Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3023c_(-)_3381386_3382633
DateThu Aug 8 16:20:19 BST 2019
Unique Job ID3c6a978a06fc81cc
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.
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
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

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