t72o_
not modelled 28.1 20
PDB header:transcription/dna
Chain: O: PDB Molecule:pho box dna (strand 1);
PDBTitle: phob(e)-sigma70(4)-(rnap-betha-flap-tip-helix)-dna transcription2 activation sub-complex
47d2v9va2
not modelled 27.7 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal fragment of elongation factor SelB
48d2fm9a1
not modelled 27.5 44
Fold:SipA N-terminal domain-like
Superfamily:SipA N-terminal domain-like
Family:SipA N-terminal domain-like
49d1bl0a2
not modelled 27.4 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
50d1smyf2
not modelled 26.9 24
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
51c2dg6A_
not modelled 25.6 24
PDB header:gene regulation
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of the putative transcriptional regulator sco55502 from streptomyces coelicolor a3(2)
52d1p4wa_
not modelled 24.6 12
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
53c3wodF_
not modelled 23.5 23
PDB header:transferase/transcription
Chain: F: PDB Molecule:rna polymerase sigma factor;
PDBTitle: rna polymerase-gp39 complex
54c5ipmF_
not modelled 23.0 13
PDB header:transcription, transferase/dna/rna
Chain: F: PDB Molecule:rna polymerase sigma factor rpos;
PDBTitle: sigmas-transcription initiation complex with 4-nt nascent rna
55d2pfxa1
not modelled 22.4 17
Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
56c2v79B_
not modelled 22.3 17
PDB header:dna binding protein
Chain: B: PDB Molecule:dna replication protein dnad;
PDBTitle: crystal structure of the n-terminal domain of dnad from bacillus2 subtilis
57d1u5ta2
not modelled 22.3 20
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Vacuolar sorting protein domain
58c5tw1F_
not modelled 22.0 13
PDB header:transcription activator/transferase/dna
Chain: F: PDB Molecule:rna polymerase sigma factor siga;
PDBTitle: crystal structure of a mycobacterium smegmatis transcription2 initiation complex with rbpa
59c2v9vA_
not modelled 21.4 17
PDB header:transcription
Chain: A: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: crystal structure of moorella thermoacetica selb(377-511)
60c2zmeA_
not modelled 21.2 25
PDB header:protein transport
Chain: A: PDB Molecule:vacuolar-sorting protein snf8;
PDBTitle: integrated structural and functional model of the human escrt-ii2 complex
61d1gjsa_
not modelled 20.9 32
Fold:immunoglobulin/albumin-binding domain-like
Superfamily:Bacterial immunoglobulin/albumin-binding domains
Family:GA module, an albumin-binding domain
62d1yioa1
not modelled 20.7 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
63c3cuqA_
not modelled 20.5 26
PDB header:protein transport
Chain: A: PDB Molecule:vacuolar-sorting protein snf8;
PDBTitle: integrated structural and functional model of the human escrt-ii2 complex
64c1x3uA_
not modelled 20.0 20
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
65d2d1ha1
not modelled 20.0 22
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
66c2mulA_
not modelled 19.8 8
PDB header:protein binding
Chain: A: PDB Molecule:e3 ubiquitin-protein ligase huwe1;
PDBTitle: solution structure of the ubm1 domain of human huwe1/arf-bp1
67c3u07A_
not modelled 18.5 11
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein vpa0106;
PDBTitle: crystal structure of the vpa0106 protein from vibrio parahaemolyticus.2 northeast structural genomics consortium target vpr106.
68c6cmvA_
not modelled 17.3 22
PDB header:gene regulation
Chain: A: PDB Molecule:transcriptional regulator lrs14-like protein;
PDBTitle: crystal structure of archaeal biofilm regulator (abfr2) from2 sulfolobus acidocaldarius
69d2p3ya1
not modelled 17.1 13
Fold:VPA0735-like
Superfamily:VPA0735-like
Family:VPA0735-like
70c2p3yA_
not modelled 17.1 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein vpa0735;
PDBTitle: crystal structure of vpa0735 from vibrio parahaemolyticus. northeast2 structural genomics target vpr109
71c4yifE_
not modelled 16.3 13
PDB header:dna binding protein
Chain: E: PDB Molecule:marr family protein rv0880;
PDBTitle: crystal structure of rv0880
72d1myla_
not modelled 15.5 25
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:Arc/Mnt-like phage repressors
73c3mklB_
not modelled 14.8 14
PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
74c2gqqB_
not modelled 14.7 19
PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
75d1b28a_
not modelled 14.2 25
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:Arc/Mnt-like phage repressors
76c3iydF_
not modelled 14.1 20
PDB header:transcription/dna
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex
77d1d5ya2
not modelled 12.0 29
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
78d2i15a1
not modelled 12.0 28
Fold:MG296-like
Superfamily:MG296-like
Family:MG296-like
79c5bqtC_
not modelled 11.8 20
PDB header:dna binding protein
Chain: C: PDB Molecule:putative hth-type transcriptional regulator trmbl2;
PDBTitle: structure of trmbl2, an archaeal chromatin protein, shows a novel mode2 of dna binding.
80c3klnC_
not modelled 11.2 22
PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
81c3lvyB_
not modelled 11.2 10
PDB header:lyase
Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family;
PDBTitle: crystal structure of carboxymuconolactone decarboxylase2 family protein smu.961 from streptococcus mutans
82c3b73A_
not modelled 10.9 18
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phih1 repressor-like protein;
PDBTitle: crystal structure of the phih1 repressor-like protein from haloarcula2 marismortui
83c3go5A_
not modelled 10.9 27
PDB header:gene regulation
Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains;
PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution
84c3h87D_
not modelled 10.8 27
PDB header:toxin/antitoxin
Chain: D: PDB Molecule:putative uncharacterized protein;
PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis
85c3zplE_
not modelled 10.8 18
PDB header:transcription/dna
Chain: E: PDB Molecule:putative marr-family transcriptional repressor;
PDBTitle: crystal structure of sco3205, a marr family transcriptional regulator2 from streptomyces coelicolor, in complex with dna
86d1heka_
not modelled 10.6 62
Fold:Retroviral matrix proteins
Superfamily:Retroviral matrix proteins
Family:EIAV matrix antigen
87c2a6eF_
not modelled 10.2 24
PDB header:transferase
Chain: F: PDB Molecule:rna polymerase sigma factor rpod;
PDBTitle: crystal structure of the t. thermophilus rna polymerase2 holoenzyme
88d1rp3a1
not modelled 9.5 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma3 domain
89c3mn2B_
not modelled 9.4 11
PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
90c3rmrA_
not modelled 9.4 29
PDB header:protein binding
Chain: A: PDB Molecule:avirulence protein;
PDBTitle: crystal structure of hyaloperonospora arabidopsidis atr1 effector2 domain
91c4ch7A_
not modelled 9.3 17
PDB header:transcription
Chain: A: PDB Molecule:nird-like protein;
PDBTitle: crystal structure of the siroheme decarboxylase nirdl
92c2nyxB_
not modelled 9.2 11
PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
93c5wurB_
not modelled 9.1 7
PDB header:metal binding protein
Chain: B: PDB Molecule:ecf rna polymerase sigma factor sigw;
PDBTitle: crystal structure of sigw in complex with its anti-sigma rsiw, an2 oxdized form
94c3r0aB_
not modelled 9.1 9
PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
95c3n41A_
not modelled 9.0 50
PDB header:viral protein
Chain: A: PDB Molecule:e3 envelope glycoprotein;
PDBTitle: crystal structure of the mature envelope glycoprotein complex2 (spontaneous cleavage) of chikungunya virus.
96d1sd4a_
not modelled 8.8 16
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
97d1d5ya1
not modelled 8.5 13
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
98c2k4bA_
not modelled 8.4 16
PDB header:dna binding protein
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: copr repressor structure
99c4proD_
not modelled 8.4 22
PDB header:serine protease
Chain: D: PDB Molecule:alpha-lytic protease;
PDBTitle: alpha-lytic protease complexed with pro region

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