Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP58006
DateTue Jul 30 13:03:56 BST 2013
Unique Job IDec23aefa4f8e1bc7
SequenceMRLAAASNEA ... Download FASTA

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:41.961 Y:52.108 Z:56.464
Model (left) based on template d2pfxa1
Top template information
Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
Confidence and coverage
Confidence: 99.9% Coverage: 36%
177 residues ( 36% of your sequence) have been modelled with 99.9% 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.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MRLAAASNEAYAASLAVSELLSCHQCGGDRGQDEELGIRIPRPLGHGPSRFIPEKEMLQV
Secondary structure 
SS confidence 
Disorder  ?????????
??
????
?
????????????????
????????
?
?
??????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  GSEDAQMHALFADSFAALGRLDNITLVMVFHPQYLESFLKTQHYLLQMDGPLPLHYRHYI
Secondary structure 
SS confidence 
Disorder  ??
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  GIMAAARHQCSYLVNLHVSDFLHVGGDPKWLNGLENAPQKLQNLGELNKVLAHRPWLITK
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  EHIEGLLKAEEHSWSLAELVHAVVLLTHYHSLASFTFGCGISPEIHCDGGHTFRPPSVSN
Secondary structure 
SS confidence 
Disorder 
?
??????????????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  YCICDITNGNHSVDEMQVNSAGNASVSDSFFEVEALMEKMRQLQECREEEEASQEEMASR
Secondary structure 
SS confidence 
Disorder  ?????
??????????????????????????
???????????????????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  FEMEKRESMFVFSSDDDEVTPARDVSRHFEDTSYGYKDFSRHGMHVPTFRVQDYCWEDHG
Secondary structure 
SS confidence 
Disorder  ?
???????????????????
???????
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  YSLVNRLYPDVGQLIDEKFHIAYNLTYNTMAMHKDVDTSMLRRAIWNYIHCMFGIRYDDY
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  DYGEINQLLDRSFKVYIKTVVCTPEKVTKRMYDSFWRQFKHSEKVHVNLLLIEARMQAEL
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........490..
Sequence  LYALRAITRYMT
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered ( 30%)
Alpha helix ( 55%)
Beta strand ( 3%)

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 2pfx chain A domain 1

3D model

Region: 46 - 230
Aligned: 177
Modelled: 177
Confidence: 99.9%
Identity: 15%
Fold: AhpD-like
Superfamily: AhpD-like
Family: Atu0492-like

Phyre2

PDB 3c1l chain B

3D model

Region: 58 - 224
Aligned: 164
Modelled: 167
Confidence: 99.9%
Identity: 19%
PDB header:oxidoreductase
Chain: B: PDB Molecule:putative antioxidant defense protein mlr4105;
PDBTitle: crystal structure of an antioxidant defense protein (mlr4105) from2 mesorhizobium loti maff303099 at 2.00 a resolution

Phyre2

PDB 2oyo chain A domain 1

3D model

Region: 49 - 224
Aligned: 168
Modelled: 168
Confidence: 99.8%
Identity: 17%
Fold: AhpD-like
Superfamily: AhpD-like
Family: Atu0492-like

Phyre2

PDB 2prr chain A domain 1

3D model

Region: 45 - 224
Aligned: 172
Modelled: 180
Confidence: 99.8%
Identity: 17%
Fold: AhpD-like
Superfamily: AhpD-like
Family: Atu0492-like

Phyre2

PDB 3lvy chain B

3D model

Region: 49 - 224
Aligned: 166
Modelled: 176
Confidence: 99.8%
Identity: 15%
PDB header:lyase
Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family;
PDBTitle: crystal structure of carboxymuconolactone decarboxylase2 family protein smu.961 from streptococcus mutans

Phyre2

PDB 2o4d chain A domain 1

3D model

Region: 85 - 224
Aligned: 135
Modelled: 140
Confidence: 99.2%
Identity: 17%
Fold: AhpD-like
Superfamily: AhpD-like
Family: Atu0492-like

Phyre2

PDB 2ouw chain A domain 1

3D model

Region: 58 - 224
Aligned: 119
Modelled: 122
Confidence: 99.0%
Identity: 17%
Fold: AhpD-like
Superfamily: AhpD-like
Family: TTHA0727-like

Phyre2

PDB 2gmy chain A domain 1

3D model

Region: 85 - 226
Aligned: 136
Modelled: 142
Confidence: 98.9%
Identity: 18%
Fold: AhpD-like
Superfamily: AhpD-like
Family: Atu0492-like

Phyre2

PDB 2qeu chain A

3D model

Region: 62 - 149
Aligned: 88
Modelled: 88
Confidence: 97.8%
Identity: 16%
PDB header:lyase
Chain: A: PDB Molecule:putative carboxymuconolactone decarboxylase;
PDBTitle: crystal structure of putative carboxymuconolactone decarboxylase2 (yp_555818.1) from burkholderia xenovorans lb400 at 1.65 a resolution

Phyre2

PDB 2cwq chain A domain 1

3D model

Region: 65 - 149
Aligned: 83
Modelled: 85
Confidence: 97.6%
Identity: 14%
Fold: AhpD-like
Superfamily: AhpD-like
Family: TTHA0727-like

Phyre2

PDB 3bey chain C

3D model

Region: 86 - 149
Aligned: 63
Modelled: 64
Confidence: 97.0%
Identity: 17%
PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:conserved protein o27018;
PDBTitle: crystal structure of the protein o27018 from methanobacterium2 thermoautotrophicum. northeast structural genomics consortium target3 tt217

Phyre2

PDB 1p8c chain D

3D model

Region: 80 - 149
Aligned: 69
Modelled: 70
Confidence: 97.0%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of tm1620 (apc4843) from thermotoga2 maritima

Phyre2

PDB 3d7i chain B

3D model

Region: 83 - 146
Aligned: 63
Modelled: 62
Confidence: 96.4%
Identity: 13%
PDB header:lyase
Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family protein;
PDBTitle: crystal structure of carboxymuconolactone decarboxylase family protein2 possibly involved in oxygen detoxification (1591455) from3 methanococcus jannaschii at 1.75 a resolution

Phyre2

PDB 1vke chain A

3D model

Region: 91 - 149
Aligned: 58
Modelled: 59
Confidence: 96.1%
Identity: 14%
Fold: AhpD-like
Superfamily: AhpD-like
Family: CMD-like

Phyre2

PDB 1vke chain B

3D model

Region: 96 - 149
Aligned: 53
Modelled: 54
Confidence: 95.7%
Identity: 15%
Fold: AhpD-like
Superfamily: AhpD-like
Family: CMD-like

Phyre2

PDB 2q0t chain A domain 1

3D model

Region: 56 - 149
Aligned: 91
Modelled: 94
Confidence: 94.3%
Identity: 15%
Fold: AhpD-like
Superfamily: AhpD-like
Family: AhpD

Phyre2

PDB 4g9q chain A

3D model

Region: 79 - 225
Aligned: 143
Modelled: 147
Confidence: 81.5%
Identity: 19%
PDB header:lyase
Chain: A: PDB Molecule:4-carboxymuconolactone decarboxylase;
PDBTitle: crystal structure of a 4-carboxymuconolactone decarboxylase

Phyre2

PDB 2r8r chain B

3D model

Region: 124 - 195
Aligned: 72
Modelled: 72
Confidence: 58.0%
Identity: 25%
PDB header:transferase
Chain: B: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the n-terminal region (19..243) of sensor protein2 kdpd from pseudomonas syringae pv. tomato str. dc3000

Phyre2

PDB 2af7 chain A domain 1

3D model

Region: 90 - 172
Aligned: 83
Modelled: 83
Confidence: 56.9%
Identity: 14%
Fold: AhpD-like
Superfamily: AhpD-like
Family: CMD-like

Phyre2

PDB 1knc chain A

3D model

Region: 83 - 218
Aligned: 131
Modelled: 136
Confidence: 44.9%
Identity: 14%
Fold: AhpD-like
Superfamily: AhpD-like
Family: AhpD

Phyre2
1
d2pfxa1
2
c3c1lB_
3
d2oyoa1
4
d2prra1
5
c3lvyB_
6
d2o4da1
7
d2ouwa1
8
d2gmya1
9
c2qeuA_
10
d2cwqa1
11
c3beyC_
12
c1p8cD_
13
c3d7iB_
14
d1vkea_
15
d1vkeb_
16
d2q0ta1
17
c4g9qA_
18
c2r8rB_
19
d2af7a1
20
d1knca_
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d2pfxa1
99.9 15 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
2c3c1lB_
99.9 19 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative antioxidant defense protein mlr4105;
PDBTitle: crystal structure of an antioxidant defense protein (mlr4105) from2 mesorhizobium loti maff303099 at 2.00 a resolution
3d2oyoa1
99.8 17 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
4d2prra1
99.8 17 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
5c3lvyB_
99.8 15 PDB header:lyase
Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family;
PDBTitle: crystal structure of carboxymuconolactone decarboxylase2 family protein smu.961 from streptococcus mutans
6d2o4da1
99.2 17 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
7d2ouwa1
99.0 17 Fold:AhpD-like
Superfamily:AhpD-like
Family:TTHA0727-like
8d2gmya1
98.9 18 Fold:AhpD-like
Superfamily:AhpD-like
Family:Atu0492-like
9c2qeuA_
97.8 16 PDB header:lyase
Chain: A: PDB Molecule:putative carboxymuconolactone decarboxylase;
PDBTitle: crystal structure of putative carboxymuconolactone decarboxylase2 (yp_555818.1) from burkholderia xenovorans lb400 at 1.65 a resolution
10d2cwqa1
97.6 14 Fold:AhpD-like
Superfamily:AhpD-like
Family:TTHA0727-like
11c3beyC_
97.0 17 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:conserved protein o27018;
PDBTitle: crystal structure of the protein o27018 from methanobacterium2 thermoautotrophicum. northeast structural genomics consortium target3 tt217
12c1p8cD_
97.0 14 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of tm1620 (apc4843) from thermotoga2 maritima
13c3d7iB_
96.4 13 PDB header:lyase
Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family protein;
PDBTitle: crystal structure of carboxymuconolactone decarboxylase family protein2 possibly involved in oxygen detoxification (1591455) from3 methanococcus jannaschii at 1.75 a resolution
14d1vkea_
96.1 14 Fold:AhpD-like
Superfamily:AhpD-like
Family:CMD-like
15d1vkeb_
95.7 15 Fold:AhpD-like
Superfamily:AhpD-like
Family:CMD-like
16d2q0ta1
94.3 15 Fold:AhpD-like
Superfamily:AhpD-like
Family:AhpD
17c4g9qA_
81.5 19 PDB header:lyase
Chain: A: PDB Molecule:4-carboxymuconolactone decarboxylase;
PDBTitle: crystal structure of a 4-carboxymuconolactone decarboxylase
18c2r8rB_
58.0 25 PDB header:transferase
Chain: B: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the n-terminal region (19..243) of sensor protein2 kdpd from pseudomonas syringae pv. tomato str. dc3000
19d2af7a1
56.9 14 Fold:AhpD-like
Superfamily:AhpD-like
Family:CMD-like
20d1knca_
44.9 14 Fold:AhpD-like
Superfamily:AhpD-like
Family:AhpD
21c1ckxA_
not modelled 37.4 40 PDB header:metal transport
Chain: A: PDB Molecule:cystic fibrosis transmembrane conductance
PDBTitle: cystic fibrosis transmembrane conductance regulator:2 solution structures of peptides based on the phe508 region,3 the most common site of disease-causing delta-f508 mutation
22c2dgxA_
not modelled 27.2 17 PDB header:rna binding protein
Chain: A: PDB Molecule:kiaa0430 protein;
PDBTitle: solution structure of the rna recognition motif in kiaa04302 protein
23c3ntsB_
not modelled 20.3 39 PDB header:transferase
Chain: B: PDB Molecule:vsdc;
PDBTitle: catalytic domain of vsdc from aeromonas hydrophila
24c1ckwA_
not modelled 18.0 31 PDB header:metal transport
Chain: A: PDB Molecule:protein (cystic fibrosis transmembrane
PDBTitle: cystic fibrosis transmembrane conductance regulator:2 solution structures of peptides based on the phe508 region,3 the most common site of disease-causing delta-f508 mutation
25c2ly8A_
not modelled 16.2 19 PDB header:chaperone
Chain: A: PDB Molecule:budding yeast chaperone scm3;
PDBTitle: the budding yeast chaperone scm3 recognizes the partially unfolded2 dimer of the centromere-specific cse4/h4 histone variant
26c3c18B_
not modelled 16.2 13 PDB header:transferase
Chain: B: PDB Molecule:nucleotidyltransferase-like protein;
PDBTitle: crystal structure of nucleotidyltransferase-like protein2 (zp_00538802.1) from exiguobacterium sibiricum 255-15 at 1.90 a3 resolution
27c2d9gA_
not modelled 15.7 27 PDB header:transcription
Chain: A: PDB Molecule:yy1-associated factor 2;
PDBTitle: solution structure of the zf-ranbp domain of yy1-associated2 factor 2
28d1id3b_
not modelled 14.3 19 Fold:Histone-fold
Superfamily:Histone-fold
Family:Nucleosome core histones
29d1kx5b_
not modelled 14.2 17 Fold:Histone-fold
Superfamily:Histone-fold
Family:Nucleosome core histones
30d2k3ka1
not modelled 13.7 13 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
31c2l5aA_
not modelled 12.7 18 PDB header:nuclear protein
Chain: A: PDB Molecule:histone h3-like centromeric protein cse4, protein scm3,
PDBTitle: structural basis for recognition of centromere specific histone h32 variant by nonhistone scm3
32c3pgwP_
not modelled 12.6 15 PDB header:splicing/dna/rna
Chain: P: PDB Molecule:u1-a;
PDBTitle: crystal structure of human u1 snrnp
33c2a3jA_
not modelled 11.9 17 PDB header:rna binding protein
Chain: A: PDB Molecule:u1 small nuclear ribonucleoprotein a;
PDBTitle: structure of urndesign, a complete computational redesign2 of human u1a protein
34c3btpA_
not modelled 11.9 35 PDB header:dna binding protein, chaperone
Chain: A: PDB Molecule:single-strand dna-binding protein;
PDBTitle: crystal structure of agrobacterium tumefaciens vire2 in complex with2 its chaperone vire1: a novel fold and implications for dna binding
35d1hw8c2
not modelled 10.8 24 Fold:Substrate-binding domain of HMG-CoA reductase
Superfamily:Substrate-binding domain of HMG-CoA reductase
Family:Substrate-binding domain of HMG-CoA reductase
36c2pehA_
not modelled 10.6 15 PDB header:protein binding
Chain: A: PDB Molecule:splicing factor 45;
PDBTitle: crystal structure of the uhm domain of human spf45 in complex with2 sf3b155-ulm5
37d1zpya1
not modelled 10.3 14 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:half-ferritin
38d1rg6a_
not modelled 9.7 22 Fold:SAM domain-like
Superfamily:SAM/Pointed domain
Family:SAM (sterile alpha motif) domain
39d1zk8a2
not modelled 9.0 12 Fold:Tetracyclin repressor-like, C-terminal domain
Superfamily:Tetracyclin repressor-like, C-terminal domain
Family:Tetracyclin repressor-like, C-terminal domain
40c3bjxB_
not modelled 8.9 16 PDB header:hydrolase
Chain: B: PDB Molecule:halocarboxylic acid dehalogenase dehi;
PDBTitle: structure of a group i haloacid dehalogenase from2 pseudomonas putida strain pp3
41d1auda_
not modelled 8.8 14 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
42c1ponB_
not modelled 8.5 38 PDB header:calcium-binding protein
Chain: B: PDB Molecule:troponin c;
PDBTitle: site iii-site iv troponin c heterodimer, nmr
43d1rz4a1
not modelled 8.3 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
44c1zzaA_
not modelled 8.1 26 PDB header:membrane protein
Chain: A: PDB Molecule:stannin;
PDBTitle: solution nmr structure of the membrane protein stannin
45d1hrti_
not modelled 8.0 35 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Leech antihemostatic proteins
Family:Hirudin-like
46c3thfA_
not modelled 7.7 27 PDB header:actin-binding protein/protein binding
Chain: A: PDB Molecule:protein shroom;
PDBTitle: crystal structure of the sd2 domain from drosophila shroom
47d2huec1
not modelled 7.4 17 Fold:Histone-fold
Superfamily:Histone-fold
Family:Nucleosome core histones
48c3kx6C_
not modelled 7.3 35 PDB header:lyase
Chain: C: PDB Molecule:fructose-bisphosphate aldolase;
PDBTitle: crystal structure of fructose-1,6-bisphosphate aldolase from babesia2 bovis at 2.1a resolution
49d4htci_
not modelled 7.1 35 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Leech antihemostatic proteins
Family:Hirudin-like
50c3k1tA_
not modelled 7.0 27 PDB header:ligase
Chain: A: PDB Molecule:glutamate--cysteine ligase gsha;
PDBTitle: crystal structure of putative gamma-glutamylcysteine synthetase2 (yp_546622.1) from methylobacillus flagellatus kt at 1.90 a3 resolution
51d1wj7a1
not modelled 6.9 32 Fold:RuvA C-terminal domain-like
Superfamily:UBA-like
Family:UBA domain
52d1nu4a_
not modelled 6.5 13 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
53c3odnA_
not modelled 6.5 15 PDB header:membrane protein
Chain: A: PDB Molecule:dally-like protein;
PDBTitle: the crystal structure of drosophila dally-like protein core domain
54c1bev4_
not modelled 6.4 29 PDB header:virus
Chain: 4: PDB Molecule:bovine enterovirus coat proteins vp1 to vp4;
PDBTitle: bovine enterovirus vg-5-27
55c2eapA_
not modelled 6.4 18 PDB header:signaling protein
Chain: A: PDB Molecule:lymphocyte cytosolic protein 2;
PDBTitle: solution structure of the n-terminal sam-domain of human2 lymphocyte cytosolic protein 2
56c2qb0D_
not modelled 6.4 23 PDB header:hydrolase regulator
Chain: D: PDB Molecule:telsam domain - lysozyme chimera;
PDBTitle: structure of the 2tel crystallization module fused to t4 lysozyme with2 an ala-gly-pro linker.
57d1jmxa2
not modelled 6.2 31 Fold:Cytochrome c
Superfamily:Cytochrome c
Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
58c3ol4B_
not modelled 6.2 46 PDB header:unknown function
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c
59d1jmsa4
not modelled 6.2 27 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:DNA polymerase beta-like
60c1rue4_
not modelled 6.0 40 PDB header:virus
Chain: 4: PDB Molecule:rhinovirus 14;
PDBTitle: rhinovirus 14 site directed mutant n1219a complexed with2 antiviral compound win 52035
61c3ajfA_
not modelled 5.8 25 PDB header:viral protein
Chain: A: PDB Molecule:non-structural protein 3;
PDBTitle: structural insigths into dsrna binding and rna silencing suppression2 by ns3 protein of rice hoja blanca tenuivirus
62d1iooa_
not modelled 5.7 17 Fold:Ribonuclease Rh-like
Superfamily:Ribonuclease Rh-like
Family:Ribonuclease Rh-like
63d1sxja1
not modelled 5.7 31 Fold:post-AAA+ oligomerization domain-like
Superfamily:post-AAA+ oligomerization domain-like
Family:DNA polymerase III clamp loader subunits, C-terminal domain
64d1ussa_
not modelled 5.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Linker histone H1/H5
65d2vana2
not modelled 5.4 9 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:DNA polymerase beta-like
66c2krcA_
not modelled 5.2 25 PDB header:transcription
Chain: A: PDB Molecule:dna-directed rna polymerase subunit delta;
PDBTitle: solution structure of the n-terminal domain of bacillus2 subtilis delta subunit of rna polymerase
67c3i3nA_
not modelled 5.1 19 PDB header:protein binding
Chain: A: PDB Molecule:kelch-like protein 11;
PDBTitle: crystal structure of the btb-back domains of human klhl11
68c1hwjB_
not modelled 5.1 24 PDB header:oxidoreductase
Chain: B: PDB Molecule:hmg-coa reductase;
PDBTitle: complex of the catalytic portion of human hmg-coa reductase2 with cerivastatin

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