Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3115_(-)_3481448_3482695
DateThu Aug 8 16:20:29 BST 2019
Unique Job ID94ae8f5f2825583c
SequenceMTSSHLIDAE ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:29.382 Y:29.828 Z:34.252
Model (left) based on template d1k78a1
Top template information
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
Confidence and coverage
Confidence: 92.9% Coverage: 12%
50 residues ( 12% of your sequence) have been modelled with 92.9% confidence by the single highest scoring template.
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Sequence analysis 

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Domain analysis [Show] 

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Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1k78a1
92.9 16
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
2d1pdnc_
92.0 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
3d6paxa1
92.0 10
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
4c6paxA_
90.7 10
PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
5d1au7a2
89.0 10
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:POU-specific domain
6d1e3oc2
88.9 15
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:POU-specific domain
7c4fcyA_
88.5 19
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposase;
PDBTitle: crystal structure of the bacteriophage mu transpososome
8c2m8eA_
86.2 17
PDB header:dna binding protein
Chain: A: PDB Molecule:sleeping beauty transposase;
PDBTitle: nmr structure of the pai subdomain of sleeping beauty transposase
9c1u78A_
85.7 21
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
10c1au7B_
85.4 11
PDB header:transcription/dna
Chain: B: PDB Molecule:protein pit-1;
PDBTitle: pit-1 mutant/dna complex
11c2r0qF_
82.3 16
PDB header:recombination/dna
Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3;
PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex
12c2k27A_
80.8 13
PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
13c1hf0A_
80.7 15
PDB header:transcription
Chain: A: PDB Molecule:octamer-binding transcription factor 1;
PDBTitle: crystal structure of the dna-binding domain of oct-1 bound to dna as a2 dimer
14d1bcoa2
79.9 28
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
15c3d1nK_
79.5 18
PDB header:transcription regulator/dna
Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1;
PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter
16c3zeyG_
78.1 14
PDB header:ribosome
Chain: G: PDB Molecule:40s ribosomal protein s13, putative;
PDBTitle: high-resolution cryo-electron microscopy structure of the trypanosoma2 brucei ribosome
17c1rp3G_
77.8 20
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
18c3l1pA_
77.7 20
PDB header:transcription/dna
Chain: A: PDB Molecule:pou domain, class 5, transcription factor 1;
PDBTitle: pou protein:dna complex
19c2xzmO_
76.2 6
PDB header:ribosome
Chain: O: PDB Molecule:rps13e;
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 1
20c3u5cN_
76.0 6
PDB header:ribosome
Chain: N: PDB Molecule:40s ribosomal protein s13;
PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution. this2 entry contains proteins of the 40s subunit, ribosome a
21c3izbO_
not modelled 75.4 7
PDB header:ribosome
Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p);
PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome
22c2gm4B_
not modelled 74.0 15
PDB header:recombination, dna
Chain: B: PDB Molecule:transposon gamma-delta resolvase;
PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna
23c3frwF_
not modelled 72.6 22
PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
24c3korD_
not modelled 70.5 21
PDB header:transcription
Chain: D: PDB Molecule:possible trp repressor;
PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus
25c1iufA_
not modelled 69.2 8
PDB header:dna binding protein
Chain: A: PDB Molecule:centromere abp1 protein;
PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein
26c2xsdC_
not modelled 68.5 15
PDB header:transcription/dna
Chain: C: PDB Molecule:pou domain, class 3, transcription factor 1;
PDBTitle: crystal structure of the dimeric oct-6 (pou3f1) pou domain2 bound to palindromic more dna
27d1jhga_
not modelled 68.1 8
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
28c6jnyA_
not modelled 62.7 15
PDB header:transcription
Chain: A: PDB Molecule:antiterminator q protein;
PDBTitle: crystal structure of bacteriophage 21 q protein
29d1xsva_
not modelled 62.6 15
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
30d1trra_
not modelled 61.3 11
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
31c1zljE_
not modelled 60.7 10
PDB header:transcription
Chain: E: PDB Molecule:dormancy survival regulator;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain
32d1yb3a1
not modelled 59.5 13
Fold:YktB/PF0168-like
Superfamily:YktB/PF0168-like
Family:PF0168-like
33d1yioa1
not modelled 57.9 10
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)
34c3hosA_
not modelled 57.4 13
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
35d1l3la1
not modelled 56.0 10
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)
36c3j20Q_
not modelled 53.5 14
PDB header:ribosome
Chain: Q: PDB Molecule:30s ribosomal protein s15p/s13e;
PDBTitle: promiscuous behavior of proteins in archaeal ribosomes revealed by2 cryo-em: implications for evolution of eukaryotic ribosomes (30s3 ribosomal subunit)
37c2jpcA_
not modelled 50.3 10
PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
38c3mzyA_
not modelled 49.4 13
PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
39c2rnjA_
not modelled 49.1 8
PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
40c1x3uA_
not modelled 47.7 10
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
41d1fsea_
not modelled 47.6 10
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)
42c3sztB_
not modelled 46.5 5
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
43d1iufa1
not modelled 46.0 11
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
44c5xyiN_
not modelled 45.9 11
PDB header:ribosome
Chain: N: PDB Molecule:40s ribosomal protein s13, putative;
PDBTitle: small subunit of trichomonas vaginalis ribosome
45c6jqsA_
not modelled 45.6 11
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding response regulator;
PDBTitle: structure of transcription factor, gere
46c3cloC_
not modelled 42.9 14
PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution
47c3c3wB_
not modelled 42.7 10
PDB header:transcription
Chain: B: PDB Molecule:two component transcriptional regulatory protein devr;
PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr
48c5ipmF_
not modelled 42.6 12
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
49c1bcoA_
not modelled 42.1 24
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
50d1a04a1
not modelled 40.7 13
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)
51c2lvsA_
not modelled 40.4 16
PDB header:dna binding protein
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: nmr solution structure of a crispr repeat binding protein
52d2bw3a2
not modelled 38.8 16
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Hermes transposase-like
53d1p4wa_
not modelled 38.2 15
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)
54c2krfB_
not modelled 38.2 11
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulatory protein coma;
PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a
55c5f64C_
not modelled 37.4 21
PDB header:transcription regulator
Chain: C: PDB Molecule:positive transcription regulator evga;
PDBTitle: putative positive transcription regulator (sensor evgs) from shigella2 flexneri
56c4kisA_
not modelled 37.0 10
PDB header:recombination/dna
Chain: A: PDB Molecule:putative integrase [bacteriophage a118];
PDBTitle: crystal structure of a lsr-dna complex
57c3qyxD_
not modelled 36.3 5
PDB header:transcription/dna
Chain: D: PDB Molecule:esx-1 secretion-associated regulator espr;
PDBTitle: crystal structure of mycobacterium tuberculosis espr in complex with a2 small dna fragment
58c3klnC_
not modelled 34.0 13
PDB header:transcription
Chain: C: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: vibrio cholerae vpst
59c2mqkA_
not modelled 33.2 11
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent target dna activator b;
PDBTitle: solution structure of n terminal domain of the mub aaa+ atpase
60d2p5ka1
not modelled 31.9 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
61c2m0nA_
not modelled 31.9 26
PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: solution structure of a duf3349 annotated protein from mycobacterium2 abscessus, mab_3403c. seattle structural genomics center for3 infectious disease target myaba.17112.a.a2
62c1e1cA_
not modelled 29.1 18
PDB header:isomerase
Chain: A: PDB Molecule:methylmalonyl-coa mutase alpha chain;
PDBTitle: methylmalonyl-coa mutase h244a mutant
63d1s7oa_
not modelled 27.6 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
64c5o8yG_
not modelled 27.2 17
PDB header:transcription
Chain: G: PDB Molecule:transcriptional regulatory protein rcsb;
PDBTitle: conformational dynamism for dna interaction in salmonella typhimurium2 rcsb response regulator.
65c5nwtM_
not modelled 27.0 11
PDB header:transferase
Chain: M: PDB Molecule:rna polymerase sigma-54 factor,rna polymerase sigma-54
PDBTitle: crystal structure of escherichia coli rna polymerase - sigma542 holoenzyme complex
66c3nf9A_
not modelled 26.9 28
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
67c5u1cD_
not modelled 26.7 22
PDB header:viral protein
Chain: D: PDB Molecule:hiv-1 integrase, sso7d chimera;
PDBTitle: structure of tetrameric hiv-1 strand transfer complex intasome
68d1f9na1
not modelled 26.2 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
69d1pbua_
not modelled 25.6 15
Fold:Ferredoxin-like
Superfamily:eEF1-gamma domain
Family:eEF1-gamma domain
70c2vbzA_
not modelled 24.9 15
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
71c4go1A_
not modelled 24.5 19
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lsrr;
PDBTitle: crystal structure of full length transcription repressor lsrr from e.2 coli.
72c6cy1B_
not modelled 24.1 13
PDB header:signaling protein
Chain: B: PDB Molecule:signal recognition particle receptor ftsy;
PDBTitle: crystal structure of signal recognition particle receptor ftsy from2 elizabethkingia anophelis
73c4if4A_
not modelled 24.0 8
PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: crystal structure of the magnesium and beryllofluoride-activated vrar2 from staphylococcus aureus
74d1stza1
not modelled 23.9 20
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
75d1b4aa1
not modelled 23.7 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Arginine repressor (ArgR), N-terminal DNA-binding domain
76d2fnaa1
not modelled 23.3 12
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Helicase DNA-binding domain
77c5z7iC_
not modelled 22.1 18
PDB header:dna binding protein/dna
Chain: C: PDB Molecule:cell cycle regulatory protein gcra;
PDBTitle: caulobacter crescentus gcra dna-binding domain(dbd)in complex with2 unmethylated dsdna
78c5zx3F_
not modelled 21.5 7
PDB header:transcription
Chain: F: PDB Molecule:ecf rna polymerase sigma factor sigh;
PDBTitle: mycobacterium tuberculosis rna polymerase holoenzyme with ecf sigma2 factor sigma h
79c6ideA_
not modelled 21.3 21
PDB header:transcription/dna
Chain: A: PDB Molecule:transcriptional regulator luxr family;
PDBTitle: crystal structure of the vibrio cholera vqma-ligand-dna complex2 provides molecular mechanisms for drug design
80c5hevC_
not modelled 20.8 10
PDB header:transcription
Chain: C: PDB Molecule:response regulator protein vrar;
PDBTitle: crystal structure of the beryllofluoride-activated liar from2 enterococcus faecium
81c2khqA_
not modelled 20.6 7
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b
82c5cz1B_
not modelled 20.4 9
PDB header:hydrolase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain of mmtv integrase
83d1z6ra1
not modelled 19.8 22
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
84c2q0oA_
not modelled 19.6 10
PDB header:transcription
Chain: A: PDB Molecule:probable transcriptional activator protein trar;
PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing
85c2bw3A_
not modelled 19.2 14
PDB header:dna recombination
Chain: A: PDB Molecule:transposase;
PDBTitle: three-dimensional structure of the hermes dna transposase
86c1h0mD_
not modelled 18.7 10
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
87d2ch5a2
not modelled 18.6 25
Fold:Ribonuclease H-like motif
Superfamily:Actin-like ATPase domain
Family:BadF/BadG/BcrA/BcrD-like
88c3c65A_
not modelled 18.3 18
PDB header:hydrolase
Chain: A: PDB Molecule:uvrabc system protein c;
PDBTitle: crystal structure of bacillus stearothermophilus uvrc 5' endonuclease2 domain
89c1r6uB_
not modelled 18.1 13
PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of an active fragment of human tryptophanyl-trna2 synthetase with cytokine activity
90c4lfuA_
not modelled 17.3 10
PDB header:dna binding protein
Chain: A: PDB Molecule:regulatory protein sdia;
PDBTitle: crystal structure of escherichia coli sdia in the space group c2
91c5uxxC_
not modelled 17.2 6
PDB header:dna binding protein/unknown function
Chain: C: PDB Molecule:rna polymerase sigma factor;
PDBTitle: co-crystal structure of the sigma factor rpoe in complex with the2 anti-sigma factor nepr from bartonella quintana
92d1g3wa1
not modelled 17.2 16
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
93c2gqqB_
not modelled 16.9 17
PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
94c2e7xA_
not modelled 16.8 18
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
95d1ku3a_
not modelled 15.9 5
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
96c4yn8A_
not modelled 15.9 15
PDB header:dna binding protein
Chain: A: PDB Molecule:response regulator chra;
PDBTitle: crystal structure of response regulator chra in heme-sensing two2 component system
97c2hteB_
not modelled 15.9 9
PDB header:transferase
Chain: B: PDB Molecule:spermidine synthase;
PDBTitle: the crystal structure of spermidine synthase from p. falciparum in2 complex with 5'-methylthioadenosine
98c4n1vA_
not modelled 15.7 11
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein hu-beta;
PDBTitle: structure of dna-binding protein hu from micoplasma spiroplasma2 melliferum
99d2isya1
not modelled 15.6 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein

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