Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP75995
DateWed Jan 25 15:21:04 GMT 2012
Unique Job IDd5f7e2f3a2abf142

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: 82%
416 residues ( 82% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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

SS confidence 



























































Disorder  ????























































Disorder confidence 



























































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






















SS confidence 



























































Disorder 
?















?
???
























?
?

????


Disorder confidence 



























































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




















SS confidence 



























































Disorder  ?????????





























??

?














?
Disorder confidence 



























































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

















SS confidence 



























































Disorder 



??

?






??
































??






Disorder confidence 



























































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
















SS confidence 



























































Disorder 



























































Disorder confidence 



























































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




















SS confidence 



























































Disorder 




























?














?













Disorder confidence 



























































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
















SS confidence 



























































Disorder 



























































Disorder confidence 



























































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






















SS confidence 



























































Disorder 









????
??










































Disorder confidence 



























































 
   .........490.........500.......
Sequence  YYFYKPVTYIDLVKIILSKPKVKVVVE
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: 40 - 489
Aligned: 416
Modelled: 428
Confidence: 100.0%
Identity: 18%
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: 61 - 486
Aligned: 364
Modelled: 375
Confidence: 100.0%
Identity: 21%
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: 245 - 492
Aligned: 246
Modelled: 248
Confidence: 100.0%
Identity: 22%
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: 244 - 492
Aligned: 247
Modelled: 249
Confidence: 100.0%
Identity: 22%
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: 249 - 500
Aligned: 249
Modelled: 252
Confidence: 100.0%
Identity: 32%
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: 244 - 489
Aligned: 239
Modelled: 246
Confidence: 100.0%
Identity: 25%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf

Phyre2

PDB 2w27 chain A

3D model

Region: 252 - 488
Aligned: 228
Modelled: 237
Confidence: 100.0%
Identity: 24%
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: 248 - 500
Aligned: 239
Modelled: 240
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 2bas chain A domain 1

3D model

Region: 252 - 499
Aligned: 242
Modelled: 248
Confidence: 100.0%
Identity: 22%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 261 - 488
Aligned: 222
Modelled: 227
Confidence: 100.0%
Identity: 18%
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: 60 - 228
Aligned: 161
Modelled: 169
Confidence: 99.7%
Identity: 7%
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: 42 - 225
Aligned: 169
Modelled: 184
Confidence: 99.5%
Identity: 8%
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: 14 - 227
Aligned: 207
Modelled: 214
Confidence: 99.4%
Identity: 7%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3i5c chain A

3D model

Region: 32 - 225
Aligned: 189
Modelled: 194
Confidence: 99.2%
Identity: 9%
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 1w25 chain A domain 3

3D model

Region: 62 - 228
Aligned: 161
Modelled: 167
Confidence: 99.2%
Identity: 6%
Fold: Ferredoxin-like
Superfamily: Nucleotide cyclase
Family: GGDEF domain

Phyre2

PDB 3icl chain A

3D model

Region: 60 - 228
Aligned: 161
Modelled: 169
Confidence: 99.2%
Identity: 6%
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: 60 - 225
Aligned: 158
Modelled: 166
Confidence: 99.2%
Identity: 4%
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 3i5a chain A

3D model

Region: 15 - 225
Aligned: 206
Modelled: 211
Confidence: 99.2%
Identity: 8%
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 3i5b chain A

3D model

Region: 60 - 227
Aligned: 163
Modelled: 168
Confidence: 99.2%
Identity: 9%
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 3mtk chain A

3D model

Region: 54 - 228
Aligned: 157
Modelled: 175
Confidence: 99.1%
Identity: 6%
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
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

c3i5cA_
15

d1w25a3
16

c3iclA_
17

c3ignA_
18

c3i5aA_
19

c3i5bA_
20

c3mtkA_
21



22



23



24



25



26



27



28



29



30



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



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






Detailed template information 

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



100.0 18 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 21 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 22 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 22 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 32 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_



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



100.0 24 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 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
9d2basa1



100.0 22 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_



100.0 18 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_



99.7 7 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
12c3ezuA_



99.5 8 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_



99.4 7 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3i5cA_



99.2 9 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
15d1w25a3



99.2 6 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
16c3iclA_



99.2 6 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
17c3ignA_



99.2 4 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
18c3i5aA_



99.2 8 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
19c3i5bA_



99.2 9 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
20c3mtkA_



99.1 6 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
21c3hvaA_



not modelled 99.1 10 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
22c3qyyB_



not modelled 99.1 4 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
23c3hvwA_



not modelled 98.6 14 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
24c3khtA_



not modelled 95.2 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
25d1mvoa_



not modelled 95.2 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
26d1ua7a2



not modelled 94.7 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
27d1p6qa_



not modelled 94.5 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
28c3hebB_



not modelled 94.5 17 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
29c2zayA_



not modelled 94.2 19 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
30d1gjwa2



not modelled 94.1 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
31d1a53a_



not modelled 93.9 12 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
32d1w25a1



not modelled 93.7 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
33c2jk1A_



not modelled 93.6 12 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
34c3edeB_



not modelled 93.4 18 PDB header:hydrolase
Chain: B: PDB Molecule:cyclomaltodextrinase;
PDBTitle: structural base for cyclodextrin hydrolysis
35d1jbea_



not modelled 93.0 19 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
36d1krwa_



not modelled 92.9 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
37c1qhoA_



not modelled 92.6 25 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
38c3q58A_



not modelled 92.4 16 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
39c2c3zA_



not modelled 92.3 13 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
40d1y0ea_



not modelled 92.2 10 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:NanE-like
41c3gt7A_



not modelled 92.1 12 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
42c2ayxA_



not modelled 92.0 17 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
43d1heya_



not modelled 92.0 20 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
44c3eulB_



not modelled 91.9 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
45c2p0oA_



not modelled 91.3 17 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
46c1jdaA_



not modelled 91.2 14 PDB header:hydrolase
Chain: A: PDB Molecule:1,4-alpha maltotetrahydrolase;
PDBTitle: maltotetraose-forming exo-amylase
47c3hdgE_



not modelled 91.0 16 PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the n-terminal domain of an2 uncharacterized protein (ws1339) from wolinella3 succinogenes
48d1yioa2



not modelled 91.0 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
49d1ny5a1



not modelled 91.0 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
50c3rqiA_



not modelled 90.8 13 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
51c1cygA_



not modelled 90.8 16 PDB header:glycosyltransferase
Chain: A: PDB Molecule:cyclodextrin glucanotransferase;
PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
52d1qkka_



not modelled 90.7 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
53c1jibA_



not modelled 90.7 24 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.
54d2guya2



not modelled 90.7 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
55c1bagA_



not modelled 90.5 14 PDB header:alpha-amylase
Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase;
PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose
56c3ucqA_



not modelled 90.5 19 PDB header:transferase
Chain: A: PDB Molecule:amylosucrase;
PDBTitle: crystal structure of amylosucrase from deinococcus geothermalis
57d1h3ga3



not modelled 90.2 18 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
58d1zesa1



not modelled 90.2 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
59c2wcsA_



not modelled 90.1 23 PDB header:hydrolase
Chain: A: PDB Molecule:alpha amylase, catalytic region;
PDBTitle: crystal structure of debranching enzyme from nostoc2 punctiforme (npde)
60c2h6rG_



not modelled 90.1 10 PDB header:isomerase
Chain: G: PDB Molecule:triosephosphate isomerase;
PDBTitle: crystal structure of triosephosphate isomerase (tim) from2 methanocaldococcus jannaschii
61c1tcmB_



not modelled 90.1 14 PDB header:glycosyltransferase
Chain: B: PDB Molecule:cyclodextrin glycosyltransferase;
PDBTitle: cyclodextrin glycosyltransferase w616a mutant from bacillus2 circulans strain 251
62c3czkA_



not modelled 90.1 20 PDB header:hydrolase
Chain: A: PDB Molecule:sucrose hydrolase;
PDBTitle: crystal structure analysis of sucrose hydrolase(suh) e322q-2 sucrose complex
63c3gl9B_



not modelled 90.0 15 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
64c3crnA_



not modelled 90.0 21 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
65d1k68a_



not modelled 89.8 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
66c3nhzA_



not modelled 89.8 15 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
67c1gjuA_



not modelled 89.7 18 PDB header:transferase
Chain: A: PDB Molecule:maltodextrin glycosyltransferase;
PDBTitle: maltosyltransferase from thermotoga maritima
68d1qhoa4



not modelled 89.7 24 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
69d1kgsa2



not modelled 89.7 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
70d1lwha2



not modelled 89.7 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
71c3cg0A_



not modelled 89.7 20 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
72d2r25b1



not modelled 89.6 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
73c2rjnA_



not modelled 89.6 15 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
74c3i42A_



not modelled 89.4 20 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
75d1ys7a2



not modelled 89.1 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
76c2pz0B_



not modelled 89.0 9 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
77d2aaaa2



not modelled 89.0 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
78d2ayxa1



not modelled 89.0 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
79c3bmwA_



not modelled 88.9 16 PDB header:transferase
Chain: A: PDB Molecule:cyclomaltodextrin glucanotransferase;
PDBTitle: cyclodextrin glycosyl transferase from thermoanerobacterium2 thermosulfurigenes em1 mutant s77p complexed with a maltoheptaose3 inhibitor
80d1dz3a_



not modelled 88.7 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
81c2zwmA_



not modelled 88.5 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
82c3b2nA_



not modelled 88.4 13 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
83d1xhfa1



not modelled 88.4 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
84d1g5aa2



not modelled 88.4 13 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
85c2qr3A_



not modelled 88.2 13 PDB header:transcription
Chain: A: PDB Molecule:two-component system response regulator;
PDBTitle: crystal structure of the n-terminal signal receiver domain of two-2 component system response regulator from bacteroides fragilis
86c3hv2B_



not modelled 88.2 12 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
87d1a04a2



not modelled 87.7 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
88c3k8kB_



not modelled 87.7 17 PDB header:membrane protein
Chain: B: PDB Molecule:alpha-amylase, susg;
PDBTitle: crystal structure of susg
89d1h5ya_



not modelled 87.5 10 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
90c3igsB_



not modelled 87.4 10 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
91d1i3ca_



not modelled 87.3 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
92c3cz5B_



not modelled 87.1 12 PDB header:transcription regulator
Chain: B: PDB Molecule:two-component response regulator, luxr family;
PDBTitle: crystal structure of two-component response regulator, luxr family,2 from aurantimonas sp. si85-9a1
93d1dbwa_



not modelled 87.1 18 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
94c1jgiA_



not modelled 86.9 13 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
95c3a47A_



not modelled 86.7 16 PDB header:hydrolase
Chain: A: PDB Molecule:oligo-1,6-glucosidase;
PDBTitle: crystal structure of isomaltase from saccharomyces cerevisiae
96c2ya0A_



not modelled 86.6 23 PDB header:hydrolase
Chain: A: PDB Molecule:putative alkaline amylopullulanase;
PDBTitle: catalytic module of the multi-modular glycogen-degrading2 pneumococcal virulence factor spua
97c3cu5B_



not modelled 86.5 12 PDB header:transcription regulator
Chain: B: PDB Molecule:two component transcriptional regulator, arac family;
PDBTitle: crystal structure of a two component transcriptional regulator arac2 from clostridium phytofermentans isdg
98d1k66a_



not modelled 86.5 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
99c3dhuC_



not modelled 86.5 16 PDB header:hydrolase
Chain: C: PDB Molecule:alpha-amylase;
PDBTitle: crystal structure of an alpha-amylase from lactobacillus2 plantarum
100d2pl1a1



not modelled 86.4 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
101d2bhua3



not modelled 86.3 22 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
102c3c3mA_



not modelled 86.3 16 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
103c2yxbA_



not modelled 86.2 17 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
104c3cnbC_



not modelled 86.2 18 PDB header:dna binding protein
Chain: C: PDB Molecule:dna-binding response regulator, merr family;
PDBTitle: crystal structure of signal receiver domain of dna binding response2 regulator protein (merr) from colwellia psychrerythraea 34h
105d2d3na2



not modelled 85.7 25 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
106c2ze0A_



not modelled 85.5 20 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-glucosidase;
PDBTitle: alpha-glucosidase gsj
107c1gviA_



not modelled 85.2 21 PDB header:hydrolase
Chain: A: PDB Molecule:maltogenic amylase;
PDBTitle: thermus maltogenic amylase in complex with beta-cd
108d1eh9a3



not modelled 85.2 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
109d1zh2a1



not modelled 84.9 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
110d1u0sy_



not modelled 84.9 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
111c2iswB_



not modelled 84.8 18 PDB header:lyase
Chain: B: PDB Molecule:putative fructose-1,6-bisphosphate aldolase;
PDBTitle: structure of giardia fructose-1,6-biphosphate aldolase in2 complex with phosphoglycolohydroxamate
112c3c97A_



not modelled 84.4 17 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
113d1hvxa2



not modelled 84.3 24 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
114c3cfyA_



not modelled 84.2 12 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
115c2qpuB_



not modelled 84.0 11 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-amylase type a isozyme;
PDBTitle: sugar tongs mutant s378p in complex with acarbose
116d1w0ma_



not modelled 83.9 13 Fold:TIM beta/alpha-barrel
Superfamily:Triosephosphate isomerase (TIM)
Family:Triosephosphate isomerase (TIM)
117c3blpX_



not modelled 83.9 10 PDB header:hydrolase
Chain: X: PDB Molecule:alpha-amylase 1;
PDBTitle: role of aromatic residues in human salivary alpha-amylase
118d1zgza1



not modelled 83.8 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
119c2z1kA_



not modelled 83.6 20 PDB header:hydrolase
Chain: A: PDB Molecule:(neo)pullulanase;
PDBTitle: crystal structure of ttha1563 from thermus thermophilus hb8
120c1zjaB_



not modelled 83.6 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)

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