Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77334
DateThu Jan 5 12:27:56 GMT 2012
Unique Job ID7bb4a9a52176b5ac

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3pjwA_
Top template information
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
Confidence and coverage
Confidence:100.0% Coverage: 62%
411 residues ( 62% 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.
549 residues ( 83%) 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKTVRESTTLYNFLGSHNPYWRLTESSDVLRFSTTETTEPDRTLQLSAEQAARIREMTVI
Secondary structure 















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Disorder  ??????


?
?





















???
????














???
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   .........70.........80.........90.........100.........110.........120
Sequence  TSSLMMSLTVDESDLSVHLVGRKINKREWAGNASAWHDTPAVARDLSHGLSFAEQVVSEA
Secondary structure 






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Disorder  ?????


???????







?
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   .........130.........140.........150.........160.........170.........180
Sequence  HSAIVILDSRGNIQRFNRLCEDYTGLKEHDVIGQSVFKLFMSRREAAASRRNNRVFFRSG
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????











?
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   .........190.........200.........210.........220.........230.........240
Sequence  NAYEVELWIPTCKGQRLFLFRNKFVHSGSGKNEIFLICSGTDITEERRAQERLRILANTD
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Disorder  ??

























































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   .........250.........260.........270.........280.........290.........300
Sequence  SITGLPNRNAMQDLIDHAINHADNNKVGVVYLDLDNFKKVNDAYGHLFGDQLLRDVSLAI
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???



































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   .........310.........320.........330.........340.........350.........360
Sequence  LSCLEHDQVLARPGGDEFLVLASNTSQSALEAMASRILTRLRLPFRIGLIEVYTSCSVGI
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   .........370.........380.........390.........400.........410.........420
Sequence  ALSPEHGSDSTAIIRHADTAMYTAKEGGRGQFCVFTPEMNQRVFEYLWLDTNLRKALEND
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   .........430.........440.........450.........460.........470.........480
Sequence  QLVIHYQPKITWRGEVRSLEALVRWQSPERGLIPPLDFISYAEESGLIVPLGRWVILDVV
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   .........490.........500.........510.........520.........530.........540
Sequence  RQVAKWRDKGINLRVAVNISARQLADQTIFTALKQVLQELNFEYCPIDVELTESCLIEND
Secondary structure 















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?

?
































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   .........550.........560.........570.........580.........590.........600
Sequence  ELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQVFVRDIHKQPVSQSLV
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???







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   .........610.........620.........630.........640.........650.........660
Sequence  RAIVAVAQALNLQVIAEGVESAKEDAFLTKNGINERQGFLFAKPMPAVAFERWYKRYLKR
Secondary structure 



















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Disorder 

























































??
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   .
Sequence  A
Secondary structure 
SS confidence 
Disorder  ?
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 3pjw chain A

3D model

Region: 223 - 646
Aligned: 411
Modelled: 424
Confidence: 100.0%
Identity: 23%
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23

Phyre2

PDB 3gfz chain B

3D model

Region: 233 - 644
Aligned: 369
Modelled: 385
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex

Phyre2

PDB 3hvb chain B

3D model

Region: 403 - 651
Aligned: 248
Modelled: 249
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa

Phyre2

PDB 3hv9 chain A

3D model

Region: 398 - 651
Aligned: 253
Modelled: 254
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa

Phyre2

PDB 3s83 chain A

3D model

Region: 409 - 657
Aligned: 246
Modelled: 249
Confidence: 100.0%
Identity: 33%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15

Phyre2

PDB 3pfm chain A

3D model

Region: 402 - 647
Aligned: 240
Modelled: 246
Confidence: 100.0%
Identity: 25%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf

Phyre2

PDB 2w27 chain A

3D model

Region: 413 - 660
Aligned: 240
Modelled: 248
Confidence: 100.0%
Identity: 17%
PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium

Phyre2

PDB 2r6o chain B

3D model

Region: 408 - 659
Aligned: 239
Modelled: 239
Confidence: 100.0%
Identity: 34%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans

Phyre2

PDB 2bas chain A domain 1

3D model

Region: 412 - 659
Aligned: 243
Modelled: 248
Confidence: 100.0%
Identity: 16%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 421 - 646
Aligned: 221
Modelled: 225
Confidence: 100.0%
Identity: 21%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes

Phyre2

PDB 1w25 chain B

3D model

Region: 221 - 397
Aligned: 177
Modelled: 177
Confidence: 100.0%
Identity: 29%
PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp

Phyre2

PDB 3ezu chain A

3D model

Region: 222 - 394
Aligned: 165
Modelled: 173
Confidence: 100.0%
Identity: 25%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution

Phyre2

PDB 3bre chain A

3D model

Region: 225 - 397
Aligned: 173
Modelled: 173
Confidence: 99.9%
Identity: 27%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3icl chain A

3D model

Region: 239 - 397
Aligned: 159
Modelled: 158
Confidence: 99.9%
Identity: 39%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c

Phyre2

PDB 3mtk chain A

3D model

Region: 232 - 401
Aligned: 163
Modelled: 170
Confidence: 99.9%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c

Phyre2

PDB 3ign chain A

3D model

Region: 235 - 394
Aligned: 160
Modelled: 156
Confidence: 99.9%
Identity: 30%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a

Phyre2

PDB 3i5b chain A

3D model

Region: 236 - 396
Aligned: 161
Modelled: 161
Confidence: 99.9%
Identity: 29%
PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa

Phyre2

PDB 3hva chain A

3D model

Region: 236 - 392
Aligned: 157
Modelled: 157
Confidence: 99.9%
Identity: 22%
PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa

Phyre2

PDB 3i5c chain A

3D model

Region: 225 - 394
Aligned: 170
Modelled: 170
Confidence: 99.9%
Identity: 28%
PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa

Phyre2

PDB 3i5a chain A

3D model

Region: 225 - 393
Aligned: 169
Modelled: 169
Confidence: 99.9%
Identity: 31%
PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae

Phyre2

PDB 3p7n chain B

3D model

Region: 112 - 292
Aligned: 180
Modelled: 180
Confidence: 99.8%
Identity: 15%
PDB header:dna binding protein
Chain: B: PDB Molecule:sensor histidine kinase;
PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis

Phyre2

PDB 2pdt chain D

3D model

Region: 89 - 222
Aligned: 125
Modelled: 125
Confidence: 99.4%
Identity: 16%
PDB header:circadian clock protein
Chain: D: PDB Molecule:vivid pas protein vvd;
PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid

Phyre2
1

c3pjwA_
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c3gfzB_
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c3hvbB_
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c3hv9A_
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c3s83A_
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c3pfmA_
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c2w27A_
8

c2r6oB_
9

d2basa1
10

c3kzpA_
11

c1w25B_
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c3ezuA_
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c3breA_
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c3iclA_
15

c3mtkA_
16

c3ignA_
17

c3i5bA_
18

c3hvaA_
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c3i5cA_
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c3i5aA_
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c3p7nB_
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c2pdtD_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3pjwA_



100.0 23 PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
2c3gfzB_



100.0 22 PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex
3c3hvbB_



100.0 25 PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa
4c3hv9A_



100.0 25 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 33 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_



100.0 25 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf
7c2w27A_



100.0 17 PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium
8c2r6oB_



100.0 34 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans
9d2basa1



100.0 16 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_



100.0 21 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes
11c1w25B_



100.0 29 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
12c3ezuA_



100.0 25 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution
13c3breA_



99.9 27 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3iclA_



99.9 39 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c
15c3mtkA_



99.9 25 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c
16c3ignA_



99.9 30 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a
17c3i5bA_



99.9 29 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
18c3hvaA_



99.9 22 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
19c3i5cA_



99.9 28 PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa
20c3i5aA_



99.9 31 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
21c3qyyB_



not modelled 99.9 28 PDB header:signaling protein/inhibitor
Chain: B: PDB Molecule:response regulator;
PDBTitle: a novel interaction mode between a microbial ggdef domain and the bis-2 (3, 5 )-cyclic di-gmp
22d1w25a3



not modelled 99.9 29 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
23c3hvwA_



not modelled 99.9 20 PDB header:lyase
Chain: A: PDB Molecule:diguanylate-cyclase (dgc);
PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c
24c3p7nB_



99.8 15 PDB header:dna binding protein
Chain: B: PDB Molecule:sensor histidine kinase;
PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis
25c2wkqA_



not modelled 99.7 15 PDB header:transferase, cell adhesion
Chain: A: PDB Molecule:nph1-1, ras-related c3 botulinum toxin substrate
PDBTitle: structure of a photoactivatable rac1 containing the lov22 c450a mutant
26c2gj3A_



not modelled 99.7 17 PDB header:transferase
Chain: A: PDB Molecule:nitrogen fixation regulatory protein;
PDBTitle: crystal structure of the fad-containing pas domain of the2 protein nifl from azotobacter vinelandii.
27c3lyxA_



not modelled 99.7 18 PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef domain protein;
PDBTitle: crystal structure of the pas domain of the protein cps_12912 from colwellia psychrerythraea. northeast structural3 genomics consortium target id csr222b
28c3mqoB_



not modelled 99.6 15 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, luxr family;
PDBTitle: the crystal structure of the pas domain in complex with isopropanol of2 a transcriptional regulator in the luxr family from burkholderia3 thailandensis to 1.7a
29c3bwlA_



not modelled 99.6 16 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of pas domain of htr-like protein from haloarcula2 marismortui
30c2v1bA_



not modelled 99.6 16 PDB header:transferase
Chain: A: PDB Molecule:nph1-1;
PDBTitle: n- and c-terminal helices of oat lov2 (404-546) are2 involved in light-induced signal transduction (room3 temperature (293k) light structure of lov2 (404-546))
31c3caxA_



not modelled 99.6 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pf0695;
PDBTitle: crystal structure of uncharacterized protein pf0695
32d1ew0a_



not modelled 99.6 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
33c2l4rA_



not modelled 99.6 10 PDB header:transport protein
Chain: A: PDB Molecule:potassium voltage-gated channel subfamily h member 2;
PDBTitle: nmr solution structure of the n-terminal pas domain of herg
34c3mxqC_



not modelled 99.6 10 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae
35c3luqC_



not modelled 99.6 15 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of a pas domain from a sensory box2 histidine kinase regulator from geobacter sulfurreducens to3 2.5a
36d1bywa_



not modelled 99.6 9 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
37d1p97a_



not modelled 99.6 8 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Hypoxia-inducible factor Hif2a, C-terminal domain
38c2r78D_



not modelled 99.6 15 PDB header:transferase
Chain: D: PDB Molecule:sensor protein;
PDBTitle: crystal structure of a domain of the sensory box sensor2 histidine kinase/response regulator from geobacter3 sulfurreducens
39d1n9la_



not modelled 99.5 14 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
40c3mfxA_



not modelled 99.5 14 PDB header:transcription
Chain: A: PDB Molecule:sensory box/ggdef family protein;
PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b
41c3f1oB_



not modelled 99.5 13 PDB header:transcription
Chain: B: PDB Molecule:aryl hydrocarbon receptor nuclear translocator;
PDBTitle: crystal structure of the high affinity heterodimer of hif22 alpha and arnt c-terminal pas domains, with an internally-3 bound artificial ligand
42c2kdkA_



not modelled 99.5 11 PDB header:transcription regulator
Chain: A: PDB Molecule:aryl hydrocarbon receptor nuclear translocator-like protein
PDBTitle: structure of human circadian clock protein bmal2 c-terminal pas domain
43c3eehA_



not modelled 99.5 10 PDB header:transferase
Chain: A: PDB Molecule:putative light and redox sensing histidine kinase;
PDBTitle: the crystal structure of the domain of the putative light and redox2 sensing histidine kinase from haloarcula marismortui
44d1jnua_



not modelled 99.5 14 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
45c3h9wA_



not modelled 99.5 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:diguanylate cyclase with pas/pac sensor;
PDBTitle: crystal structure of the n-terminal domain of diguanylate cyclase with2 pas/pac sensor (maqu_2914) from marinobacter aquaeolei, northeast3 structural genomics consortium target mqr66c
46c2z6dB_



not modelled 99.5 13 PDB header:transferase
Chain: B: PDB Molecule:phototropin-2;
PDBTitle: crystal structure of lov1 domain of phototropin2 from2 arabidopsis thaliana
47c3oloB_



not modelled 99.5 11 PDB header:transferase
Chain: B: PDB Molecule:two-component sensor histidine kinase;
PDBTitle: crystal structure of a pas domain from two-component sensor histidine2 kinase
48c2pr6A_



not modelled 99.5 18 PDB header:flavoprotein, signaling protein
Chain: A: PDB Molecule:blue-light photoreceptor;
PDBTitle: structural basis for light-dependent signaling in the dimeric lov2 photosensor ytva (light structure)
49c3k3dA_



not modelled 99.5 11 PDB header:signaling protein
Chain: A: PDB Molecule:protein rv1364c/mt1410;
PDBTitle: the n-terminal pas domain crystal structure of rv1364c from2 mycobacterium tuberculosis at 2.3 angstrom
50c3b33A_



not modelled 99.5 16 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus
51c2vlgD_



not modelled 99.5 12 PDB header:transferase
Chain: D: PDB Molecule:sporulation kinase a;
PDBTitle: kina pas-a domain, homodimer
52c3mr0B_



not modelled 99.5 14 PDB header:transcription regulator
Chain: B: PDB Molecule:sensory box histidine kinase/response regulator;
PDBTitle: crystal structure of sensory box histidine kinase/response regulator2 from burkholderia thailandensis e264
53c1v9yA_



not modelled 99.4 20 PDB header:signaling protein
Chain: A: PDB Molecule:heme pas sensor protein;
PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form)
54d1v9ya_



not modelled 99.4 20 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
55c2pdtD_



99.4 16 PDB header:circadian clock protein
Chain: D: PDB Molecule:vivid pas protein vvd;
PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid
56c3mjqB_



not modelled 99.4 12 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the pas domain of q24qt8_deshy protein from2 desulfitobacterium hafniense. northeast structural genomics3 consortium target dhr85c.
57c3kx0X_



not modelled 99.4 11 PDB header:signaling protein
Chain: X: PDB Molecule:uncharacterized protein rv1364c/mt1410;
PDBTitle: crystal structure of the pas domain of rv1364c
58d1y28a_



not modelled 99.4 21 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
59c3gdiB_



not modelled 99.4 10 PDB header:transcription
Chain: B: PDB Molecule:period circadian protein homolog 2;
PDBTitle: mammalian clock protein mper2 - crystal struture of a pas2 domain fragment
60d1xj3a1



not modelled 99.3 20 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
61c3fg8B_



not modelled 99.3 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein rha05790;
PDBTitle: crystal structure of pas domain of rha05790
62c2qkpD_



not modelled 99.3 9 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of c-terminal domain of smu_1151c from streptococcus2 mutans
63c3rtyA_



not modelled 99.3 15 PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: structure of an enclosed dimer formed by the drosophila period protein
64c3icyB_



not modelled 99.3 10 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:sensor protein;
PDBTitle: the crystal structure of sensory box histidine2 kinase/response regulator domain from chlorobium tepidum3 tls
65d1nwza_



not modelled 99.3 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
66c3njaC_



not modelled 99.3 16 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:probable ggdef family protein;
PDBTitle: the crystal structure of the pas domain of a ggdef family protein from2 chromobacterium violaceum atcc 12472.
67c2jheB_



not modelled 99.2 8 PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)
68c3gecA_



not modelled 99.2 10 PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: crystal structure of a tandem pas domain fragment of2 drosophila period
69c3fc7B_



not modelled 99.2 18 PDB header:transferase
Chain: B: PDB Molecule:htr-like protein;
PDBTitle: the crystal structure of a domain of htr-like protein from haloarcula2 marismortui atcc 43049
70d1oj5a_



not modelled 99.1 11 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PAS domain of steroid receptor coactivator 1A, NCo-A1
71c3ewkA_



not modelled 99.1 18 PDB header:flavoprotein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos
72d1otda_



not modelled 99.1 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
73d1ll8a_



not modelled 99.1 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:N-terminal PAS domain of Pas kinase
74d1mzua_



not modelled 99.1 16 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
75c3a0rA_



not modelled 99.0 18 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of histidine kinase thka (tm1359) in complex with2 response regulator protein trra (tm1360)
76c3a0vA_



not modelled 99.0 17 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)
77c2w0nA_



not modelled 99.0 14 PDB header:transferase
Chain: A: PDB Molecule:sensor protein dcus;
PDBTitle: plasticity of pas domain and potential role for signal2 transduction in the histidine-kinase dcus
78c1wa9A_



not modelled 99.0 10 PDB header:circadian rhythm
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: crystal structure of the pas repeat region of the2 drosophila clock protein period
79d1xfna1



not modelled 98.9 19 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
80c3cloC_



not modelled 98.8 16 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
81c2oolA_



not modelled 98.4 14 PDB header:signaling protein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the chromophore-binding domain of an unusual2 bacteriophytochrome rpbphp3 from r. palustris
82c2o9bA_



not modelled 98.1 13 PDB header:transferase
Chain: A: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of bacteriophytochrome chromophore binding domain
83c2veaA_



not modelled 97.3 12 PDB header:transferase
Chain: A: PDB Molecule:phytochrome-like protein cph1;
PDBTitle: the complete sensory module of the cyanobacterial2 phytochrome cph1 in the pr-state.
84d1p6qa_



not modelled 96.8 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
85d1mvoa_



not modelled 96.8 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
86d1zesa1



not modelled 96.6 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
87c2ayxA_



not modelled 96.5 18 PDB header:transferase
Chain: A: PDB Molecule:sensor kinase protein rcsc;
PDBTitle: solution structure of the e.coli rcsc c-terminus (residues2 700-949) containing linker region and phosphoreceiver3 domain
88c2zayA_



not modelled 96.4 23 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
89c3q58A_



not modelled 96.4 15 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
90d2ayxa1



not modelled 96.3 18 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
91c3khtA_



not modelled 96.2 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
92d1w25a1



not modelled 96.2 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
93c3hebB_



not modelled 96.1 15 PDB header:transcription regulator
Chain: B: PDB Molecule:response regulator receiver domain protein (chey);
PDBTitle: crystal structure of response regulator receiver domain from2 rhodospirillum rubrum
94d1xhfa1



not modelled 96.0 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
95d2a9pa1



not modelled 95.9 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
96d1jbea_



not modelled 95.9 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
97d1krwa_



not modelled 95.8 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
98c2qr3A_



not modelled 95.8 13 PDB header:transcription
Chain: A: PDB Molecule:two-component system response regulator;
PDBTitle: crystal structure of the n-terminal signal receiver domain of two-2 component system response regulator from bacteroides fragilis
99d1qkka_



not modelled 95.7 18 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
100d1heya_



not modelled 95.7 18 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
101c3gt7A_



not modelled 95.6 16 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
102c2rjnA_



not modelled 95.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
103c3nhzA_



not modelled 95.6 16 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
104c2yxbA_



not modelled 95.6 16 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
105c3cnbC_



not modelled 95.5 18 PDB header:dna binding protein
Chain: C: PDB Molecule:dna-binding response regulator, merr family;
PDBTitle: crystal structure of signal receiver domain of dna binding response2 regulator protein (merr) from colwellia psychrerythraea 34h
106c3t6kB_



not modelled 95.4 17 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator receiver;
PDBTitle: crystal structure of a hypothetical response regulator (caur_3799)2 from chloroflexus aurantiacus j-10-fl at 1.86 a resolution
107c3c2wB_



not modelled 95.4 8 PDB header:signaling protein
Chain: B: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of the photosensory core domain of p.2 aeruginosa bacteriophytochrome pabphp in the pfr state
108d1k66a_



not modelled 95.2 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
109c3hv2B_



not modelled 95.1 13 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator/hd domain protein;
PDBTitle: crystal structure of signal receiver domain of hd domain-2 containing protein from pseudomonas fluorescens pf-5
110c3cg0A_



not modelled 95.1 17 PDB header:lyase
Chain: A: PDB Molecule:response regulator receiver modulated diguanylate cyclase
PDBTitle: crystal structure of signal receiver domain of modulated diguanylate2 cyclase from desulfovibrio desulfuricans g20, an example of alternate3 folding
111c2jk1A_



not modelled 95.1 13 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
112d1mb3a_



not modelled 95.0 19 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
113d1yioa2



not modelled 95.0 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
114c3c97A_



not modelled 95.0 14 PDB header:signaling protein, transferase
Chain: A: PDB Molecule:signal transduction histidine kinase;
PDBTitle: crystal structure of the response regulator receiver domain2 of a signal transduction histidine kinase from aspergillus3 oryzae
115d1dz3a_



not modelled 95.0 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
116c3crnA_



not modelled 94.9 15 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver domain protein, chey-like;
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
117c3i42A_



not modelled 94.8 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:response regulator receiver domain protein (chey-
PDBTitle: structure of response regulator receiver domain (chey-like)2 from methylobacillus flagellatus
118d1ny5a1



not modelled 94.8 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
119c2zwmA_



not modelled 94.7 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
120c3b2nA_



not modelled 94.7 11 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus

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



Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0