Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP38097
DateThu Jan 5 11:57:56 GMT 2012
Unique Job ID623c96788c4fa1d5

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: 37%
411 residues ( 37% 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.
786 residues ( 71%) 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  MSKQSQHVLIALPHPLLHLVSLGLVSFIFTLFSLELSQFGTQLAPLWFPTSIMMVAFYRH
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Disorder  ??????


























?

?????
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   .........70.........80.........90.........100.........110.........120
Sequence  AGRMWPGIALSCSLGNIAASILLFSTSSLNMTWTTINIVEAVVGAVLLRKLLPWYNPLQN
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???














???????
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   .........130.........140.........150.........160.........170.........180
Sequence  LADWLRLALGSAIVPPLLGGVLVVLLTPGDDPLRAFLIWVLSESIGALALVPLGLLFKPH
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??
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   .........190.........200.........210.........220.........230.........240
Sequence  YLLRHRNPRLLFESLLTLAITLTLSWLSMLYLPWPFTFIIVLLMWSAVRLPRMEAFLIFL
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Disorder  ??
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   .........250.........260.........270.........280.........290.........300
Sequence  TTVMMVSLMMAADPSLLATPRTYLMSHMPWLPFLLILLPANIMTMVMYAFRAERKHISES
Secondary structure 
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?

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   .........310.........320.........330.........340.........350.........360
Sequence  ETHFRNAMEYSAIGMALVGTEGQWLQTNKALCQFLGYSQEELRGLTFQQLTWPEDLNKDL
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   .........370.........380.........390.........400.........410.........420
Sequence  QQVEKLISGEINTYSMEKRYYNRNGDVVWALLAVSLVRHTDGTPLYFIAQIEDINELKRT
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   .........430.........440.........450.........460.........470.........480
Sequence  EQVNQQLMERITLANEAGGIGIWEWELKPNIFSWDKRMFELYEIPPHIKPNWQVWYECVL
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   .........490.........500.........510.........520.........530.........540
Sequence  PEDRQHAEKVIRDSLQSRSPFKLEFRITVKDGIRHIRALANRVLNKEGEVERLLGINMDM
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   .........550.........560.........570.........580.........590.........600
Sequence  TEVKQLNEALFQEKERLHITLDSIGEAVVCIDMAMKITFMNPVAEKMSGWTQEEALGVPL
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   .........610.........620.........630.........640.........650.........660
Sequence  LTVLHITFGDNGPLMENIYSADTSRSAIEQDVVLHCRSGGSYDVHYSITPLSTLDGSNIG
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   .........670.........680.........690.........700.........710.........720
Sequence  SVLVIQDVTESRKMLRQLSYSASHDALTHLANRASFEKQLRILLQTVNSTHQRHALVFID
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   .........730.........740.........750.........760.........770.........780
Sequence  LDRFKAVNDSAGHAAGDALLRELASLMLSMLRSSDVLARLGGDEFGLLLPDCNVESARFI
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   .........790.........800.........810.........820.........830.........840
Sequence  ATRIISAVNDYHFIWEGRVHRVGASAGITLIDDNNHQAAEVMSQADIACYASKNGGRGRV
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   .........850.........860.........870.........880.........890.........900
Sequence  TVYEPQQAAAHSERAAMSLDEQWRMIKENQLMMLAHGVASPRIPEARNLWLISLKLWSCE
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   .........910.........920.........930.........940.........950.........960
Sequence  GEIIDEQTFRRSFSDPALSHALDRRVFHEFFQQAAKAVASKGISISLPLSVAGLSSATLV
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  NDLLEQLENSPLPPRLLHLIIPAEAILDHAESVQKLRLAGCRIVLSQVGRDLQIFNSLKA
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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  NMADYLLLDGELCANVQGNLMDEMLITIIQGHAQRLGMKTIAGPVVLPLVMDTLSGIGVD
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   .........1090.........1100.....
Sequence  LIYGEVIADAQPLDLLVNSSYFAIN
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???????
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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: 668 - 1092
Aligned: 411
Modelled: 425
Confidence: 100.0%
Identity: 20%
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: 678 - 1090
Aligned: 368
Modelled: 385
Confidence: 100.0%
Identity: 13%
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: 858 - 1096
Aligned: 237
Modelled: 239
Confidence: 100.0%
Identity: 20%
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: 844 - 1096
Aligned: 251
Modelled: 253
Confidence: 100.0%
Identity: 20%
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: 858 - 1099
Aligned: 238
Modelled: 242
Confidence: 100.0%
Identity: 18%
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: 852 - 1092
Aligned: 237
Modelled: 241
Confidence: 100.0%
Identity: 19%
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: 860 - 1092
Aligned: 227
Modelled: 233
Confidence: 100.0%
Identity: 11%
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: 857 - 1099
Aligned: 230
Modelled: 231
Confidence: 100.0%
Identity: 17%
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: 861 - 1092
Aligned: 227
Modelled: 232
Confidence: 100.0%
Identity: 11%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 1w25 chain B

3D model

Region: 666 - 845
Aligned: 180
Modelled: 180
Confidence: 100.0%
Identity: 31%
PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp

Phyre2

PDB 3kzp chain A

3D model

Region: 870 - 1093
Aligned: 219
Modelled: 223
Confidence: 100.0%
Identity: 12%
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 3ezu chain A

3D model

Region: 617 - 842
Aligned: 215
Modelled: 226
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: 670 - 845
Aligned: 176
Modelled: 176
Confidence: 100.0%
Identity: 30%
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: 684 - 845
Aligned: 162
Modelled: 161
Confidence: 100.0%
Identity: 29%
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 3ign chain A

3D model

Region: 680 - 842
Aligned: 163
Modelled: 159
Confidence: 100.0%
Identity: 34%
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: 681 - 844
Aligned: 164
Modelled: 164
Confidence: 100.0%
Identity: 32%
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 3i5a chain A

3D model

Region: 670 - 841
Aligned: 172
Modelled: 172
Confidence: 100.0%
Identity: 30%
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 3hva chain A

3D model

Region: 681 - 841
Aligned: 161
Modelled: 161
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa

Phyre2

PDB 1w25 chain A domain 3

3D model

Region: 687 - 846
Aligned: 160
Modelled: 160
Confidence: 100.0%
Identity: 32%
Fold: Ferredoxin-like
Superfamily: Nucleotide cyclase
Family: GGDEF domain

Phyre2

PDB 3i5c chain A

3D model

Region: 664 - 843
Aligned: 180
Modelled: 180
Confidence: 100.0%
Identity: 29%
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 3rty chain A

3D model

Region: 310 - 562
Aligned: 242
Modelled: 242
Confidence: 99.9%
Identity: 12%
PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: structure of an enclosed dimer formed by the drosophila period protein

Phyre2

PDB 3gec chain A

3D model

Region: 312 - 566
Aligned: 233
Modelled: 233
Confidence: 99.8%
Identity: 13%
PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: crystal structure of a tandem pas domain fragment of2 drosophila period

Phyre2

PDB 1wa9 chain A

3D model

Region: 312 - 563
Aligned: 245
Modelled: 245
Confidence: 99.8%
Identity: 11%
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

Phyre2

PDB 3gdi chain B

3D model

Region: 312 - 556
Aligned: 218
Modelled: 218
Confidence: 99.8%
Identity: 11%
PDB header:transcription
Chain: B: PDB Molecule:period circadian protein homolog 2;
PDBTitle: mammalian clock protein mper2 - crystal struture of a pas2 domain fragment

Phyre2

PDB 2wkq chain A

3D model

Region: 306 - 433
Aligned: 127
Modelled: 127
Confidence: 99.7%
Identity: 19%
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

Phyre2

PDB 3p7n chain B

3D model

Region: 555 - 739
Aligned: 183
Modelled: 183
Confidence: 99.7%
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 3cax chain A

3D model

Region: 294 - 428
Aligned: 128
Modelled: 128
Confidence: 99.7%
Identity: 9%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pf0695;
PDBTitle: crystal structure of uncharacterized protein pf0695

Phyre2
1

c3pjwA_
2

c3gfzB_
3

c3hvbB_
4

c3hv9A_
5

c3s83A_
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c3pfmA_
7

c2w27A_
8

c2r6oB_
9

d2basa1
10

c1w25B_
11

c3kzpA_
12

c3ezuA_
13

c3breA_
14

c3iclA_
15

c3ignA_
16

c3i5bA_
17

c3i5aA_
18

c3hvaA_
19

d1w25a3
20

c3i5cA_
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c3rtyA_
25

c3gecA_
26

c1wa9A_
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c3gdiB_
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c2wkqA_
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c3p7nB_
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c3caxA_
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Detailed template information 

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



100.0 20 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 13 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 20 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 20 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 18 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_



100.0 19 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 11 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 17 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 11 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c1w25B_



100.0 31 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
11c3kzpA_



100.0 12 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
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_



100.0 30 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3iclA_



100.0 29 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
15c3ignA_



100.0 34 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
16c3i5bA_



100.0 32 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
17c3i5aA_



100.0 30 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
18c3hvaA_



100.0 25 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
19d1w25a3



100.0 32 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
20c3i5cA_



100.0 29 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
21c3qyyB_



not modelled 99.9 26 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
22c3mtkA_



not modelled 99.9 19 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
23c3hvwA_



not modelled 99.9 17 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
24c3rtyA_



99.9 12 PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: structure of an enclosed dimer formed by the drosophila period protein
25c3gecA_



99.8 13 PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: crystal structure of a tandem pas domain fragment of2 drosophila period
26c1wa9A_



99.8 11 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
27c3gdiB_



99.8 11 PDB header:transcription
Chain: B: PDB Molecule:period circadian protein homolog 2;
PDBTitle: mammalian clock protein mper2 - crystal struture of a pas2 domain fragment
28c3ewkA_



not modelled 99.8 16 PDB header:flavoprotein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos
29c2wkqA_



99.7 19 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
30c3p7nB_



99.7 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
31d1ew0a_



not modelled 99.7 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
32c3caxA_



99.7 9 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pf0695;
PDBTitle: crystal structure of uncharacterized protein pf0695
33c2gj3A_



not modelled 99.7 21 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.
34c3bwlA_



not modelled 99.7 19 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of pas domain of htr-like protein from haloarcula2 marismortui
35c2v1bA_



not modelled 99.7 19 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))
36c2r78D_



not modelled 99.6 22 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
37c3f1oB_



not modelled 99.6 15 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
38c3lyxA_



not modelled 99.6 17 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
39d1p97a_



not modelled 99.6 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Hypoxia-inducible factor Hif2a, C-terminal domain
40c3mqoB_



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
41c3luqC_



not modelled 99.6 18 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
42c2kdkA_



not modelled 99.6 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
43c3mr0B_



not modelled 99.6 20 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
44c3mxqC_



not modelled 99.6 12 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae
45c2pr6A_



not modelled 99.6 19 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)
46c3mfxA_



not modelled 99.6 16 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
47d1n9la_



not modelled 99.6 18 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
48c2vlgD_



not modelled 99.6 18 PDB header:transferase
Chain: D: PDB Molecule:sporulation kinase a;
PDBTitle: kina pas-a domain, homodimer
49d1bywa_



not modelled 99.6 21 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
50c2l4rA_



not modelled 99.5 20 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
51d1jnua_



not modelled 99.5 16 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
52c3h9wA_



not modelled 99.5 18 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
53c3mjqB_



not modelled 99.5 22 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.
54c3eehA_



not modelled 99.5 16 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
55c2z6dB_



not modelled 99.5 18 PDB header:transferase
Chain: B: PDB Molecule:phototropin-2;
PDBTitle: crystal structure of lov1 domain of phototropin2 from2 arabidopsis thaliana
56c3k3dA_



not modelled 99.5 12 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
57c1v9yA_



not modelled 99.5 22 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)
58d1v9ya_



not modelled 99.5 22 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
59d1y28a_



not modelled 99.5 18 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
60c3icyB_



not modelled 99.5 11 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
61c3kx0X_



not modelled 99.4 13 PDB header:signaling protein
Chain: X: PDB Molecule:uncharacterized protein rv1364c/mt1410;
PDBTitle: crystal structure of the pas domain of rv1364c
62c3oloB_



not modelled 99.4 20 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
63c3njaC_



not modelled 99.4 18 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.
64d1xj3a1



not modelled 99.4 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
65c3b33A_



not modelled 99.4 12 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
66c2pdtD_



not modelled 99.4 15 PDB header:circadian clock protein
Chain: D: PDB Molecule:vivid pas protein vvd;
PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid
67c2qkpD_



not modelled 99.3 13 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
68c3fg8B_



not modelled 99.3 11 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein rha05790;
PDBTitle: crystal structure of pas domain of rha05790
69d1oj5a_



not modelled 99.3 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PAS domain of steroid receptor coactivator 1A, NCo-A1
70d1nwza_



not modelled 99.3 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
71c2jheB_



not modelled 99.3 19 PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)
72c3fc7B_



not modelled 99.3 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
73d1ll8a_



not modelled 99.2 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:N-terminal PAS domain of Pas kinase
74c3cloC_



not modelled 99.2 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
75d1otda_



not modelled 99.2 14 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
76d1mzua_



not modelled 99.1 9 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
77c3a0rA_



not modelled 99.1 14 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)
78c3a0vA_



not modelled 99.0 16 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)
79c2w0nA_



not modelled 98.9 16 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
80d1xfna1



not modelled 98.9 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
81c2oolA_



not modelled 98.7 10 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 98.6 12 PDB header:transferase
Chain: A: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of bacteriophytochrome chromophore binding domain
83c2veaA_



not modelled 98.5 10 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.
84c3c2wB_



not modelled 96.4 16 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
85c3eulB_



not modelled 95.9 13 PDB header:transcription
Chain: B: PDB Molecule:possible nitrate/nitrite response transcriptional
PDBTitle: structure of the signal receiver domain of the putative2 response regulator narl from mycobacterium tuberculosis
86c2qv6D_



not modelled 95.8 22 PDB header:hydrolase
Chain: D: PDB Molecule:gtp cyclohydrolase iii;
PDBTitle: gtp cyclohydrolase iii from m. jannaschii (mj0145)2 complexed with gtp and metal ions
87c3khtA_



not modelled 95.7 11 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
88c3hebB_



not modelled 95.4 12 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
89c2zayA_



not modelled 95.3 14 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
90d1mvoa_



not modelled 95.3 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
91d1p6qa_



not modelled 95.2 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
92d1w25a1



not modelled 95.0 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
93c3b2nA_



not modelled 94.9 17 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
94d1krwa_



not modelled 94.8 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
95c2ayxA_



not modelled 94.5 15 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
96d2oola2



not modelled 94.4 10 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
97c2qr3A_



not modelled 94.4 10 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
98c3t6kB_



not modelled 94.3 14 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
99d2o9ca2



not modelled 94.3 17 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
100d1ny5a1



not modelled 94.2 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
101c3cg0A_



not modelled 94.2 18 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
102d1jbea_



not modelled 94.1 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
103d1heya_



not modelled 94.0 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
104d1u0sy_



not modelled 93.8 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
105c2rjnA_



not modelled 93.2 9 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
106c3lteH_



not modelled 93.1 11 PDB header:transcription
Chain: H: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator (signal receiver domain) from2 bermanella marisrubri
107c2jrlA_



not modelled 93.0 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: solution structure of the beryllofluoride-activated ntrc4 receiver2 domain dimer
108d1dz3a_



not modelled 92.9 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
109d1i3ca_



not modelled 92.8 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
110d1dbwa_



not modelled 92.7 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
111d1zesa1



not modelled 92.7 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
112d2ayxa1



not modelled 92.7 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
113c2jk1A_



not modelled 92.7 10 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
114d1qkka_



not modelled 92.6 20 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
115c3gt7A_



not modelled 92.5 13 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
116c2yxbA_



not modelled 92.5 12 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
117d2pl1a1



not modelled 92.4 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
118c3gl9B_



not modelled 92.4 8 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator;
PDBTitle: the structure of a histidine kinase-response regulator2 complex sheds light into two-component signaling and3 reveals a novel cis autophosphorylation mechanism
119c3hv2B_



not modelled 92.1 11 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
120c2qxyB_



not modelled 91.9 16 PDB header:transcription
Chain: B: PDB Molecule:response regulator;
PDBTitle: crystal structure of a response regulator from thermotoga2 maritima

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