Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3413c_(-)_3832326_3833225
DateFri Aug 9 18:20:08 BST 2019
Unique Job ID538a8af8d9f489b0
SequenceMREFGNPLGD ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:27.439 Y:33.225 Z:34.121
Model (left) based on template c3vepC_
Top template information
PDB header:membrane protein/transcription
Chain: C: PDB Molecule:uncharacterized protein rv3413c/mt3522;
PDBTitle: crystal structure of sigd4 in complex with its negative regulator rsda
Confidence and coverage
Confidence: 98.9% Coverage: 16%
47 residues ( 16% of your sequence) have been modelled with 98.9% 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.
Warning: 65% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted.
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
1c3vepC_
98.9 100
PDB header:membrane protein/transcription
Chain: C: PDB Molecule:uncharacterized protein rv3413c/mt3522;
PDBTitle: crystal structure of sigd4 in complex with its negative regulator rsda
2c3vepX_
98.8 100
PDB header:membrane protein/transcription
Chain: X: PDB Molecule:uncharacterized protein rv3413c/mt3522;
PDBTitle: crystal structure of sigd4 in complex with its negative regulator rsda
3c4malB_
93.2 25
PDB header:unknown function
Chain: B: PDB Molecule:motility protein fimv;
PDBTitle: tpr3 of fimv from p. aeruginosa (pao1)
4c4fx5A_
74.0 12
PDB header:blood clotting
Chain: A: PDB Molecule:von willebrand factor type a;
PDBTitle: von willebrand factor type a from catenulispora acidiphila
5c3dzaB_
68.5 11
PDB header:unknown function
Chain: B: PDB Molecule:uncharacterized putative membrane protein;
PDBTitle: crystal structure of a putative membrane protein of unknown function2 (yfdx) from klebsiella pneumoniae subsp. at 1.65 a resolution
6c6a09C_
68.0 11
PDB header:unknown function
Chain: C: PDB Molecule:yfdx protein;
PDBTitle: salmonella typhi yfdx in the p222 space group
7d256ba_
65.4 17
Fold:Four-helical up-and-down bundle
Superfamily:Cytochromes
Family:Cytochrome b562
8c4er9A_
63.7 11
PDB header:electron transport
Chain: A: PDB Molecule:soluble cytochrome b562;
PDBTitle: crystal structure of cytochrome b562 from salmonella enterica subsp.2 enterica serovar typhimurium str. 14028s
9c4l6rA_
56.0 12
PDB header:membrane protein
Chain: A: PDB Molecule:soluble cytochrome b562 and glucagon receptor chimera;
PDBTitle: structure of the class b human glucagon g protein coupled receptor
10c1wcrA_
53.5 12
PDB header:transferase
Chain: A: PDB Molecule:pts system, n, n'-diacetylchitobiose-specific
PDBTitle: trimeric structure of the enzyme iia from escherichia coli2 phosphotransferase system specific for n,n'-3 diacetylchitobiose
11c3l8rA_
52.4 10
PDB header:transferase
Chain: A: PDB Molecule:putative pts system, cellobiose-specific iia
PDBTitle: the crystal structure of ptca from s. mutans
12d2e2aa_
51.7 17
Fold:Spectrin repeat-like
Superfamily:Enzyme IIa from lactose specific PTS, IIa-lac
Family:Enzyme IIa from lactose specific PTS, IIa-lac
13c2kc7A_
51.3 30
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bfr218_protein;
PDBTitle: solution nmr structure of bacteroides fragilis protein2 bf1650. northeast structural genomics consortium target3 bfr218
14c4fm3B_
50.6 15
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized hypothetical protein;
PDBTitle: crystal structure of a duf4398 family protein (pa2901) from2 pseudomonas aeruginosa pao1 at 2.47 a resolution
15d1vh6a_
47.3 13
Fold:Four-helical up-and-down bundle
Superfamily:Flagellar export chaperone FliS
Family:Flagellar export chaperone FliS
16c1vh6A_
47.3 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:flagellar protein flis;
PDBTitle: crystal structure of a flagellar protein
17c6iiuA_
47.2 16
PDB header:signaling protein
Chain: A: PDB Molecule:soluble cytochrome b562,thromboxane a2 receptor,rubredoxin,
PDBTitle: crystal structure of the human thromboxane a2 receptor bound to2 ramatroban
18c3zsuA_
43.8 13
PDB header:photosynthesis
Chain: A: PDB Molecule:tll2057 protein;
PDBTitle: structure of the cyanoq protein from thermosynechococcus elongatus
19c3k1iA_
43.2 6
PDB header:chaperone
Chain: A: PDB Molecule:flagellar protein;
PDBTitle: crystal strcture of flis-hp1076 complex in h. pylori
20c5b3hD_
42.3 19
PDB header:transcription
Chain: D: PDB Molecule:protein scarecrow;
PDBTitle: the crystal structure of the jackdaw/idd10 bound to the heterodimeric2 shr-scr complex
21c5fimA_
not modelled 38.7 16
PDB header:unknown function
Chain: A: PDB Molecule:ygau;
PDBTitle: the structure of kbp.k from e. coli
22c3ls1A_
not modelled 38.5 9
PDB header:photosynthesis
Chain: A: PDB Molecule:sll1638 protein;
PDBTitle: crystal structure of cyanobacterial psbq from synechocystis2 sp. pcc 6803 complexed with zn2+
23c3k1sE_
not modelled 38.1 17
PDB header:transferase
Chain: E: PDB Molecule:pts system, cellobiose-specific iia component;
PDBTitle: crystal structure of the pts cellobiose specific enzyme iia from2 bacillus anthracis
24c4uicA_
not modelled 38.0 17
PDB header:sugar binding protein
Chain: A: PDB Molecule:surface layer protein;
PDBTitle: crystal structure of the s-layer protein rsbsc(31-844)
25d2gy9t1
not modelled 36.0 26
Fold:Spectrin repeat-like
Superfamily:Ribosomal protein S20
Family:Ribosomal protein S20
26c2ra1A_
not modelled 33.1 17
PDB header:sugar binding protein
Chain: A: PDB Molecule:surface layer protein;
PDBTitle: crystal structure of the n-terminal part of the bacterial s-layer2 protein sbsc
27c6g7oA_
not modelled 33.0 16
PDB header:membrane protein
Chain: A: PDB Molecule:alkaline ceramidase 3,soluble cytochrome b562;
PDBTitle: crystal structure of human alkaline ceramidase 3 (acer3) at 2.72 angstrom resolution
28c5xefA_
not modelled 32.9 9
PDB header:chaperone
Chain: A: PDB Molecule:flagellar protein flis;
PDBTitle: crystal structure of flagellar chaperone from bacteria
29c4cqiA_
not modelled 31.3 18
PDB header:structural protein
Chain: A: PDB Molecule:tubulin-binding cofactor a;
PDBTitle: crystal structure of recombinant tubulin-binding cofactor a2 (tbca) from leishmania major
30c2pv7B_
not modelled 29.4 9
PDB header:isomerase, oxidoreductase
Chain: B: PDB Molecule:t-protein [includes: chorismate mutase (ec 5.4.99.5) (cm)
PDBTitle: crystal structure of chorismate mutase / prephenate dehydrogenase2 (tyra) (1574749) from haemophilus influenzae rd at 2.00 a resolution
31d2cpra1
not modelled 27.9 17
Fold:SAM domain-like
Superfamily:HRDC-like
Family:EXOSC10 HRDC domain-like
32d2uubt1
not modelled 27.5 21
Fold:Spectrin repeat-like
Superfamily:Ribosomal protein S20
Family:Ribosomal protein S20
33c5o5jT_
not modelled 26.3 15
PDB header:ribosome
Chain: T: PDB Molecule:30s ribosomal protein s20;
PDBTitle: structure of the 30s small ribosomal subunit from mycobacterium2 smegmatis
34c2rpaA_
not modelled 25.9 9
PDB header:hydrolase
Chain: A: PDB Molecule:katanin p60 atpase-containing subunit a1;
PDBTitle: the solution structure of n-terminal domain of microtubule severing2 enzyme
35c6p2iA_
not modelled 24.2 9
PDB header:oxidoreductase, biosynthetic protein
Chain: A: PDB Molecule:glycerate dehydrogenase;
PDBTitle: acyclic imino acid reductase (bsp5) in complex with nadph and d-arg
36c5oxeA_
not modelled 23.9 38
PDB header:virus
Chain: A: PDB Molecule:major virion protein;
PDBTitle: structure of major capsid protein vp1 of aeropyrum pernix bacilliform2 virus 1 apbv1
37c6grjG_
not modelled 23.1 7
PDB header:toxin
Chain: G: PDB Molecule:ahlb;
PDBTitle: structure of the ahlb pore of the tripartite alpha-pore forming toxin,2 ahl, from aeromonas hydrophila.
38c6fkhe_
not modelled 21.9 18
PDB header:membrane protein
Chain: E: PDB Molecule:atp synthase subunit alpha, chloroplastic;
PDBTitle: chloroplast f1fo conformation 2
39c3u8pB_
not modelled 20.5 17
PDB header:fluorescent protein, electron transport
Chain: B: PDB Molecule:cytochrome b562 integral fusion with enhanced green
PDBTitle: cytochrome b562 integral fusion with egfp
40d2np3a1
not modelled 20.4 28
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
41c5b3hB_
not modelled 20.2 18
PDB header:transcription
Chain: B: PDB Molecule:protein short-root;
PDBTitle: the crystal structure of the jackdaw/idd10 bound to the heterodimeric2 shr-scr complex
42c2rt6A_
not modelled 20.1 15
PDB header:dna binding protein
Chain: A: PDB Molecule:primosomal replication protein n'';
PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for pric n-2 terminal domain
43d2f1ka1
not modelled 19.5 16
Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:TyrA dimerization domain-like
44c3gw4B_
not modelled 18.3 18
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of uncharacterized protein from deinococcus2 radiodurans. northeast structural genomics consortium target drr162b.
45c6q45P_
not modelled 17.8 10
PDB header:hydrolase
Chain: P: PDB Molecule:atp synthase epsilon chain;
PDBTitle: f1-atpase from fusobacterium nucleatum
46c1nzeA_
not modelled 17.7 11
PDB header:oxidoreductase
Chain: A: PDB Molecule:oxygen-evolving enhancer protein 3;
PDBTitle: crystal structure of psbq polypeptide of photosystem ii2 from higher plants
47d1nzea_
not modelled 17.7 11
Fold:Four-helical up-and-down bundle
Superfamily:Oxygen-evolving enhancer protein 3,
Family:Oxygen-evolving enhancer protein 3,
48d1y7ma2
not modelled 17.3 24
Fold:LysM domain
Superfamily:LysM domain
Family:LysM domain
49d1yt3a2
not modelled 17.3 26
Fold:SAM domain-like
Superfamily:HRDC-like
Family:RNase D C-terminal domains
50c2mkxA_
not modelled 16.9 27
PDB header:hydrolase
Chain: A: PDB Molecule:autolysin;
PDBTitle: solution structure of lysm the peptidoglycan binding domain of2 autolysin atla from enterococcus faecalis
51c2y8nC_
not modelled 16.7 14
PDB header:lyase
Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit;
PDBTitle: crystal structure of glycyl radical enzyme
52c5i2gB_
not modelled 16.2 25
PDB header:lyase
Chain: B: PDB Molecule:diol dehydratase;
PDBTitle: 1,2-propanediol dehydration in roseburia inulinivorans; structural2 basis for substrate and enantiomer selectivity
53c4or2A_
not modelled 16.2 18
PDB header:signaling protein
Chain: A: PDB Molecule:soluble cytochrome b562, metabotropic glutamate receptor 1;
PDBTitle: human class c g protein-coupled metabotropic glutamate receptor 1 in2 complex with a negative allosteric modulator
54c6ch3B_
not modelled 15.9 13
PDB header:structural protein
Chain: B: PDB Molecule:flagellar secretion chaperone flis,flagellin;
PDBTitle: crystal structure of the cytoplasmic domain of flha and flis-flic2 complex
55c4ntxC_
not modelled 15.6 35
PDB header:transport protein/toxin
Chain: C: PDB Molecule:basic phospholipase a2 homolog tx-beta;
PDBTitle: structure of acid-sensing ion channel in complex with snake toxin and2 amiloride
56d1orjb_
not modelled 14.6 15
Fold:Four-helical up-and-down bundle
Superfamily:Flagellar export chaperone FliS
Family:Flagellar export chaperone FliS
57d1fe5a_
not modelled 14.3 41
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
58d1m8ra_
not modelled 13.9 29
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
59c4gfjA_
not modelled 13.6 12
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase v;
PDBTitle: crystal structure of topo-78, an n-terminal 78kda fragment of2 topoisomerase v
60c4uz2D_
not modelled 13.3 26
PDB header:hydrolase
Chain: D: PDB Molecule:cell wall-binding endopeptidase-related protein;
PDBTitle: crystal structure of the n-terminal lysm domains from the putative2 nlpc/p60 d,l endopeptidase from t. thermophilus
61c5wzmA_
not modelled 13.3 24
PDB header:hydrolase/inhibitor
Chain: A: PDB Molecule:group iie secretory phospholipase a2;
PDBTitle: crystal structure of human secreted phospholipase a2 group iie
62c4xa8A_
not modelled 13.1 16
PDB header:oxidoreductase
Chain: A: PDB Molecule:d-isomer specific 2-hydroxyacid dehydrogenase nad-binding;
PDBTitle: crystal structure of d-isomer specific 2-hydroxyacid dehydrogenase2 from xanthobacter autotrophicus py2
63c3zpjA_
not modelled 13.1 20
PDB header:unknown function
Chain: A: PDB Molecule:ton_1535;
PDBTitle: crystal structure of ton1535 from thermococcus onnurineus na1
64c5a8jA_
not modelled 12.7 23
PDB header:transcription
Chain: A: PDB Molecule:vwa2;
PDBTitle: crystal structure of the arnb paralog vwa2 from2 sulfolobus acidocaldarius
65c5k2lA_
not modelled 12.7 20
PDB header:hydrolase
Chain: A: PDB Molecule:chitinase, lysozyme;
PDBTitle: crystal structure of lysm domain from volvox carteri chitinase
66d1g2xa_
not modelled 12.6 35
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
67c3mxzA_
not modelled 12.6 21
PDB header:chaperone
Chain: A: PDB Molecule:tubulin-specific chaperone a;
PDBTitle: crystal structure of tubulin folding cofactor a from arabidopsis2 thaliana
68d2pv7a1
not modelled 12.5 9
Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:TyrA dimerization domain-like
69c2lbgA_
not modelled 12.4 38
PDB header:membrane protein
Chain: A: PDB Molecule:major prion protein;
PDBTitle: structure of the chr of the prion protein in dpc micelles
70d2a26a1
not modelled 12.2 16
Fold:Long alpha-hairpin
Superfamily:Calcyclin-binding protein-like
Family:Siah interacting protein N terminal domain-like
71d1p7oa_
not modelled 12.1 41
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
72c4fnvA_
not modelled 11.8 32
PDB header:lyase
Chain: A: PDB Molecule:heparinase iii protein, heparitin sulfate lyase;
PDBTitle: crystal structure of heparinase iii
73d1g0za_
not modelled 11.7 41
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
74d1s6ba_
not modelled 11.7 35
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
75c6f5dH_
not modelled 11.6 15
PDB header:hydrolase
Chain: H: PDB Molecule:atp synthase subunit delta, mitochondrial;
PDBTitle: trypanosoma brucei f1-atpase
76c2r5sB_
not modelled 11.4 26
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein vp0806;
PDBTitle: the crystal structure of a domain of protein vp0806 (unknown function)2 from vibrio parahaemolyticus rimd 2210633
77d1po8a_
not modelled 11.4 35
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
78c2momC_
not modelled 11.3 13
PDB header:membrane protein
Chain: C: PDB Molecule:lysosome-associated membrane glycoprotein 2;
PDBTitle: structural insights of tm domain of lamp-2a in dpc micelles
79c2momB_
not modelled 11.3 13
PDB header:membrane protein
Chain: B: PDB Molecule:lysosome-associated membrane glycoprotein 2;
PDBTitle: structural insights of tm domain of lamp-2a in dpc micelles
80d1poaa_
not modelled 11.3 35
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
81c2w6jH_
not modelled 11.2 14
PDB header:hydrolase
Chain: H: PDB Molecule:f1-atpase delta subunit;
PDBTitle: low resolution structures of bovine mitochondrial f1-atpase during2 controlled dehydration: hydration state 5.
82c2djpA_
not modelled 11.1 35
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein sb145;
PDBTitle: the solution structure of the lysm domain of human2 hypothetical protein sb145
83c5gjqR_
not modelled 11.1 11
PDB header:hydrolase
Chain: R: PDB Molecule:26s proteasome non-atpase regulatory subunit 6;
PDBTitle: structure of the human 26s proteasome bound to usp14-ubal
84c2rq7A_
not modelled 11.0 18
PDB header:hydrolase
Chain: A: PDB Molecule:atp synthase epsilon chain;
PDBTitle: solution structure of the epsilon subunit chimera combining2 the n-terminal beta-sandwich domain from t. elongatus bp-13 f1 and the c-terminal alpha-helical domain from spinach4 chloroplast f1
85c2ke3A_
not modelled 11.0 67
PDB header:hydrolase
Chain: A: PDB Molecule:neuroendocrine convertase 1;
PDBTitle: pc1/3 dcsg sorting domain in chaps
86d1e0ga_
not modelled 11.0 22
Fold:LysM domain
Superfamily:LysM domain
Family:LysM domain
87d2f4la1
not modelled 10.9 42
Fold:CUB-like
Superfamily:Acetamidase/Formamidase-like
Family:Acetamidase/Formamidase-like
88c5b7jA_
not modelled 10.9 32
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:switch-activating protein 1;
PDBTitle: structure model of sap1-dna complex
89d1ijla_
not modelled 10.9 29
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
90c3myfB_
not modelled 10.9 11
PDB header:transferase
Chain: B: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of the hpt domain from the hpt sensor hybrid2 histidine kinase from shewanella to 1.80a
91d1g4ia_
not modelled 10.7 41
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
92c5fayA_
not modelled 10.7 14
PDB header:lyase
Chain: A: PDB Molecule:choline trimethylamine-lyase;
PDBTitle: y208f mutant of choline tma-lyase
93c2e76D_
not modelled 10.4 9
PDB header:photosynthesis
Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus
94c2rhfA_
not modelled 10.3 25
PDB header:hydrolase
Chain: A: PDB Molecule:dna helicase recq;
PDBTitle: d. radiodurans recq hrdc domain 3
95c4ebzA_
not modelled 10.0 10
PDB header:transferase
Chain: A: PDB Molecule:chitin elicitor receptor kinase 1;
PDBTitle: crystal structure of the ectodomain of a receptor like kinase
96d1mh2a_
not modelled 10.0 29
Fold:Phospholipase A2, PLA2
Superfamily:Phospholipase A2, PLA2
Family:Vertebrate phospholipase A2
97c4ymrB_
not modelled 10.0 20
PDB header:protein transport
Chain: B: PDB Molecule:protein snx21;
PDBTitle: crystal structure of the domain swapped pxb/tpr domain of mouse snx21
98c2l9yA_
not modelled 10.0 24
PDB header:sugar binding protein
Chain: A: PDB Molecule:cvnh-lysm lectin;
PDBTitle: solution structure of the mocvnh-lysm module from the rice blast2 fungus magnaporthe oryzae protein (mgg_03307)
99c2fynO_
not modelled 9.9 11
PDB header:oxidoreductase
Chain: O: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: crystal structure analysis of the double mutant rhodobacter2 sphaeroides bc1 complex

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