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I-TASSER results for job id Rv3780

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.10 4 3ag4P CDL Rep, Mult 49,52,56,60,131,134,135
20.07 3 3zqeB DXC Rep, Mult 55,62,78,85
30.05 2 2einC CDL Rep, Mult 49,53,56
40.05 2 4ryoA MPG Rep, Mult 57,119,126
50.02 1 3j000 PEV Rep, Mult 101,103,107
60.02 1 1b0nA ZN Rep, Mult 52,110
70.02 1 3n3uA ZN Rep, Mult 90,99
80.02 1 3k2sB POV Rep, Mult 86,89,90,93
90.02 1 3o01B DXC Rep, Mult 57,61,74,77,81
100.02 1 3o02B JN3 Rep, Mult 126,129,130,133
110.02 1 2bhwA CLA Rep, Mult 68,70
120.02 1 2a68F MG Rep, Mult 60,64
130.02 1 3asnP CDL Rep, Mult 49,52,53,134

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0601lgfA0.4315.060.0310.6911.14.-.-NA
20.0601occA0.4365.620.0310.7581.9.3.182
30.0601n6bA0.3904.990.0310.6011.14.14.1NA
40.0601pfuA0.3904.460.0500.6076.1.1.10NA
50.0601pg0A0.4165.230.0500.7146.1.1.10NA
60.0601z11A0.4694.770.0740.7301.14.14.142,142
70.0602w0aA0.3565.190.0470.5961.14.13.70NA
80.0602ohyB0.3984.400.0280.6185.4.3.6NA
90.0601q5eA0.4375.050.0900.6911.14.-.-NA
100.0601w0eA0.3585.340.0590.5841.14.13.67,1.14.14.1NA
110.0601z0hB0.2896.690.0430.6353.4.24.69NA
120.0601q3qA0.4394.980.0620.7303.6.4.9NA
130.0602nztA0.4224.670.1180.6292.7.1.1NA
140.0601ygeA0.4344.770.0800.6911.13.11.12NA
150.0601clqA0.4334.870.0460.6912.7.7.7128,130
160.0601no3A0.4415.010.0720.7191.13.11.12NA
170.0602r25A0.4343.940.0540.6072.7.13.360,93
180.0602iukA0.4374.780.0860.6971.13.11.12NA
190.0601qleC0.5083.420.0810.6911.9.3.1105

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.580.6140.630.990.625ietA GO:0000502 GO:0005618 GO:0005886 GO:0022624 GO:0051260 GO:0061136 GO:0070628 GO:1901800
10.210.4212.780.590.515ieuB GO:0000502 GO:0005618 GO:0005886 GO:0022624 GO:0051260 GO:0061136 GO:0070628 GO:1901800
20.070.4394.170.100.634onsC GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
30.070.5263.820.080.721st6A GO:0001725 GO:0002009 GO:0002162 GO:0003779 GO:0005198 GO:0005623 GO:0005737 GO:0005743 GO:0005856 GO:0005886 GO:0005903 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005916 GO:0005925 GO:0005927 GO:0007155 GO:0008013 GO:0015629 GO:0016020 GO:0017166 GO:0030018 GO:0030032 GO:0030054 GO:0030334 GO:0030486 GO:0031594 GO:0031625 GO:0034333 GO:0034394 GO:0042383 GO:0042803 GO:0043034 GO:0043234 GO:0043297 GO:0045121 GO:0045294 GO:0045296 GO:0048675 GO:0051015 GO:0051371 GO:0051393 GO:0070062 GO:0070527 GO:0090136 GO:0090636 GO:0090637 GO:0097110 GO:0098723 GO:1903561 GO:1990357
40.070.5064.370.040.763bo0A GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
50.070.5083.960.060.724p9tA GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
60.070.4704.910.050.782yxrA GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
70.070.4944.710.060.773jc21 GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
80.070.5114.560.050.782wwbA GO:0005783 GO:0005789 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0030176 GO:0045047
90.070.3885.640.060.703mp7A GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0065002
100.060.3874.650.060.583ll9B GO:0000166 GO:0005524 GO:0008299 GO:0016301 GO:0016310 GO:0016740 GO:0102043
110.060.4274.340.050.634k1nA GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
120.060.3274.680.100.511sj8A GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
130.060.3835.620.030.713dinC GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
140.060.4174.320.070.614k1oA GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
150.060.4944.900.090.784iggB GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034332 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0051015 GO:0051149 GO:0051291 GO:0071681 GO:0090136 GO:0098641 GO:2000146 GO:2001045 GO:2001240 GO:2001241
160.060.3645.260.010.622ww9A GO:0005048 GO:0005783 GO:0005789 GO:0006614 GO:0006810 GO:0008320 GO:0015031 GO:0016020 GO:0016021 GO:0071261 GO:0071806
170.060.3606.030.050.723dl8G GO:0005622 GO:0005886 GO:0006605 GO:0006810 GO:0015031 GO:0016020 GO:0016021 GO:0043952 GO:0065002
180.060.3235.250.020.542h34A GO:0000166 GO:0004672 GO:0004674 GO:0005524 GO:0005576 GO:0005886 GO:0006468 GO:0009405 GO:0016020 GO:0016021 GO:0016301 GO:0016310 GO:0016740 GO:0043085 GO:0043086 GO:0045717 GO:0046777 GO:0051409


Consensus prediction of GO terms
 
Molecular Function GO:0070628
GO-Score 0.67
Biological Processes GO:1901800 GO:0051260
GO-Score 0.67 0.67
Cellular Component GO:0005886 GO:0005618 GO:0022624
GO-Score 0.73 0.67 0.67

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.