Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76129
DateThu Jan 5 12:19:21 GMT 2012
Unique Job IDce3b1ce95588dcdd

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: 52%
412 residues ( 52% 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.
694 residues ( 87%) 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  MKLTDADNAADGIFFPALEQNMMGAVLINENDEVMFFNPAAEKLWGYKREEVIGNNIDML
Secondary structure 
















SS confidence 



























































Disorder  ??

























































Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  IPRDLRPAHPEYIRHNREGGKARVEGMSRELQLEKKDGSKIWTRFALSKVSAEGKVYYLA
Secondary structure 














SS confidence 



























































Disorder 















































?










Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  LVRDASVEMAQKEQTRQLIIAVDHLDRPVIVLDPERHIVQCNRAFTEMFGYCISEASGMQ
Secondary structure 















SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........190.........200.........210.........220.........230.........240
Sequence  PDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQN
Secondary structure 


















SS confidence 



























































Disorder 






















?
?

































Disorder confidence 



























































 
   .........250.........260.........270.........280.........290.........300
Sequence  LVMTFSDITEERQIRQLEGNILAAMCSSPPFHEMGEIICRNIESVLNESHVSLFALRNGM
Secondary structure 











SS confidence 



























































Disorder 

























































?
Disorder confidence 



























































 
   .........310.........320.........330.........340.........350.........360
Sequence  PIHWASSSHGAEIQNAQSWSATIRQRDGAPAGILQIKTSSGAETSAFIERVADISQHMAA
Secondary structure 



























SS confidence 



























































Disorder 





?






?
??



















?

















???
Disorder confidence 



























































 
   .........370.........380.........390.........400.........410.........420
Sequence  LALEQEKSRQHIEQLIQFDPMTGLPNRNNLHNYLDDLVDKAVSPVVYLIGVDHIQDVIDS
Secondary structure 
























SS confidence 



























































Disorder  ???
























































Disorder confidence 



























































 
   .........430.........440.........450.........460.........470.........480
Sequence  LGYAWADQALLEVVNRFREKLKPDQYLCRIEGTQFVLVSLENDVSNITQIADELRNVVSK
Secondary structure 
















SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........490.........500.........510.........520.........530.........540
Sequence  PIMIDDKPFPLTLSIGISYDLGKNRDYLLSTAHNAMDYIRKNGGNGWQFFSPAMNEMVKE
Secondary structure 
















SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........550.........560.........570.........580.........590.........600
Sequence  RLVLGAALKEAISNNQLKLVYQPQIFAETGELYGIEALARWHDPLHGHVPPSRFIPLAEE
Secondary structure 























SS confidence 



























































Disorder 



























































Disorder confidence 



























































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


















SS confidence 



























































Disorder 







































?

?















Disorder confidence 



























































 
   .........670.........680.........690.........700.........710.........720
Sequence  GHQLTVEITESMMMEHDTEIFKRIQILRDMGVGLSVDDFGTGFSGLSRLVSLPVTEIKID
Secondary structure 














SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........730.........740.........750.........760.........770.........780
Sequence  KSFVDRCLTEKRILALLEAITSIGQSLNLTVVAEGVETKEQFEMLRKIHCRVIQGYFFSR
Secondary structure 





















SS confidence 



























































Disorder 





???


















































Disorder confidence 



























































 
   .........790.........
Sequence  PLPAEEIPGWMSSVLPLKI
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: 359 - 783
Aligned: 412
Modelled: 425
Confidence: 100.0%
Identity: 25%
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: 372 - 781
Aligned: 366
Modelled: 383
Confidence: 100.0%
Identity: 20%
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: 538 - 788
Aligned: 249
Modelled: 251
Confidence: 100.0%
Identity: 26%
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: 533 - 787
Aligned: 253
Modelled: 255
Confidence: 100.0%
Identity: 26%
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: 542 - 794
Aligned: 250
Modelled: 253
Confidence: 100.0%
Identity: 34%
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: 540 - 784
Aligned: 238
Modelled: 245
Confidence: 100.0%
Identity: 27%
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: 547 - 783
Aligned: 228
Modelled: 237
Confidence: 100.0%
Identity: 20%
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: 542 - 795
Aligned: 240
Modelled: 241
Confidence: 100.0%
Identity: 33%
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: 547 - 794
Aligned: 242
Modelled: 248
Confidence: 100.0%
Identity: 19%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 556 - 783
Aligned: 222
Modelled: 227
Confidence: 100.0%
Identity: 19%
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: 361 - 532
Aligned: 172
Modelled: 172
Confidence: 100.0%
Identity: 25%
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: 361 - 529
Aligned: 161
Modelled: 169
Confidence: 100.0%
Identity: 19%
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: 364 - 532
Aligned: 169
Modelled: 169
Confidence: 100.0%
Identity: 24%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3i5a chain A

3D model

Region: 364 - 528
Aligned: 165
Modelled: 165
Confidence: 100.0%
Identity: 24%
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 3mtk chain A

3D model

Region: 371 - 535
Aligned: 160
Modelled: 165
Confidence: 100.0%
Identity: 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

Phyre2

PDB 3icl chain A

3D model

Region: 378 - 532
Aligned: 155
Modelled: 154
Confidence: 100.0%
Identity: 28%
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 3i5b chain A

3D model

Region: 375 - 531
Aligned: 157
Modelled: 157
Confidence: 100.0%
Identity: 22%
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 3i5c chain A

3D model

Region: 351 - 529
Aligned: 179
Modelled: 179
Confidence: 100.0%
Identity: 20%
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 3qyy chain B

3D model

Region: 371 - 529
Aligned: 150
Modelled: 150
Confidence: 100.0%
Identity: 20%
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

Phyre2

PDB 3ign chain A

3D model

Region: 374 - 529
Aligned: 156
Modelled: 152
Confidence: 100.0%
Identity: 21%
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 3rty chain A

3D model

Region: 24 - 256
Aligned: 224
Modelled: 224
Confidence: 99.9%
Identity: 11%
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 3ewk chain A

3D model

Region: 25 - 247
Aligned: 218
Modelled: 218
Confidence: 99.9%
Identity: 19%
PDB header:flavoprotein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos

Phyre2

PDB 3gec chain A

3D model

Region: 24 - 259
Aligned: 218
Modelled: 218
Confidence: 99.9%
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 3gdi chain B

3D model

Region: 24 - 258
Aligned: 211
Modelled: 211
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 1ew0 chain A

3D model

Region: 1 - 126
Aligned: 126
Modelled: 126
Confidence: 99.8%
Identity: 27%
Fold: Profilin-like
Superfamily: PYP-like sensor domain (PAS domain)
Family: Heme-binding PAS domain

Phyre2

PDB 1wa9 chain A

3D model

Region: 24 - 260
Aligned: 230
Modelled: 230
Confidence: 99.8%
Identity: 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

Phyre2

PDB 3p7n chain B

3D model

Region: 136 - 429
Aligned: 182
Modelled: 182
Confidence: 99.8%
Identity: 17%
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 1h5y chain A

3D model

Region: 737 - 797
Aligned: 61
Modelled: 61
Confidence: 91.2%
Identity: 20%
Fold: TIM beta/alpha-barrel
Superfamily: Ribulose-phoshate binding barrel
Family: Histidine biosynthesis enzymes

Phyre2
1

c3pjwA_
2

c3gfzB_
3

c3hvbB_
4

c3hv9A_
5

c3s83A_
6

c3pfmA_
7

c2w27A_
8

c2r6oB_
9

d2basa1
10

c3kzpA_
11

c1w25B_
12

c3ezuA_
13

c3breA_
14

c3i5aA_
15

c3mtkA_
16

c3iclA_
17

c3i5bA_
18

c3i5cA_
19

c3qyyB_
20

c3ignA_
21



22



23



24

c3rtyA_
25

c3ewkA_
26

c3gecA_
27

c3gdiB_
28

d1ew0a_
29

c1wa9A_
30

c3p7nB_
31



32



33



34



35



36



37



38



39



40



41



42



43



44



45



46



47



48



49



50



51



52



53



54



55



56



57



58



59



60



61



62



63



64



65



66



67



68



69



70



71



72



73



74



75



76



77



78



79



80



81



82



83



84



85



86



87



88



89



90



91



92



93



94



95



96



97



98



99



100



101



102



103



104



105



106



107



108



109



110



111



112



113



114



115

d1h5ya_
116



117



118



119



120



121



122



123



124



125



126



127



128



129



130



131



132



133



134



135



136



137



138



139



140



141



142



143



144



145



146



147



148



149



150



151



152



153



154



155



156



157



158



159



160



161



162



163



164



165



166



167



168



169



170



171



172



173



174



175



176



177



178



179



180



181



182



183



184



185



186



187



188



189



190



191



192



193



194



195



196



197



198



199



200



201



202



203



204



205



206



207



208



209



210



211



212



213



214



215



216



217



218



219



220



221



222



223



224



225



226



227



228



229



230



231



232



233



234



235



236



237



238



239



240



241



242



243



244



245



246



247



248



249



250



251



252



253



254



255



256



257



258



259



260



261



262



263



264



265



266



267



268



269



270



271



272



273



274



275



276



277



278



279



280



281



282



283



284



285



286



287



288



289



290



291



292



293



294



295



296



297



298



299



300



301



302



303



304



305



306



307



308



309



310



311



312



313



314



315



316



317



318



319



320



321



322



323



324



325



326



327



328



329



330



331



332



333



334



335



336



337



338



339



340



341



342



343



344



345



346



347



348



349



350



351



352



353



354



355



356



357



358



359



360



361



362



363



364



365



366



367



368



369



370



371



372



373



374



375



376



377



378



379



380



381



382



383



384



385



386



387



388



389



390



391



392



393



394



395



396



397



398



399



400



401



402



403



404



405



406



407



408



409



410



411



412



413



414



415



416



417



418



419



420



421



422



423



424



425



426



427



428



429



430



431



432



433



434



435



436



437



438



439



440



441



442



443



444



445



446



447



448



449



450



451



452



453



454



455



456



457



458



459



460



461



462



463



464



465



466



467



468



469



470



471



472



473



474



475



476



477



478



479



480



481



482



483



484



485



486



487



488



489



490






Detailed template information 

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



100.0 25 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 20 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 26 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 26 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 34 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_



100.0 27 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 20 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 33 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 19 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_



100.0 19 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 25 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 19 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 24 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3i5aA_



100.0 24 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
15c3mtkA_



100.0 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
16c3iclA_



100.0 28 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
17c3i5bA_



100.0 22 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
18c3i5cA_



100.0 20 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
19c3qyyB_



100.0 20 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
20c3ignA_



100.0 21 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
21c3hvaA_



not modelled 100.0 20 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
22d1w25a3



not modelled 100.0 26 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
23c3hvwA_



not modelled 99.9 21 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 11 PDB header:circadian clock protein
Chain: A: PDB Molecule:period circadian protein;
PDBTitle: structure of an enclosed dimer formed by the drosophila period protein
25c3ewkA_



99.9 19 PDB header:flavoprotein
Chain: A: PDB Molecule:sensor protein;
PDBTitle: structure of the redox sensor domain of methylococcus capsulatus2 (bath) mmos
26c3gecA_



99.9 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
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
28d1ew0a_



99.8 27 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
29c1wa9A_



99.8 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
30c3p7nB_



99.8 17 PDB header:dna binding protein
Chain: B: PDB Molecule:sensor histidine kinase;
PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis
31c2pr6A_



not modelled 99.7 22 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)
32d1y28a_



not modelled 99.7 22 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
33c2r78D_



not modelled 99.7 18 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
34c3bwlA_



not modelled 99.7 18 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of pas domain of htr-like protein from haloarcula2 marismortui
35c2wkqA_



not modelled 99.7 20 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
36c1v9yA_



not modelled 99.7 100 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)
37d1v9ya_



not modelled 99.7 100 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
38c3mfxA_



not modelled 99.7 10 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
39c2v1bA_



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))
40c3mqoB_



not modelled 99.7 14 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
41c3mjqB_



not modelled 99.7 24 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.
42c3oloB_



not modelled 99.7 12 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
43d1xj3a1



not modelled 99.6 26 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Heme-binding PAS domain
44c2gj3A_



not modelled 99.6 23 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.
45c3b33A_



not modelled 99.6 14 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
46c3luqC_



not modelled 99.6 13 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
47c3mxqC_



not modelled 99.6 14 PDB header:transferase
Chain: C: PDB Molecule:sensor protein;
PDBTitle: crystal structure of sensory box sensor histidine kinase from vibrio2 cholerae
48c3lyxA_



not modelled 99.6 20 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
49c3caxA_



not modelled 99.6 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pf0695;
PDBTitle: crystal structure of uncharacterized protein pf0695
50c3mr0B_



not modelled 99.6 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
51d1p97a_



not modelled 99.5 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Hypoxia-inducible factor Hif2a, C-terminal domain
52c2l4rA_



not modelled 99.5 19 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
53d1n9la_



not modelled 99.5 20 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
54c3f1oB_



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
55c2vlgD_



not modelled 99.5 18 PDB header:transferase
Chain: D: PDB Molecule:sporulation kinase a;
PDBTitle: kina pas-a domain, homodimer
56d1jnua_



not modelled 99.5 22 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
57d1bywa_



not modelled 99.5 22 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:Flavin-binding PAS domain
58c3k3dA_



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
59c3fg8B_



not modelled 99.5 17 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein rha05790;
PDBTitle: crystal structure of pas domain of rha05790
60c2z6dB_



not modelled 99.5 19 PDB header:transferase
Chain: B: PDB Molecule:phototropin-2;
PDBTitle: crystal structure of lov1 domain of phototropin2 from2 arabidopsis thaliana
61d1ll8a_



not modelled 99.4 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:N-terminal PAS domain of Pas kinase
62c2kdkA_



not modelled 99.4 12 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
63c3kx0X_



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
64c3eehA_



not modelled 99.4 17 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
65d1nwza_



not modelled 99.4 14 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
66c3h9wA_



not modelled 99.4 16 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
67c3fc7B_



not modelled 99.3 16 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
68c3icyB_



not modelled 99.3 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
69c2qkpD_



not modelled 99.3 11 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
70d1mzua_



not modelled 99.3 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
71d1otda_



not modelled 99.3 15 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
72c2jheB_



not modelled 99.2 12 PDB header:transcription
Chain: B: PDB Molecule:transcription regulator tyrr;
PDBTitle: n-terminal domain of tyrr transcription factor (residues 1 -2 190)
73d1oj5a_



not modelled 99.1 9 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PAS domain of steroid receptor coactivator 1A, NCo-A1
74c2pdtD_



not modelled 99.1 17 PDB header:circadian clock protein
Chain: D: PDB Molecule:vivid pas protein vvd;
PDBTitle: 2.3 angstrom structure of phosphodiesterase treated vivid
75c3njaC_



not modelled 99.1 10 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.
76d1xfna1



not modelled 99.0 13 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:PYP-like
77c3a0vA_



not modelled 99.0 15 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m)
78c2o9bA_



not modelled 99.0 10 PDB header:transferase
Chain: A: PDB Molecule:bacteriophytochrome;
PDBTitle: crystal structure of bacteriophytochrome chromophore binding domain
79c3a0rA_



not modelled 98.9 17 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)
80c2veaA_



not modelled 98.9 7 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.
81c2oolA_



not modelled 98.9 11 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
82c2w0nA_



not modelled 98.9 18 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
83c3cloC_



not modelled 98.8 13 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
84c3c2wB_



not modelled 97.7 11 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
85c2qv6D_



not modelled 97.3 17 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
86d2o9ca2



not modelled 95.8 12 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
87d1mvoa_



not modelled 95.7 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
88c3khtA_



not modelled 95.7 10 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
89d2oola2



not modelled 95.6 6 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
90c3hebB_



not modelled 95.4 14 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
91d1krwa_



not modelled 95.0 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
92c2zayA_



not modelled 94.8 15 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
93c2ayxA_



not modelled 94.7 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
94d2veaa3



not modelled 94.6 10 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
95c2jk1A_



not modelled 94.5 8 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
96d1w25a1



not modelled 94.4 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
97d1p6qa_



not modelled 94.3 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
98d3c2wa3



not modelled 93.7 16 Fold:Profilin-like
Superfamily:PYP-like sensor domain (PAS domain)
Family:BphP N-terminal domain-like
99d1u0sy_



not modelled 93.6 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
100c3crnA_



not modelled 93.1 13 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
101d1jbea_



not modelled 93.0 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
102c2rjnA_



not modelled 93.0 12 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
103c3b2nA_



not modelled 93.0 12 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
104d2r25b1



not modelled 92.6 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
105c3nhzA_



not modelled 92.4 13 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
106c2j48A_



not modelled 92.4 16 PDB header:transferase
Chain: A: PDB Molecule:two-component sensor kinase;
PDBTitle: nmr structure of the pseudo-receiver domain of the cika2 protein.
107d1ny5a1



not modelled 92.2 18 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
108d1dz3a_



not modelled 92.1 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
109c2zwmA_



not modelled 92.0 11 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
110c3gt7A_



not modelled 92.0 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
111d1yioa2



not modelled 91.8 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
112d1nvma2



not modelled 91.7 12 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:HMGL-like
113c3c97A_



not modelled 91.7 11 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
114c3eulB_



not modelled 91.4 11 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
115d1h5ya_



91.2 20 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
116c3gl9B_



not modelled 91.2 13 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
117d1k68a_



not modelled 91.0 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
118c3i42A_



not modelled 90.8 16 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
119c3hv2B_



not modelled 90.7 14 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
120d1zesa1



not modelled 90.6 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related

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