Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionA1L3C1
DateWed Jul 10 14:09:30 BST 2013
Unique Job ID1b9611dfa23384b1
SequenceMKGGRDLKAA ... Download FASTA

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:27.479 Y:23.102 Z:25.694
Model (left) based on template c1eb0A_
Top template information
PDB header:chaperone
Chain: A: PDB Molecule:urease accessory protein uree;
PDBTitle: crystal structure of bacillus pasteurii uree at 1.85 a,2 phased by siras. type i crystal form.
Confidence and coverage
Confidence: 52.7% Coverage: 17%
35 residues ( 17% of your sequence) have been modelled with 52.7% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKGGRDLKAARGGADRPLAPAYAPCRPGRLQRHLLSGEFDQLRDFPIFESNFVQVTRFGE
Secondary structure 
SS confidence 
Disorder  ?????????????????????????
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  VANKVTMGVAASSPALELPDLLLLAGPDKENGHLQLLGLFPLQFVQLFVHDESRQQLKVK
Secondary structure 
SS confidence 
Disorder 
???
???
?
?????
??
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  FRTGRAFYLQLRSPPETLDCEFGRWVRLLYRLRFHSPTCAVPFTHEDTAPEEEEEEEEEE
Secondary structure 
SS confidence 
Disorder 
?????
???????????????????
Disorder confidence 
 
   .........190.........200.........210..
Sequence  EEEEVKEGQLQPPEFQATEARLDPQVSELWGL
Secondary structure 
SS confidence 
Disorder  ????????????????????????????????
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered ( 46%)
Alpha helix ( 21%)
Beta strand ( 28%)

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 1eb0 chain A

3D model

Region: 102 - 138
Aligned: 35
Modelled: 37
Confidence: 52.7%
Identity: 11%
PDB header:chaperone
Chain: A: PDB Molecule:urease accessory protein uree;
PDBTitle: crystal structure of bacillus pasteurii uree at 1.85 a,2 phased by siras. type i crystal form.

Phyre2

PDB 2kk8 chain A

3D model

Region: 110 - 133
Aligned: 24
Modelled: 24
Confidence: 46.8%
Identity: 25%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein at4g05270;
PDBTitle: nmr solution structure of a putative uncharacterized protein2 obtained from arabidopsis thaliana: northeast structural3 genomics consortium target ar3449a

Phyre2

PDB 1gmu chain B

3D model

Region: 103 - 138
Aligned: 34
Modelled: 36
Confidence: 45.8%
Identity: 29%
PDB header:metallochaperone
Chain: B: PDB Molecule:uree;
PDBTitle: structure of uree

Phyre2

PDB 1ear chain A domain 1

3D model

Region: 102 - 138
Aligned: 35
Modelled: 37
Confidence: 45.7%
Identity: 11%
Fold: Urease metallochaperone UreE, N-terminal domain
Superfamily: Urease metallochaperone UreE, N-terminal domain
Family: Urease metallochaperone UreE, N-terminal domain

Phyre2

PDB 1v61 chain A

3D model

Region: 79 - 160
Aligned: 77
Modelled: 82
Confidence: 40.0%
Identity: 14%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Pleckstrin-homology domain (PH domain)

Phyre2

PDB 1omw chain A domain 2

3D model

Region: 79 - 149
Aligned: 63
Modelled: 66
Confidence: 40.0%
Identity: 29%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Pleckstrin-homology domain (PH domain)

Phyre2

PDB 1gmu chain A domain 1

3D model

Region: 103 - 131
Aligned: 29
Modelled: 29
Confidence: 38.7%
Identity: 28%
Fold: Urease metallochaperone UreE, N-terminal domain
Superfamily: Urease metallochaperone UreE, N-terminal domain
Family: Urease metallochaperone UreE, N-terminal domain

Phyre2

PDB 3q3f chain A

3D model

Region: 111 - 141
Aligned: 30
Modelled: 31
Confidence: 36.5%
Identity: 30%
PDB header:hydrolase, protein binding
Chain: A: PDB Molecule:ribonuclease/ubiquitin chimeric protein;
PDBTitle: engineering domain-swapped binding interfaces by mutually exclusive2 folding: insertion of ubiquitin into position 103 of barnase

Phyre2

PDB 3ny0 chain D

3D model

Region: 100 - 142
Aligned: 43
Modelled: 43
Confidence: 31.3%
Identity: 23%
PDB header:metal binding protein
Chain: D: PDB Molecule:urease accessory protein uree;
PDBTitle: crystal structure of uree from helicobacter pylori (ni2+ bound form)

Phyre2

PDB 2kdi chain A

3D model

Region: 110 - 133
Aligned: 24
Modelled: 24
Confidence: 28.1%
Identity: 29%
PDB header:signaling protein
Chain: A: PDB Molecule:ubiquitin, vacuolar protein sorting-associated
PDBTitle: solution structure of a ubiquitin/uim fusion protein

Phyre2

PDB 2kzk chain A

3D model

Region: 38 - 78
Aligned: 38
Modelled: 41
Confidence: 25.5%
Identity: 29%
PDB header:protein transport
Chain: A: PDB Molecule:uncharacterized protein yol083w;
PDBTitle: solution structure of alpha-mannosidase binding domain of atg34

Phyre2

PDB 2ltm chain A

3D model

Region: 19 - 64
Aligned: 43
Modelled: 46
Confidence: 25.1%
Identity: 21%
PDB header:electron transport
Chain: A: PDB Molecule:nfu1 iron-sulfur cluster scaffold homolog, mitochondrial;
PDBTitle: solution nmr structure of nfu1 iron-sulfur cluster scaffold homolog2 from homo sapiens, northeast structural genomics consortium (nesg)3 target hr2876b

Phyre2

PDB 3a8q chain B

3D model

Region: 110 - 150
Aligned: 36
Modelled: 36
Confidence: 24.1%
Identity: 17%
PDB header:signaling protein
Chain: B: PDB Molecule:t-lymphoma invasion and metastasis-inducing
PDBTitle: low-resolution crystal structure of the tiam2 phccex domain

Phyre2

PDB 2kzb chain A

3D model

Region: 38 - 78
Aligned: 38
Modelled: 41
Confidence: 22.3%
Identity: 26%
PDB header:protein transport
Chain: A: PDB Molecule:autophagy-related protein 19;
PDBTitle: solution structure of alpha-mannosidase binding domain of atg19

Phyre2

PDB 1ttn chain A domain 1

3D model

Region: 113 - 135
Aligned: 23
Modelled: 23
Confidence: 22.0%
Identity: 30%
Fold: beta-Grasp (ubiquitin-like)
Superfamily: Ubiquitin-like
Family: Ubiquitin-related

Phyre2

PDB 1ttn chain A

3D model

Region: 113 - 135
Aligned: 23
Modelled: 23
Confidence: 22.0%
Identity: 30%
PDB header:signaling protein
Chain: A: PDB Molecule:dendritic cell-derived ubiquitin-like protein;
PDBTitle: solution structure of the ubiquitin-like domain of human dc-2 ubp from dendritic cells

Phyre2

PDB 2fwk chain B

3D model

Region: 99 - 131
Aligned: 29
Modelled: 33
Confidence: 16.1%
Identity: 17%
PDB header:dna binding protein
Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5;
PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5

Phyre2

PDB 2q22 chain A domain 1

3D model

Region: 63 - 73
Aligned: 11
Modelled: 11
Confidence: 15.7%
Identity: 18%
Fold: Ava3019-like
Superfamily: Ava3019-like
Family: Ava3019-like

Phyre2

PDB 2kcj chain A

3D model

Region: 99 - 161
Aligned: 58
Modelled: 58
Confidence: 12.5%
Identity: 14%
PDB header:membrane protein
Chain: A: PDB Molecule:pleckstrin homology domain-containing family a
PDBTitle: solution structure of fapp1 ph domain

Phyre2

PDB 1w1h chain A

3D model

Region: 95 - 150
Aligned: 48
Modelled: 56
Confidence: 12.2%
Identity: 21%
Fold: PH domain-like barrel
Superfamily: PH domain-like
Family: Pleckstrin-homology domain (PH domain)

Phyre2
1
c1eb0A_
2
c2kk8A_
3
c1gmuB_
4
d1eara1
5
d1v61a_
6
d1omwa2
7
d1gmua1
8
c3q3fA_
9
c3ny0D_
10
c2kdiA_
11
c2kzkA_
12
c2ltmA_
13
c3a8qB_
14
c2kzbA_
15
d1ttna1
16
c1ttnA_
17
c2fwkB_
18
d2q22a1
19
c2kcjA_
20
d1w1ha_
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1eb0A_
52.7 11 PDB header:chaperone
Chain: A: PDB Molecule:urease accessory protein uree;
PDBTitle: crystal structure of bacillus pasteurii uree at 1.85 a,2 phased by siras. type i crystal form.
2c2kk8A_
46.8 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein at4g05270;
PDBTitle: nmr solution structure of a putative uncharacterized protein2 obtained from arabidopsis thaliana: northeast structural3 genomics consortium target ar3449a
3c1gmuB_
45.8 29 PDB header:metallochaperone
Chain: B: PDB Molecule:uree;
PDBTitle: structure of uree
4d1eara1
45.7 11 Fold:Urease metallochaperone UreE, N-terminal domain
Superfamily:Urease metallochaperone UreE, N-terminal domain
Family:Urease metallochaperone UreE, N-terminal domain
5d1v61a_
40.0 14 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Pleckstrin-homology domain (PH domain)
6d1omwa2
40.0 29 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Pleckstrin-homology domain (PH domain)
7d1gmua1
38.7 28 Fold:Urease metallochaperone UreE, N-terminal domain
Superfamily:Urease metallochaperone UreE, N-terminal domain
Family:Urease metallochaperone UreE, N-terminal domain
8c3q3fA_
36.5 30 PDB header:hydrolase, protein binding
Chain: A: PDB Molecule:ribonuclease/ubiquitin chimeric protein;
PDBTitle: engineering domain-swapped binding interfaces by mutually exclusive2 folding: insertion of ubiquitin into position 103 of barnase
9c3ny0D_
31.3 23 PDB header:metal binding protein
Chain: D: PDB Molecule:urease accessory protein uree;
PDBTitle: crystal structure of uree from helicobacter pylori (ni2+ bound form)
10c2kdiA_
28.1 29 PDB header:signaling protein
Chain: A: PDB Molecule:ubiquitin, vacuolar protein sorting-associated
PDBTitle: solution structure of a ubiquitin/uim fusion protein
11c2kzkA_
25.5 29 PDB header:protein transport
Chain: A: PDB Molecule:uncharacterized protein yol083w;
PDBTitle: solution structure of alpha-mannosidase binding domain of atg34
12c2ltmA_
25.1 21 PDB header:electron transport
Chain: A: PDB Molecule:nfu1 iron-sulfur cluster scaffold homolog, mitochondrial;
PDBTitle: solution nmr structure of nfu1 iron-sulfur cluster scaffold homolog2 from homo sapiens, northeast structural genomics consortium (nesg)3 target hr2876b
13c3a8qB_
24.1 17 PDB header:signaling protein
Chain: B: PDB Molecule:t-lymphoma invasion and metastasis-inducing
PDBTitle: low-resolution crystal structure of the tiam2 phccex domain
14c2kzbA_
22.3 26 PDB header:protein transport
Chain: A: PDB Molecule:autophagy-related protein 19;
PDBTitle: solution structure of alpha-mannosidase binding domain of atg19
15d1ttna1
22.0 30 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
16c1ttnA_
22.0 30 PDB header:signaling protein
Chain: A: PDB Molecule:dendritic cell-derived ubiquitin-like protein;
PDBTitle: solution structure of the ubiquitin-like domain of human dc-2 ubp from dendritic cells
17c2fwkB_
16.1 17 PDB header:dna binding protein
Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5;
PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5
18d2q22a1
15.7 18 Fold:Ava3019-like
Superfamily:Ava3019-like
Family:Ava3019-like
19c2kcjA_
12.5 14 PDB header:membrane protein
Chain: A: PDB Molecule:pleckstrin homology domain-containing family a
PDBTitle: solution structure of fapp1 ph domain
20d1w1ha_
12.2 21 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Pleckstrin-homology domain (PH domain)
21d2fwka1
not modelled 11.9 16 Fold:Sm-like fold
Superfamily:Sm-like ribonucleoproteins
Family:Sm motif of small nuclear ribonucleoproteins, SNRNP
22c3swnA_
not modelled 11.7 24 PDB header:rna binding protein
Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5;
PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings
23c2d9xA_
not modelled 11.4 23 PDB header:lipid transport
Chain: A: PDB Molecule:oxysterol binding protein-related protein 11;
PDBTitle: solution structure of the ph domain of oxysterol binding2 protein-related protein 11 from human
24c3a8nA_
not modelled 10.9 22 PDB header:signaling protein
Chain: A: PDB Molecule:t-lymphoma invasion and metastasis-inducing
PDBTitle: crystal structure of the tiam1 phccex domain
25d2ffma1
not modelled 9.4 10 Fold:Hypothetical protein SAV1430
Superfamily:Hypothetical protein SAV1430
Family:Hypothetical protein SAV1430
26d2h7aa1
not modelled 9.4 64 Fold:YcgL-like
Superfamily:YcgL-like
Family:YcgL-like
27c2auwB_
not modelled 9.1 12 PDB header:unknown function
Chain: B: PDB Molecule:hypothetical protein ne0471;
PDBTitle: crystal structure of putative dna binding protein ne0471 from2 nitrosomonas europaea atcc 19718
28d1wiaa_
not modelled 9.0 14 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
29d1b33n_
not modelled 8.5 36 Fold:Allophycocyanin linker chain (domain)
Superfamily:Allophycocyanin linker chain (domain)
Family:Allophycocyanin linker chain (domain)
30d1zaka2
not modelled 8.1 25 Fold:Rubredoxin-like
Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain
Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
31d1oqya4
not modelled 8.0 21 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
32c1cq0A_
not modelled 7.3 75 PDB header:de novo protein
Chain: A: PDB Molecule:protein (new hypothalamic neuropeptide/orexin-
PDBTitle: solution structure of a human hypocretin-2/orexin-2 b'solution structure of a human hypocretin-2/orexin-b '
33d1baka_
not modelled 7.0 27 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Pleckstrin-homology domain (PH domain)
34c2ojrA_
not modelled 6.7 26 PDB header:protein binding
Chain: A: PDB Molecule:ubiquitin;
PDBTitle: structure of ubiquitin solved by sad using the lanthanide-2 binding tag
35c3qwmA_
not modelled 6.6 11 PDB header:signaling protein
Chain: A: PDB Molecule:iq motif and sec7 domain-containing protein 1;
PDBTitle: crystal structure of gep100, the plextrin homology domain of iq motif2 and sec7 domain-containing protein 1 isoform a
36c2z4dA_
not modelled 6.5 50 PDB header:nuclear protein
Chain: A: PDB Molecule:26s proteasome regulatory subunit rpn13;
PDBTitle: nmr structures of yeast proteasome component rpn13
37d1droa_
not modelled 6.4 34 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:Pleckstrin-homology domain (PH domain)
38c2o4wA_
not modelled 6.1 29 PDB header:hydrolase
Chain: A: PDB Molecule:lysozyme;
PDBTitle: t4 lysozyme circular permutant
39d1d3ba_
not modelled 5.9 20 Fold:Sm-like fold
Superfamily:Sm-like ribonucleoproteins
Family:Sm motif of small nuclear ribonucleoproteins, SNRNP
40c2p0fA_
not modelled 5.8 34 PDB header:ligand binding protein
Chain: A: PDB Molecule:rho gtpase-activating protein 9;
PDBTitle: arhgap9 ph domain in complex with ins(1,3,5)p3
41c2kzrA_
not modelled 5.7 21 PDB header:hydrolase
Chain: A: PDB Molecule:ubiquitin thioesterase otu1;
PDBTitle: solution nmr structure of ubiquitin thioesterase otu1 (ec 3.1.2.-)2 from mus musculus, northeast structural genomics consortium target3 mmt2a
42d1o6wa1
not modelled 5.6 33 Fold:WW domain-like
Superfamily:WW domain
Family:WW domain
43d1ogwa_
not modelled 5.5 32 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
44d1iyfa_
not modelled 5.4 15 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Ubiquitin-like
Family:Ubiquitin-related
45c1z2mA_
not modelled 5.3 23 PDB header:signaling protein
Chain: A: PDB Molecule:interferon, alpha-inducible protein (clone ifi-
PDBTitle: crystal structure of isg15, the interferon-induced2 ubiquitin cross reactive protein

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