Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP37649
DateThu Jan 5 11:56:21 GMT 2012
Unique Job ID5d49611a64f5ca83

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%
409 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.
579 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  MRVSRSLTIKQMAMVAAVVLVFVFIFCTVLLFHLVQQNRYNTATQLESIARSVREPLSSA
Secondary structure 


SS confidence 



























































Disorder  ??????















































??



Disorder confidence 



























































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





















SS confidence 



























































Disorder 

??











???????








?????????????????




???
??
Disorder confidence 



























































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







SS confidence 



























































Disorder 
???
??
???
















































Disorder confidence 



























































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




















SS confidence 



























































Disorder 













????????






?????

























Disorder confidence 



























































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
























SS confidence 



























































Disorder 
























??
































Disorder confidence 



























































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



















SS confidence 



























































Disorder 



























































Disorder confidence 



























































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













SS confidence 



























































Disorder 



























































Disorder confidence 



























































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






















SS confidence 



























































Disorder 



























































Disorder confidence 



























































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












SS confidence 



























































Disorder 


























?

?




























Disorder confidence 



























































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































SS confidence 



























































Disorder 



























































Disorder confidence 



























































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
















SS confidence 



























































Disorder 


























































?
Disorder confidence 



























































 
   ..
Sequence  EK
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: 226 - 650
Aligned: 409
Modelled: 425
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: 237 - 648
Aligned: 366
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: 406 - 655
Aligned: 247
Modelled: 250
Confidence: 100.0%
Identity: 24%
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: 406 - 655
Aligned: 247
Modelled: 250
Confidence: 100.0%
Identity: 24%
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: 410 - 661
Aligned: 246
Modelled: 252
Confidence: 100.0%
Identity: 35%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15

Phyre2

PDB 2w27 chain A

3D model

Region: 414 - 650
Aligned: 229
Modelled: 237
Confidence: 100.0%
Identity: 21%
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 3pfm chain A

3D model

Region: 408 - 650
Aligned: 234
Modelled: 243
Confidence: 100.0%
Identity: 26%
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 2bas chain A domain 1

3D model

Region: 413 - 661
Aligned: 244
Modelled: 249
Confidence: 100.0%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 2r6o chain B

3D model

Region: 410 - 658
Aligned: 233
Modelled: 236
Confidence: 100.0%
Identity: 31%
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 3kzp chain A

3D model

Region: 424 - 651
Aligned: 220
Modelled: 227
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: 231 - 400
Aligned: 170
Modelled: 170
Confidence: 100.0%
Identity: 18%
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: 233 - 397
Aligned: 156
Modelled: 165
Confidence: 100.0%
Identity: 18%
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: 222 - 400
Aligned: 178
Modelled: 179
Confidence: 99.9%
Identity: 21%
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: 244 - 400
Aligned: 157
Modelled: 156
Confidence: 99.9%
Identity: 25%
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 3i5a chain A

3D model

Region: 236 - 396
Aligned: 160
Modelled: 161
Confidence: 99.9%
Identity: 18%
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 3ign chain A

3D model

Region: 240 - 398
Aligned: 159
Modelled: 155
Confidence: 99.9%
Identity: 13%
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 3mtk chain A

3D model

Region: 237 - 404
Aligned: 161
Modelled: 168
Confidence: 99.9%
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 3hva chain A

3D model

Region: 241 - 396
Aligned: 156
Modelled: 156
Confidence: 99.9%
Identity: 20%
PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa

Phyre2

PDB 3i5b chain A

3D model

Region: 241 - 399
Aligned: 159
Modelled: 159
Confidence: 99.9%
Identity: 17%
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: 216 - 397
Aligned: 182
Modelled: 182
Confidence: 99.9%
Identity: 17%
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 3pjv chain D

3D model

Region: 29 - 156
Aligned: 122
Modelled: 120
Confidence: 98.6%
Identity: 16%
PDB header:lyase
Chain: D: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain

Phyre2

PDB 2asx chain A domain 1

3D model

Region: 181 - 236
Aligned: 53
Modelled: 53
Confidence: 92.7%
Identity: 25%
Fold: HAMP domain-like
Superfamily: HAMP domain-like
Family: HAMP domain

Phyre2

PDB 1h5y chain A

3D model

Region: 604 - 662
Aligned: 59
Modelled: 59
Confidence: 84.6%
Identity: 27%
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

c2w27A_
7

c3pfmA_
8

d2basa1
9

c2r6oB_
10

c3kzpA_
11

c1w25B_
12

c3ezuA_
13

c3breA_
14

c3iclA_
15

c3i5aA_
16

c3ignA_
17

c3mtkA_
18

c3hvaA_
19

c3i5bA_
20

c3i5cA_
21



22



23



24

c3pjvD_
25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41



42



43



44



45



46



47

d2asxa1
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



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

d1h5ya_
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






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 24 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 24 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 35 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c2w27A_



100.0 21 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
7c3pfmA_



100.0 26 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
8d2basa1



100.0 18 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
9c2r6oB_



100.0 31 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
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 18 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 18 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 21 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3iclA_



99.9 25 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
15c3i5aA_



99.9 18 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
16c3ignA_



99.9 13 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
17c3mtkA_



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
18c3hvaA_



99.9 20 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
19c3i5bA_



99.9 17 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
20c3i5cA_



99.9 17 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 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
22d1w25a3



not modelled 99.9 18 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
23c3hvwA_



not modelled 99.9 18 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
24c3pjvD_



98.6 16 PDB header:lyase
Chain: D: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain
25c3p7nB_



not modelled 97.4 9 PDB header:dna binding protein
Chain: B: PDB Molecule:sensor histidine kinase;
PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis
26c3khtA_



not modelled 96.0 13 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
27c2p0oA_



not modelled 95.6 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein duf871;
PDBTitle: crystal structure of a conserved protein from locus ef_2437 in2 enterococcus faecalis with an unknown function
28d1mvoa_



not modelled 95.3 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
29c3hebB_



not modelled 95.2 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
30d1p6qa_



not modelled 95.2 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
31c2pz0B_



not modelled 95.1 11 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
32c3q58A_



not modelled 94.8 17 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
33c2zayA_



not modelled 94.8 13 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
34d1w25a1



not modelled 94.7 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
35c2c3zA_



not modelled 94.7 18 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of a truncated variant of indole-3-2 glycerol phosphate synthase from sulfolobus solfataricus
36d1a53a_



not modelled 94.6 20 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
37c3qvqB_



not modelled 93.9 16 PDB header:hydrolase
Chain: B: PDB Molecule:phosphodiesterase olei02445;
PDBTitle: the structure of an oleispira antarctica phosphodiesterase olei024452 in complex with the product sn-glycerol-3-phosphate
38c3igsB_



not modelled 93.8 12 PDB header:isomerase
Chain: B: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase 2;
PDBTitle: structure of the salmonella enterica n-acetylmannosamine-6-phosphate2 2-epimerase
39d1i3ca_



not modelled 93.7 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
40d1zesa1



not modelled 93.6 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
41d1jbea_



not modelled 93.5 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
42c3gt7A_



not modelled 93.4 10 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
43c3qjaA_



not modelled 93.4 20 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of the mycobacterium tuberculosis indole-3-glycerol2 phosphate synthase (trpc) in apo form
44d1ny5a1



not modelled 93.3 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
45d1zh2a1



not modelled 93.0 20 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
46d1heya_



not modelled 92.7 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
47d2asxa1



92.7 25 Fold:HAMP domain-like
Superfamily:HAMP domain-like
Family:HAMP domain
48d1krwa_



not modelled 92.7 19 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
49d2guya2



not modelled 92.6 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
50d1h3ga3



not modelled 92.4 23 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
51d1xm3a_



not modelled 92.3 11 Fold:TIM beta/alpha-barrel
Superfamily:ThiG-like
Family:ThiG-like
52c3i42A_



not modelled 92.2 18 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
53d1k66a_



not modelled 92.2 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
54c3b2nA_



not modelled 92.2 14 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
55c3dhuC_



not modelled 92.1 21 PDB header:hydrolase
Chain: C: PDB Molecule:alpha-amylase;
PDBTitle: crystal structure of an alpha-amylase from lactobacillus2 plantarum
56d1qkka_



not modelled 92.1 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
57c3cg0A_



not modelled 91.8 21 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
58c3nhzA_



not modelled 91.6 18 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
59c3lnrA_



not modelled 91.5 14 PDB header:signaling protein
Chain: A: PDB Molecule:aerotaxis transducer aer2;
PDBTitle: crystal structure of poly-hamp domains from the p. aeruginosa soluble2 receptor aer2
60d2pl1a1



not modelled 91.3 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
61c3czkA_



not modelled 91.1 22 PDB header:hydrolase
Chain: A: PDB Molecule:sucrose hydrolase;
PDBTitle: crystal structure analysis of sucrose hydrolase(suh) e322q-2 sucrose complex
62c2rjnA_



not modelled 91.0 13 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
63d1g5aa2



not modelled 91.0 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
64d1ua7a2



not modelled 91.0 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
65c2yxbA_



not modelled 90.9 15 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
66c3hv2B_



not modelled 90.9 8 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
67d1eh9a3



not modelled 90.9 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
68d1a04a2



not modelled 90.9 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
69c3ffsC_



not modelled 90.8 12 PDB header:oxidoreductase
Chain: C: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: the crystal structure of cryptosporidium parvum inosine-5'-2 monophosphate dehydrogenase
70d1ys7a2



not modelled 90.6 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
71d1dz3a_



not modelled 90.6 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
72c1cjkA_



not modelled 90.5 9 PDB header:lyase/lyase/signaling protein
Chain: A: PDB Molecule:adenylate cyclase, type v;
PDBTitle: complex of gs-alpha with the catalytic domains of mammalian adenylyl2 cyclase: complex with adenosine 5'-(alpha thio)-triphosphate (rp),3 mg, and mn
73d2ayxa1



not modelled 90.5 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
74c3c3mA_



not modelled 90.1 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of the n-terminal domain of response regulator2 receiver protein from methanoculleus marisnigri jr1
75c1jgiA_



not modelled 90.1 12 PDB header:transferase
Chain: A: PDB Molecule:amylosucrase;
PDBTitle: crystal structure of the active site mutant glu328gln of2 amylosucrase from neisseria polysaccharea in complex with3 the natural substrate sucrose
76d1dbwa_



not modelled 90.0 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
77d2bhua3



not modelled 90.0 23 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
78c3eulB_



not modelled 89.9 17 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
79c1cygA_



not modelled 89.8 14 PDB header:glycosyltransferase
Chain: A: PDB Molecule:cyclodextrin glucanotransferase;
PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
80d1yioa2



not modelled 89.6 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
81c3a47A_



not modelled 89.6 21 PDB header:hydrolase
Chain: A: PDB Molecule:oligo-1,6-glucosidase;
PDBTitle: crystal structure of isomaltase from saccharomyces cerevisiae
82c3edeB_



not modelled 89.5 16 PDB header:hydrolase
Chain: B: PDB Molecule:cyclomaltodextrinase;
PDBTitle: structural base for cyclodextrin hydrolysis
83c2jk1A_



not modelled 89.5 12 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
84c1zjaB_



not modelled 89.3 16 PDB header:isomerase
Chain: B: PDB Molecule:trehalulose synthase;
PDBTitle: crystal structure of the trehalulose synthase mutb from2 pseudomonas mesoacidophila mx-45 (triclinic form)
85c3rqiA_



not modelled 89.3 19 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein;
PDBTitle: crystal structure of a response regulator protein from burkholderia2 pseudomallei with a phosphorylated aspartic acid, calcium ion and3 citrate
86d1azsa_



not modelled 89.2 9 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:Adenylyl and guanylyl cyclase catalytic domain
87d1vd6a1



not modelled 89.1 16 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Glycerophosphoryl diester phosphodiesterase
88c2wcsA_



not modelled 89.0 23 PDB header:hydrolase
Chain: A: PDB Molecule:alpha amylase, catalytic region;
PDBTitle: crystal structure of debranching enzyme from nostoc2 punctiforme (npde)
89c2ayxA_



not modelled 89.0 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
90d2aaaa2



not modelled 88.9 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
91d1u0sy_



not modelled 88.9 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
92c3cnbC_



not modelled 88.7 20 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
93c1qhoA_



not modelled 88.6 20 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
94d2a9pa1



not modelled 88.6 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
95d1cgta4



not modelled 88.6 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
96c3cg4A_



not modelled 88.4 17 PDB header:structural genomics, unknown function
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
97d1cyga4



not modelled 88.4 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
98d1gjwa2



not modelled 88.4 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
99c3ch0A_



not modelled 88.4 24 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphoryl diester phosphodiesterase2 (yp_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution
100c2zwmA_



not modelled 88.2 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
101c1gcyA_



not modelled 88.1 8 PDB header:hydrolase
Chain: A: PDB Molecule:glucan 1,4-alpha-maltotetrahydrolase;
PDBTitle: high resolution crystal structure of maltotetraose-forming2 exo-amylase
102d1xi3a_



not modelled 88.0 14 Fold:TIM beta/alpha-barrel
Superfamily:Thiamin phosphate synthase
Family:Thiamin phosphate synthase
103d1lwha2



not modelled 88.0 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
104d1pama4



not modelled 87.9 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
105c1tcmB_



not modelled 87.7 14 PDB header:glycosyltransferase
Chain: B: PDB Molecule:cyclodextrin glycosyltransferase;
PDBTitle: cyclodextrin glycosyltransferase w616a mutant from bacillus2 circulans strain 251
106d1kgsa2



not modelled 87.6 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
107c2h6rG_



not modelled 87.5 17 PDB header:isomerase
Chain: G: PDB Molecule:triosephosphate isomerase;
PDBTitle: crystal structure of triosephosphate isomerase (tim) from2 methanocaldococcus jannaschii
108c3cfyA_



not modelled 87.5 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative luxo repressor protein;
PDBTitle: crystal structure of signal receiver domain of putative luxo2 repressor protein from vibrio parahaemolyticus
109d1m7xa3



not modelled 87.4 27 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
110c3crnA_



not modelled 87.4 12 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
111d1xhfa1



not modelled 87.3 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
112c3f6cB_



not modelled 87.3 19 PDB header:dna binding protein
Chain: B: PDB Molecule:positive transcription regulator evga;
PDBTitle: crystal structure of n-terminal domain of positive transcription2 regulator evga from escherichia coli
113c2qv6D_



not modelled 87.1 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
114d1e43a2



not modelled 87.1 25 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
115d1qhoa4



not modelled 87.1 28 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
116d1m53a2



not modelled 87.0 15 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
117d1ea9c3



not modelled 87.0 23 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
118d2gjpa2



not modelled 86.9 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
119c1jibA_



not modelled 86.9 25 PDB header:hydrolase
Chain: A: PDB Molecule:neopullulanase;
PDBTitle: complex of alpha-amylase ii (tva ii) from thermoactinomyces2 vulgaris r-47 with maltotetraose based on a crystal soaked3 with maltohexaose.
120c3rlhA_



not modelled 86.8 16 PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of a class ii phospholipase d from loxosceles2 intermedia venom

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