Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionQ9JMT8
DateThu Jan 5 12:38:13 GMT 2012
Unique Job ID6f93e95dcb3cc3a6

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: 93%
329 residues ( 93% 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  MNTIKIKLNLIDYDSIVNIEFPCLLSEIEIELLSQLLKGYSVNEISKRRNRSIKTVSCQK
Secondary structure 
SS confidence 
Disorder  ????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  MKLYKKLNVKSDLTLWRDVFLRFKAYLQPKNIICDNFNSSVLPVVSSKGESMAHYNIYYQ
Secondary structure 
SS confidence 
Disorder 
??
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PIYNAKNGNIAGCDVTIALKNSDGSAFALDSDRINYNPNDNKVSYLFGHINKLFSPIKNN
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LPHGFFITININPEDILTCDIERECLHFIKVFGTERIRLVLQFSTKEELYIIRRYQSSLR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  RIRNNNVYLSLNDFGMGYAELSHLQNIPFSYVNLHKTMFHDIESNSLTDIIATTIIDLSK
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350...
Sequence  QLHIDVIADGIETKKQAGYMIERGVKYLKGIALSSPLPADAFVRKLLASLKQV
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: 2 - 339
Aligned: 329
Modelled: 338
Confidence: 100.0%
Identity: 12%
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: 60 - 336
Aligned: 267
Modelled: 277
Confidence: 100.0%
Identity: 15%
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: 102 - 342
Aligned: 239
Modelled: 241
Confidence: 100.0%
Identity: 11%
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: 89 - 342
Aligned: 252
Modelled: 254
Confidence: 100.0%
Identity: 11%
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: 102 - 349
Aligned: 244
Modelled: 248
Confidence: 100.0%
Identity: 17%
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: 96 - 339
Aligned: 240
Modelled: 242
Confidence: 100.0%
Identity: 16%
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: 105 - 338
Aligned: 228
Modelled: 234
Confidence: 100.0%
Identity: 16%
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: 101 - 349
Aligned: 238
Modelled: 248
Confidence: 100.0%
Identity: 24%
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: 105 - 352
Aligned: 243
Modelled: 248
Confidence: 100.0%
Identity: 16%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 114 - 338
Aligned: 222
Modelled: 224
Confidence: 100.0%
Identity: 13%
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: 5 - 89
Aligned: 85
Modelled: 85
Confidence: 99.0%
Identity: 13%
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: 5 - 87
Aligned: 80
Modelled: 83
Confidence: 98.6%
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 3icl chain A

3D model

Region: 3 - 91
Aligned: 89
Modelled: 89
Confidence: 98.4%
Identity: 17%
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 3bre chain A

3D model

Region: 6 - 91
Aligned: 86
Modelled: 86
Confidence: 98.4%
Identity: 10%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3mtk chain A

3D model

Region: 5 - 91
Aligned: 84
Modelled: 87
Confidence: 98.3%
Identity: 26%
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 1w25 chain A domain 3

3D model

Region: 3 - 91
Aligned: 89
Modelled: 89
Confidence: 98.2%
Identity: 11%
Fold: Ferredoxin-like
Superfamily: Nucleotide cyclase
Family: GGDEF domain

Phyre2

PDB 3hva chain A

3D model

Region: 2 - 88
Aligned: 87
Modelled: 87
Confidence: 98.2%
Identity: 10%
PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa

Phyre2

PDB 3i5a chain A

3D model

Region: 6 - 88
Aligned: 83
Modelled: 83
Confidence: 98.1%
Identity: 11%
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: 2 - 89
Aligned: 88
Modelled: 88
Confidence: 98.1%
Identity: 10%
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 3hvw chain A

3D model

Region: 6 - 91
Aligned: 86
Modelled: 86
Confidence: 97.9%
Identity: 6%
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

Phyre2
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c3pjwA_
2
c3gfzB_
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c3hvbB_
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c3hv9A_
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c3s83A_
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c3pfmA_
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c2w27A_
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c2r6oB_
9
d2basa1
10
c3kzpA_
11
c1w25B_
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c3ezuA_
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c3iclA_
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c3breA_
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c3mtkA_
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d1w25a3
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c3hvaA_
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c3i5aA_
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c3ignA_
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c3hvwA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3pjwA_
100.0 12 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 15 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 11 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 11 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_
100.0 17 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_
100.0 16 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 16 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 24 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans
9d2basa1
100.0 16 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_
100.0 13 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_
99.0 13 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
12c3ezuA_
98.6 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
13c3iclA_
98.4 17 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
14c3breA_
98.4 10 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
15c3mtkA_
98.3 26 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
16d1w25a3
98.2 11 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
17c3hvaA_
98.2 10 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
18c3i5aA_
98.1 11 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
19c3ignA_
98.1 10 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
20c3hvwA_
97.9 6 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
21c3i5bA_
not modelled 97.6 13 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
22c3i5cA_
not modelled 97.5 10 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
23c3qyyB_
not modelled 97.2 19 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
24d1mvoa_
not modelled 96.2 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
25c3khtA_
not modelled 96.1 11 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
26d1p6qa_
not modelled 95.6 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
27d1zesa1
not modelled 95.5 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
28d1w25a1
not modelled 95.5 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
29c2zayA_
not modelled 95.3 14 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
30d1krwa_
not modelled 94.7 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
31d1jbea_
not modelled 94.7 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
32c3q58A_
not modelled 94.7 18 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
33d1heya_
not modelled 94.5 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
34c3eulB_
not modelled 94.3 10 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
35c3gt7A_
not modelled 94.1 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
36c3gl9B_
not modelled 94.1 11 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
37c2jk1A_
not modelled 93.9 7 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
38d1dbwa_
not modelled 93.9 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
39c3hebB_
not modelled 93.9 13 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
40c2ayxA_
not modelled 93.6 14 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
41d1yioa2
not modelled 93.2 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
42d1kgsa2
not modelled 93.2 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
43c3nhzA_
not modelled 93.1 12 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
44d1ua7a2
not modelled 93.1 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
45c3crnA_
not modelled 93.0 10 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
46d1xhfa1
not modelled 92.8 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
47c2p0oA_
not modelled 92.8 15 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
48d2pl1a1
not modelled 92.8 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
49c2zwmA_
not modelled 92.6 9 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
50c2rjnA_
not modelled 92.6 12 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
51d1y0ea_
not modelled 92.6 11 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:NanE-like
52d1dz3a_
not modelled 92.6 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
53d2a9pa1
not modelled 92.5 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
54c2qr3A_
not modelled 92.5 14 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
55d1zh2a1
not modelled 92.3 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
56c3cu5B_
not modelled 92.3 11 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
57d2ayxa1
not modelled 92.2 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
58d1zgza1
not modelled 92.1 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
59d1qkka_
not modelled 92.1 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
60c3cnbC_
not modelled 92.1 16 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
61d1ny5a1
not modelled 91.9 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
62d1ys7a2
not modelled 91.9 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
63c3edeB_
not modelled 91.9 12 PDB header:hydrolase
Chain: B: PDB Molecule:cyclomaltodextrinase;
PDBTitle: structural base for cyclodextrin hydrolysis
64d1kkoa1
not modelled 91.5 10 Fold:TIM beta/alpha-barrel
Superfamily:Enolase C-terminal domain-like
Family:D-glucarate dehydratase-like
65d1k66a_
not modelled 91.1 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
66d2r25b1
not modelled 91.0 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
67c3i42A_
not modelled 90.9 9 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
68c2pz0B_
not modelled 90.9 14 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
69c1qhoA_
not modelled 90.2 18 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
70d1gjwa2
not modelled 90.1 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
71d1a53a_
not modelled 90.0 15 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
72c2c3zA_
not modelled 89.7 15 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
73d1k68a_
not modelled 89.6 7 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
74c3rqiA_
not modelled 89.4 12 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
75c3hv2B_
not modelled 89.3 13 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator/hd domain protein;
PDBTitle: crystal structure of signal receiver domain of hd domain-2 containing protein from pseudomonas fluorescens pf-5
76d1u0sy_
not modelled 89.2 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
77d1a04a2
not modelled 89.1 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
78c3t6kB_
not modelled 89.0 8 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator receiver;
PDBTitle: crystal structure of a hypothetical response regulator (caur_3799)2 from chloroflexus aurantiacus j-10-fl at 1.86 a resolution
79d1mb3a_
not modelled 89.0 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
80c3nhmA_
not modelled 89.0 13 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of a response regulator from myxococcus xanthus
81c3ucqA_
not modelled 88.9 10 PDB header:transferase
Chain: A: PDB Molecule:amylosucrase;
PDBTitle: crystal structure of amylosucrase from deinococcus geothermalis
82c2yxbA_
not modelled 88.8 8 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
83c1jdaA_
not modelled 88.6 8 PDB header:hydrolase
Chain: A: PDB Molecule:1,4-alpha maltotetrahydrolase;
PDBTitle: maltotetraose-forming exo-amylase
84c3b2nA_
not modelled 88.6 11 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
85c1gcyA_
not modelled 88.4 10 PDB header:hydrolase
Chain: A: PDB Molecule:glucan 1,4-alpha-maltotetrahydrolase;
PDBTitle: high resolution crystal structure of maltotetraose-forming2 exo-amylase
86c1bagA_
not modelled 88.3 15 PDB header:alpha-amylase
Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase;
PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose
87d1gcya2
not modelled 88.2 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
88c3dzdA_
not modelled 88.2 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of sigma54 activator ntrc4 in the inactive2 state
89c3cfyA_
not modelled 87.9 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
90d1h3ga3
not modelled 87.7 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
91d1tz9a_
not modelled 87.6 17 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:UxuA-like
92c2jrlA_
not modelled 87.5 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: solution structure of the beryllofluoride-activated ntrc4 receiver2 domain dimer
93c3grcD_
not modelled 86.9 6 PDB header:transferase
Chain: D: PDB Molecule:sensor protein, kinase;
PDBTitle: crystal structure of a sensor protein from polaromonas sp.2 js666
94d2guya2
not modelled 86.7 7 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
95d1g5aa2
not modelled 86.5 13 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
96d1xrsb1
not modelled 86.4 12 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
97d1i3ca_
not modelled 86.4 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
98c3t8yA_
not modelled 86.3 12 PDB header:hydrolase
Chain: A: PDB Molecule:chemotaxis response regulator protein-glutamate
PDBTitle: crystal structure of the response regulator domain of thermotoga2 maritima cheb
99c3bw2A_
not modelled 85.8 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-nitropropane dioxygenase;
PDBTitle: crystal structures and site-directed mutagenesis study of nitroalkane2 oxidase from streptomyces ansochromogenes
100c3gr7A_
not modelled 85.8 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dehydrogenase;
PDBTitle: structure of oye from geobacillus kaustophilus, hexagonal2 crystal form
101d1peya_
not modelled 85.6 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
102c1cygA_
not modelled 85.5 12 PDB header:glycosyltransferase
Chain: A: PDB Molecule:cyclodextrin glucanotransferase;
PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
103c3c3mA_
not modelled 85.4 10 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
104d1xi3a_
not modelled 85.4 14 Fold:TIM beta/alpha-barrel
Superfamily:Thiamin phosphate synthase
Family:Thiamin phosphate synthase
105c3igsB_
not modelled 85.4 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
106c3czkA_
not modelled 85.0 8 PDB header:hydrolase
Chain: A: PDB Molecule:sucrose hydrolase;
PDBTitle: crystal structure analysis of sucrose hydrolase(suh) e322q-2 sucrose complex
107c1jgiA_
not modelled 84.6 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
108c1jibA_
not modelled 84.5 19 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.
109c1tcmB_
not modelled 84.3 11 PDB header:glycosyltransferase
Chain: B: PDB Molecule:cyclodextrin glycosyltransferase;
PDBTitle: cyclodextrin glycosyltransferase w616a mutant from bacillus2 circulans strain 251
110d2aaaa2
not modelled 84.0 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
111c3bmwA_
not modelled 83.5 11 PDB header:transferase
Chain: A: PDB Molecule:cyclomaltodextrin glucanotransferase;
PDBTitle: cyclodextrin glycosyl transferase from thermoanerobacterium2 thermosulfurigenes em1 mutant s77p complexed with a maltoheptaose3 inhibitor
112d1rd5a_
not modelled 83.4 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
113c3bdkB_
not modelled 83.4 15 PDB header:lyase
Chain: B: PDB Molecule:d-mannonate dehydratase;
PDBTitle: crystal structure of streptococcus suis mannonate2 dehydratase complexed with substrate analogue
114c3ilhA_
not modelled 83.4 14 PDB header:transcription regulator
Chain: A: PDB Molecule:two component response regulator;
PDBTitle: crystal structure of two component response regulator from cytophaga2 hutchinsonii
115c2wcsA_
not modelled 83.3 17 PDB header:hydrolase
Chain: A: PDB Molecule:alpha amylase, catalytic region;
PDBTitle: crystal structure of debranching enzyme from nostoc2 punctiforme (npde)
116d1lwha2
not modelled 83.2 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
117c2j48A_
not modelled 83.1 8 PDB header:transferase
Chain: A: PDB Molecule:two-component sensor kinase;
PDBTitle: nmr structure of the pseudo-receiver domain of the cika2 protein.
118d1bf2a3
not modelled 82.9 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
119c3f6cB_
not modelled 82.8 11 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
120d1qhoa4
not modelled 82.8 18 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain

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
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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