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I-TASSER results for job id Rv0790c

[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
10.12 6 4f8hC LMD Rep, Mult 89,92
20.06 3 3ltwA HLZ Rep, Mult 98,100,101,142,145,227
30.04 2 1so2D MG Rep, Mult 136,151
40.04 2 2f4oA III Rep, Mult 69,83,84,85,136,137
50.04 2 1j95A TBA Rep, Mult 30,52
60.02 1 1ea4J NUC Rep, Mult 14,15,17
70.02 1 3d5d7 MG Rep, Mult 103,119
80.02 1 1g0dA SO4 Rep, Mult 103,147
90.02 1 3nteB FE Rep, Mult 46,150
100.02 1 4rku4 CLA Rep, Mult 45,48
110.02 1 4ej7A CA Rep, Mult 187,192
120.02 1 3zweA FUC Rep, Mult 142,147
130.02 1 4l9sA CA Rep, Mult 52,54
140.02 1 1h1lB MG Rep, Mult 54,58
150.02 1 2o01G CLA Rep, Mult 194,195

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
10.0601t9gC0.4085.920.0680.6821.3.99.3NA
20.0602qnoA0.4016.640.0740.7773.2.1.435
30.0601is2A0.4155.150.0450.6241.3.3.6NA
40.0602q3zA0.5184.560.0980.7192.3.2.13NA
50.0601g0dA0.5164.780.0880.7192.3.2.1384,136,151
60.0601xc6A0.4116.270.0540.7233.2.1.2386
70.0601f13A0.5134.670.0920.7152.3.2.1384,136,151
80.0603mddA0.4075.830.0680.6781.3.99.314,216,219
90.0602bszA0.4534.080.0540.5952.3.1.584,136,151
100.0601kv3A0.5184.690.0760.7192.3.2.1384,136,151
110.0601ivhA0.4115.940.0460.7111.3.99.1098
120.0602ebaA0.4145.760.0470.6941.3.99.7NA
130.0603d9wA0.4784.090.0630.6402.3.1.584,136,151
140.0601ukwA0.4135.850.0580.6901.3.99.3NA
150.0601bucA0.4245.800.0260.7071.3.99.2NA
160.0601l2aE0.4076.200.0480.7233.2.1.4NA
170.0601bucB0.4165.700.0520.6941.3.99.2NA
180.0602pg0A0.4065.650.0570.6781.3.99.398
190.0601e2tA0.4524.020.0640.5912.3.1.11884,136,151

(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
00.180.5134.670.090.711f13A GO:0002576 GO:0003810 GO:0005576 GO:0005737 GO:0007596 GO:0007599 GO:0016740 GO:0016746 GO:0018149 GO:0031093 GO:0042060 GO:0046872 GO:0072562
10.070.5184.560.100.722q3zA GO:0003810 GO:0005737 GO:0005739 GO:0005783 GO:0005829 GO:0005925 GO:0007200 GO:0016740 GO:0016746 GO:0018149 GO:0031012 GO:0031226 GO:0032471 GO:0043065 GO:0043277 GO:0045785 GO:0046872 GO:0051561 GO:0060445 GO:0060662 GO:0070062
20.070.5204.650.080.721l9mB GO:0003810 GO:0003824 GO:0005509 GO:0005737 GO:0006464 GO:0016740 GO:0016746 GO:0018149 GO:0030216 GO:0031069 GO:0031234 GO:0031424 GO:0043163 GO:0046872 GO:0051262 GO:0070062
30.070.5134.550.080.714pygA GO:0003810 GO:0005737 GO:0005739 GO:0005783 GO:0005829 GO:0005925 GO:0007200 GO:0016740 GO:0016746 GO:0018149 GO:0031012 GO:0031226 GO:0032471 GO:0043065 GO:0043277 GO:0045785 GO:0046872 GO:0051561 GO:0060445 GO:0060662 GO:0070062
40.070.5164.780.090.721g0dA GO:0003810 GO:0016740 GO:0016746 GO:0018149 GO:0046872
50.070.4694.660.100.653s3sA GO:0003810 GO:0005737 GO:0005739 GO:0005783 GO:0005829 GO:0005925 GO:0007200 GO:0016740 GO:0016746 GO:0018149 GO:0031012 GO:0031226 GO:0032471 GO:0043065 GO:0043277 GO:0045785 GO:0046872 GO:0051561 GO:0060445 GO:0060662 GO:0070062
60.060.3226.280.020.585a63A GO:0002262 GO:0004175 GO:0005765 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0005925 GO:0006508 GO:0006509 GO:0007219 GO:0007220 GO:0008233 GO:0016020 GO:0016021 GO:0016485 GO:0031293 GO:0042098 GO:0042470 GO:0042987 GO:0043065 GO:0043085 GO:0048013 GO:0050435 GO:0050673 GO:0070062
70.060.3276.570.030.623ucpA GO:0046872 GO:0055114
80.060.3196.490.080.594uisA GO:0002262 GO:0004175 GO:0005765 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0005925 GO:0006508 GO:0006509 GO:0007219 GO:0007220 GO:0008233 GO:0016020 GO:0016021 GO:0016485 GO:0031293 GO:0042098 GO:0042470 GO:0042987 GO:0043065 GO:0043085 GO:0048013 GO:0050435 GO:0050673 GO:0070062
90.060.2786.340.030.513czmB GO:0003824 GO:0004459 GO:0005975 GO:0016491 GO:0016616 GO:0019752 GO:0055114
100.060.2936.080.040.512aryA GO:0004198 GO:0005509 GO:0005622 GO:0005737 GO:0005739 GO:0005764 GO:0005829 GO:0005886 GO:0005925 GO:0006508 GO:0008092 GO:0008233 GO:0008234 GO:0008284 GO:0016020 GO:0016241 GO:0016540 GO:0016787 GO:0022617 GO:0032801 GO:0046872 GO:0060056 GO:0070062
110.060.2816.310.030.504mwaF GO:0003824 GO:0005506 GO:0008299 GO:0016114 GO:0016491 GO:0019288 GO:0044237 GO:0046429 GO:0046872 GO:0051536 GO:0051539 GO:0055114
120.060.2806.590.060.544q9nA GO:0004319 GO:0016491 GO:0055114
130.060.2526.710.040.504upcA GO:0002262 GO:0004175 GO:0005765 GO:0005783 GO:0005794 GO:0005886 GO:0005887 GO:0005925 GO:0006508 GO:0006509 GO:0007219 GO:0007220 GO:0008233 GO:0016020 GO:0016021 GO:0016485 GO:0031293 GO:0042098 GO:0042470 GO:0042987 GO:0043065 GO:0043085 GO:0048013 GO:0050435 GO:0050673 GO:0070062
140.060.3155.850.040.534aw6A GO:0004222 GO:0005634 GO:0005637 GO:0005783 GO:0005789 GO:0006508 GO:0006998 GO:0008233 GO:0008235 GO:0008237 GO:0016020 GO:0016021 GO:0016787 GO:0030327 GO:0046872 GO:0070062 GO:0071586
150.060.3245.960.030.554r2bA GO:0005215 GO:0006810
160.060.2495.510.080.413ibxA GO:0006772 GO:0009228 GO:0009229 GO:0016787 GO:0050334
170.060.3055.700.040.502p0rA GO:0004198 GO:0005509 GO:0005622 GO:0005737 GO:0006508 GO:0007586 GO:0008233 GO:0008234 GO:0016787 GO:0046872
180.060.2574.450.070.363a0bV GO:0005506 GO:0009055 GO:0009523 GO:0009579 GO:0015979 GO:0016020 GO:0018063 GO:0019684 GO:0020037 GO:0022904 GO:0042651 GO:0046872 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0003810 GO:0046872
GO-Score 0.37 0.37
Biological Processes GO:0018149 GO:0045055 GO:0007599 GO:0042060 GO:0050817
GO-Score 0.37 0.36 0.36 0.36 0.36
Cellular Component GO:1903561 GO:0005615 GO:0034774 GO:0031091
GO-Score 0.37 0.36 0.36 0.36

(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.