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I-TASSER results for job id Rv1341

[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 2 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
10.85 41 2q16A ITT Rep, Mult 11,12,13,16,48,60,76,77,78,92,93,125,158,159,160,161,181,186,187
20.19 8 3tquB CA Rep, Mult 48,76,93
30.07 5 2j4eD POP Rep, Mult 11,12,13,16,48,60,93
40.03 2 2j4eC MG Rep, Mult 46,48
50.01 1 2dvp0 III Rep, Mult 52,54,82,83,85,86,122,124,126,145,167
60.01 1 2pyu0 III Rep, Mult 51,52,53,54,55,58,62,85,86,124,126,134,137,139
70.01 1 2car0 III Rep, Mult 48,49,50,51,59,84,85,87,91,94,95,111,112,114,117,118
80.01 1 1b780 III Rep, Mult 48,49,50,59,63,84,85,87,88,91,94,111,112

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
10.4602pyuA0.9061.330.4410.9563.6.1.1553,78,89,93,158,160,187
20.3892carA0.8072.230.3050.9123.6.1.1916,19,76,159,161,174,184,186
30.0602vroB0.4625.220.0910.7451.2.1.3NA
40.0602gzmA0.4754.840.0910.7305.1.1.311
50.0601b78A0.8311.590.2640.8923.6.1.1516,77,92,157,161,187
60.0601vp2A0.8371.770.3260.9173.6.1.1513,16,53,78,89,93,125,157,160,162
70.0601o9jA0.3156.130.0380.5931.2.1.313
80.0601bxsA0.4605.210.0670.7301.2.1.3613
90.0601cddA0.3694.960.0400.5782.1.2.2NA
100.0601a4sA0.4644.950.0710.7111.2.1.8,1.2.1.3NA
110.0601escA0.4694.800.0630.7163.1.1.-NA
120.0601zuwC0.4634.940.0900.7265.1.1.311
130.0603cmmC0.4795.440.0620.8386.3.2.19NA
140.0602cfiA0.4634.530.0380.6811.5.1.6NA
150.0601up7A0.4694.530.0840.6863.2.1.86NA
160.0601ortI0.4675.110.0490.7352.1.3.3NA
170.0601a1sA0.4685.000.0880.7452.1.3.3187
180.0601c2tA0.4654.280.0750.6522.1.2.2NA
190.0603hfsB0.4635.140.0880.7401.3.1.77NA
200.0602o2pA0.4665.000.0880.7261.5.1.616
210.0602ve5H0.4644.960.0690.7111.2.1.860

(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
00.620.9290.920.420.953tquA GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
10.620.9061.330.440.962pyuA GO:0000166 GO:0000287 GO:0005829 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
20.500.8311.590.260.891b78A GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
30.500.8282.330.360.954bnqA GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
40.500.8361.760.330.923s86A GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
50.410.8072.230.300.912carA GO:0000166 GO:0005737 GO:0005829 GO:0006193 GO:0009117 GO:0009143 GO:0009204 GO:0016787 GO:0035870 GO:0036220 GO:0036222 GO:0046872 GO:0047429 GO:0051276 GO:0055086
60.410.7802.330.300.902dvnA GO:0000166 GO:0006163 GO:0009117 GO:0009143 GO:0016787 GO:0017111 GO:0046872 GO:0047429
70.070.4374.940.120.704bkqA GO:0004318 GO:0006629 GO:0006631 GO:0006633 GO:0016491 GO:0051287 GO:0055114
80.070.4195.320.100.714f2pB GO:0003824 GO:0008652 GO:0008782 GO:0008930 GO:0009086 GO:0009116 GO:0009164 GO:0016787 GO:0019284 GO:0019509
90.060.4315.290.090.714gmgA GO:0000166 GO:0016491 GO:0055114
100.060.4265.230.060.702fn8A GO:0005886 GO:0015145 GO:0015749 GO:0016021
110.060.3366.100.060.635bxpA GO:0004553 GO:0004563 GO:0005975 GO:0008152 GO:0016020 GO:0016021 GO:0016787 GO:0016798 GO:0047403
120.060.3725.390.050.633b50A GO:0006810 GO:0008643 GO:0030288 GO:0042597
130.060.3705.630.050.644mnpA GO:0006810 GO:0030288
140.060.3326.070.090.624qqaA GO:0009405 GO:0015485
150.060.3966.180.040.764c20B GO:0005737 GO:0005975 GO:0005996 GO:0006004 GO:0008736 GO:0016853 GO:0016861 GO:0019317 GO:0030145 GO:0042355 GO:0046872
160.060.4134.620.090.642gvqD GO:0000162 GO:0000287 GO:0003824 GO:0004048 GO:0005829 GO:0008152 GO:0008652 GO:0009073 GO:0016740 GO:0016757 GO:0046872
170.060.3476.370.060.653gh4A GO:0004553 GO:0004563 GO:0005975
180.060.3365.640.050.602a5jA GO:0000139 GO:0000166 GO:0005525 GO:0005783 GO:0005789 GO:0005794 GO:0005886 GO:0006810 GO:0007264 GO:0015031 GO:0016020 GO:0016192 GO:0045921 GO:0070062


Consensus prediction of GO terms
 
Molecular Function GO:0017111 GO:0047429 GO:0000166 GO:0000287
GO-Score 0.98 0.98 0.98 0.62
Biological Processes GO:0006163 GO:0009143
GO-Score 0.98 0.98
Cellular Component GO:0005829
GO-Score 0.62

(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.