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I-TASSER results for job id Rv2077c

[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 7 5lx2A III Rep, Mult 57,58,61,67,124,127,134,135,187,188,191,195,244,248,251
20.11 6 2btpA III Rep, Mult 61,67,127,134,135,187,188,191,194,195,244,248,251
30.04 2 1c6fA AR Rep, Mult 5,8,19
40.04 2 2o98A FSC Rep, Mult 50,54,57,121,125,233,234,237,238
50.04 2 2j62B GSZ Rep, Mult 110,113
60.04 2 3rdhC 3RD Rep, Mult 61,127,184,188,242
70.04 2 2a01B AC9 Rep, Mult 56,60
80.02 1 1lghA DET Rep, Mult 20,27
90.02 1 2i0mA ZN Rep, Mult 98,102
100.02 1 3eqaA UUU Rep, Mult 24,25,26,85,88,90
110.02 1 1z08D MG Rep, Mult 1,4
120.02 1 2id3A CA Rep, Mult 32,99

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
10.0601hn0A0.4575.820.0640.7184.2.2.20140
20.0601h54B0.4545.450.0480.6662.4.1.8NA
30.0601occA0.4406.490.0470.7311.9.3.1NA
40.0602ri9B0.4555.100.0370.6623.2.1.113NA
50.0601l2aE0.5075.620.0420.7403.2.1.4NA
60.0602vn4A0.4975.240.0650.7253.2.1.3NA
70.0601i8qA0.4835.850.0630.7684.2.2.162,70
80.0601m56A0.4555.920.0350.7061.9.3.1NA
90.0601dl2A0.4774.970.0460.6753.2.1.113184
100.0602jg0A0.4525.520.0690.6783.2.1.28NA
110.0601ug9A0.5135.350.0800.7553.2.1.70NA
120.0601ojnA0.4705.000.0320.6754.2.2.1NA
130.0601cb8A0.4575.710.0410.7094.2.2.5NA
140.0602eabA0.4925.230.0750.7123.2.1.63133
150.0601nxcA0.4725.200.0390.6843.2.1.113184
160.0601js4A0.4585.560.0600.6753.2.1.4NA
170.0601h12A0.4545.230.0320.6533.2.1.8NA
180.0601f1sA0.4815.930.0520.7684.2.2.1NA
190.0601w6jA0.4485.970.0560.6945.4.99.7185

(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
00.100.5233.010.030.612o98B GO:0019904
10.070.5252.960.060.614j6sB GO:0000086 GO:0005080 GO:0005159 GO:0005737 GO:0005739 GO:0005829 GO:0005925 GO:0006469 GO:0006605 GO:0008426 GO:0009966 GO:0016020 GO:0019904 GO:0030659 GO:0030971 GO:0031988 GO:0032869 GO:0043209 GO:0044822 GO:0045664 GO:0048167 GO:0061024 GO:0070062 GO:0071901 GO:1900740
20.070.4522.780.060.521a37A GO:0005615 GO:0005634 GO:0005737 GO:0005925 GO:0008134 GO:0019901 GO:0019904 GO:0031625 GO:0042470 GO:0042802 GO:0044822 GO:0051683 GO:0070062 GO:0072562 GO:0090168
30.070.5004.120.060.653m73A GO:0005886 GO:0006810 GO:0006811 GO:0016020 GO:0016021 GO:0046677 GO:0046690 GO:0055085
40.070.5514.800.040.744um2A GO:0000184 GO:0000333 GO:0000723 GO:0000781 GO:0003677 GO:0004518 GO:0004519 GO:0004521 GO:0005634 GO:0005694 GO:0005697 GO:0005730 GO:0005737 GO:0005829 GO:0006406 GO:0016787 GO:0032210 GO:0035145 GO:0035303 GO:0042162 GO:0043021 GO:0046872 GO:0070034 GO:0070182 GO:0090305 GO:0090502 GO:1904354
50.070.5115.090.050.701ya0B GO:0000184 GO:0005634 GO:0005737 GO:0005829 GO:0006406 GO:0035303 GO:0042162 GO:0045111 GO:0051721
60.070.5193.070.020.613axyC GO:0005634 GO:0005737 GO:0019904
70.070.5182.880.060.602c74A GO:0002028 GO:0003779 GO:0005159 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006713 GO:0006886 GO:0014704 GO:0017080 GO:0019899 GO:0019904 GO:0021762 GO:0030659 GO:0035259 GO:0042921 GO:0044325 GO:0045664 GO:0045893 GO:0046982 GO:0048167 GO:0050774 GO:0061024 GO:0070062 GO:0086010 GO:1900740 GO:2000649
80.070.5102.890.060.592br9A GO:0000086 GO:0001764 GO:0003064 GO:0005737 GO:0005739 GO:0005829 GO:0005871 GO:0005913 GO:0005925 GO:0006605 GO:0015459 GO:0016020 GO:0016032 GO:0019899 GO:0019904 GO:0021762 GO:0021766 GO:0021987 GO:0023026 GO:0030424 GO:0030659 GO:0031625 GO:0032403 GO:0035308 GO:0035329 GO:0035556 GO:0042470 GO:0042826 GO:0043154 GO:0044325 GO:0044822 GO:0046982 GO:0050815 GO:0051219 GO:0060306 GO:0061024 GO:0070062 GO:0086013 GO:0086091 GO:0098609 GO:0098641 GO:1900034 GO:1900740 GO:1901016 GO:1902309
90.070.5092.900.050.592npmA GO:0019904
100.070.5163.050.040.602btpA GO:0005737 GO:0005739 GO:0005829 GO:0005925 GO:0006605 GO:0007264 GO:0008022 GO:0016020 GO:0019904 GO:0021762 GO:0030659 GO:0034766 GO:0043234 GO:0044325 GO:0045892 GO:0047485 GO:0061024 GO:0070062 GO:0071889 GO:1900740
110.070.5033.110.030.594dx0A GO:0019904
120.070.4984.690.060.663zheB GO:0000184 GO:0005634 GO:0005737
130.070.5013.240.040.604jc3A GO:0000079 GO:0001836 GO:0003334 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0006469 GO:0006977 GO:0007165 GO:0008426 GO:0008630 GO:0010482 GO:0010839 GO:0019901 GO:0019904 GO:0030216 GO:0030307 GO:0030659 GO:0031424 GO:0043154 GO:0043588 GO:0045606 GO:0046827 GO:0051219 GO:0051726 GO:0061024 GO:0061436 GO:0070062 GO:0071901 GO:0098609 GO:0098641 GO:1900740
140.070.5122.940.060.594zdrA GO:0000166 GO:0000287 GO:0001558 GO:0001894 GO:0001944 GO:0002039 GO:0004672 GO:0004674 GO:0005524 GO:0005615 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0005925 GO:0006468 GO:0006605 GO:0006914 GO:0006915 GO:0006974 GO:0007049 GO:0007050 GO:0007165 GO:0007283 GO:0007286 GO:0007409 GO:0008134 GO:0008285 GO:0010212 GO:0010508 GO:0010941 GO:0016020 GO:0016301 GO:0016310 GO:0016740 GO:0019901 GO:0019904 GO:0030010 GO:0030111 GO:0030154 GO:0030168 GO:0030275 GO:0030295 GO:0030308 GO:0030511 GO:0030659 GO:0031625 GO:0032147 GO:0036398 GO:0036399 GO:0042470 GO:0042593 GO:0042802 GO:0043066 GO:0043276 GO:0043488 GO:0044822 GO:0045059 GO:0046777 GO:0046872 GO:0048814 GO:0050731 GO:0050772 GO:0050852 GO:0051055 GO:0051645 GO:0051683 GO:0051896 GO:0060070 GO:0060770 GO:0061024 GO:0070062 GO:0071493 GO:0071902 GO:0072332 GO:0072562 GO:0090168 GO:0097484 GO:0098609 GO:0098641 GO:1900182 GO:1900740 GO:1901796 GO:1904262
150.070.4614.220.060.604dnkB GO:0000165 GO:0003714 GO:0005634 GO:0005737 GO:0005739 GO:0005829 GO:0005913 GO:0005925 GO:0006605 GO:0008022 GO:0016020 GO:0016032 GO:0017053 GO:0019899 GO:0019904 GO:0030659 GO:0032403 GO:0035308 GO:0035329 GO:0042470 GO:0042826 GO:0043085 GO:0043234 GO:0043488 GO:0045744 GO:0045892 GO:0048471 GO:0050815 GO:0051219 GO:0051220 GO:0051291 GO:0061024 GO:0070062 GO:0098609 GO:0098641 GO:1900740
160.070.4652.970.050.544f7rD GO:0019904
170.070.4554.100.080.593efzB GO:0019904
180.060.3974.230.040.502gw1A GO:0005739 GO:0005741 GO:0005742 GO:0006626 GO:0006886 GO:0015266 GO:0015450 GO:0016020 GO:0016021 GO:0030150 GO:0030943 GO:0031307 GO:0045039


Consensus prediction of GO terms
 
Molecular Function GO:0005515
GO-Score 0.45
Biological Processes GO:0071901 GO:0032869 GO:0048167 GO:0045664 GO:1900740 GO:0006605 GO:0000086 GO:0090168 GO:0051683 GO:0046690 GO:0046677 GO:0055085 GO:0006811 GO:0006406 GO:1904354 GO:0035303 GO:0032210 GO:0090502 GO:0000184
GO-Score 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07
Cellular Component GO:0044424
GO-Score 0.38

(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.