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I-TASSER results for job id Rv1269c

[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
10.06 4 3f1eC MG Rep, Mult 63,66
20.06 4 3lpeB ZN Rep, Mult 70,75,84,123
30.05 3 1z3a0 III Rep, Mult 57,61,68,71
40.05 3 1dftA CD Rep, Mult 66,70,75,84
50.03 2 3m4oA C7P Rep, Mult 17,18,21
60.03 2 4gqtA ZN Rep, Mult 59,63
70.03 2 2hvwA DDN Rep, Mult 36,37,39,55,58,61,62,63,100,101
80.03 2 2bx2L ZN Rep, Mult 70,75
90.03 2 1pl0D BW2 Rep, Mult 39,58,59,60
100.02 1 4k4aB 0FQ Rep, Mult 16,20,39,40
110.02 1 4x23P III Rep, Mult 13,16
120.02 1 2ggpB CU1 Rep, Mult 75,83,84
130.02 1 3n0aA CA Rep, Mult 90,113
140.02 1 1oz0B PO4 Rep, Mult 42,43,51,52
150.02 1 1smyF MG Rep, Mult 8,12,42
160.02 1 4h83F BCT Rep, Mult 2,118
170.02 1 1qiyL IPH Rep, Mult 106,109

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
10.0663ijfX0.5423.170.1210.7503.5.4.567
20.0661r5tA0.5593.390.0480.8233.5.4.563
30.0662d30A0.5403.720.1200.7823.5.4.563
40.0661vq2A0.6033.400.1040.8553.5.4.1284,88
50.0661mq0A0.5393.650.1240.7823.5.4.563
60.0601qbaA0.4993.650.0610.7583.2.1.5289
70.0601aldA0.4994.680.0550.8794.1.2.13NA
80.0601xfbA0.5004.650.0360.8794.1.2.13NA
90.0603dmoA0.5583.610.1330.8063.5.4.563
100.0602obcB0.6173.270.1270.8791.1.1.193,3.5.4.2627,32,63
110.0603dmoD0.5603.630.1320.8063.5.4.538
120.0601cttA0.5133.190.1210.7343.5.4.538,82,84
130.0601jtkA0.5483.540.1350.7823.5.4.563
140.0602z3iA0.5443.310.0810.7663.5.4.23NA
150.0601fdjA0.4954.680.0820.8794.1.2.13NA
160.0601ox7B0.6203.370.1080.8953.5.4.180
170.0602qubA0.5113.860.0680.8313.1.1.359
180.0601zabA0.5523.750.1430.7983.5.4.563
190.0601c7sA0.4754.970.0700.8873.2.1.52NA
200.0602w4lE0.6153.230.1110.8633.5.4.1238,89
210.0601xdmB0.4074.720.0720.7344.1.2.13NA
220.0602wanA0.4963.470.0530.7343.2.1.41NA
230.0601fbaA0.4964.700.0730.8794.1.2.13NA
240.0601xdmY0.4054.640.0820.7264.1.2.1397

(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
00.100.6453.200.090.913dh1A GO:0002100 GO:0003824 GO:0005654 GO:0006400 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717 GO:0052718
10.100.6433.210.120.902g6vB GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
20.090.6623.090.080.922nx8A GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
30.090.6353.020.120.874g3mA GO:0003824 GO:0005829 GO:0008152 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
40.080.6373.190.120.891wwrC GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0019239 GO:0046872 GO:0052717
50.080.6423.190.100.903zpcA GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0016491 GO:0016787 GO:0046872 GO:0050661 GO:0055114
60.080.6353.190.150.891z3aA GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
70.080.6413.150.140.892b3jC GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
80.080.6263.450.110.902hxvA GO:0000166 GO:0003824 GO:0008270 GO:0008703 GO:0008835 GO:0009231 GO:0009451 GO:0016491 GO:0016787 GO:0019239 GO:0046872 GO:0055114
90.080.6073.420.110.852g84A GO:0003824 GO:0008270 GO:0016787 GO:0046872
100.070.6203.370.110.901ox7B GO:0003824 GO:0004131 GO:0008270 GO:0008655 GO:0009451 GO:0016787 GO:0019858 GO:0044206 GO:0046087 GO:0046872
110.070.6153.230.110.862w4lE GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
120.070.6133.200.110.852w4lC GO:0003824 GO:0004132 GO:0005829 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046134 GO:0046872 GO:0070062
130.070.6033.400.100.851vq2A GO:0003824 GO:0004132 GO:0006220 GO:0008152 GO:0008270 GO:0009165 GO:0016787 GO:0046872
140.070.6263.010.120.854p9cA GO:0000166 GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
150.070.6142.980.150.852a8nB GO:0002100 GO:0003824 GO:0008033 GO:0008251 GO:0008270 GO:0016787 GO:0046872 GO:0052717
160.070.5593.390.050.821r5tA GO:0003824 GO:0004126 GO:0005634 GO:0005737 GO:0005829 GO:0006216 GO:0006217 GO:0008270 GO:0008655 GO:0009972 GO:0016787 GO:0042802 GO:0046872
170.070.6063.440.100.862hvwA GO:0003824 GO:0004132 GO:0006220 GO:0008270 GO:0016787 GO:0046872
180.070.5543.350.150.761wkqA GO:0003824 GO:0006144 GO:0006147 GO:0008270 GO:0008892 GO:0009451 GO:0016787 GO:0019239 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0008251 GO:0008270 GO:0016616 GO:0000166 GO:0050662
GO-Score 0.50 0.38 0.35 0.35 0.35
Biological Processes GO:0002097 GO:0042727 GO:0006771 GO:0042364
GO-Score 0.50 0.35 0.35 0.35
Cellular Component GO:0052718 GO:0005654 GO:0005829
GO-Score 0.10 0.10 0.09

(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.