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I-TASSER results for job id Rv2567

[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
10.04 2 1qr2A FAD Rep, Mult 212,274
20.04 2 4q54D CLA Rep, Mult 136,137,141
30.04 2 4wakB BCT Rep, Mult 130,133
40.02 1 3vggA GLC Rep, Mult 207,209
50.02 1 2oroA SO3 Rep, Mult 123,377
60.02 1 2bptA III Rep, Mult 123,126,127,130,131,159,162
70.02 1 2a69P MG Rep, Mult 74,78
80.02 1 1lm1A F3S Rep, Mult 212,213,214,215,217,219,220,222,226,227
90.02 1 3f9oA CO3 Rep, Mult 302,318
100.02 1 3nl3A MG Rep, Mult 274,291
110.02 1 3e25A MG Rep, Mult 318,323
120.02 1 4yfkC 4C6 Rep, Mult 398,402
130.02 1 1h39C C8E Rep, Mult 553,554
140.02 1 1f59A III Rep, Mult 130,133,134,137,138,167,170,174
150.02 1 3e27A MG Rep, Mult 291,315
160.02 1 2muwB 3LW Rep, Mult 610,613
170.02 1 1rfuF ZN Rep, Mult 188,199
180.02 1 2ed4B NAD Rep, Mult 378,381
190.02 1 1u6g0 III Rep, Mult 119,122,126,156,157
200.02 1 2e5dA NCA Rep, Mult 143,145

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
10.0601z1wA0.3137.620.0320.4533.4.11.-127,159
20.0602qllA0.2928.190.0390.4472.4.1.1135
30.0603ebgA0.3597.700.0470.5163.4.11.-NA
40.0601u22A0.2977.960.0570.4452.1.1.14NA
50.0602gtqA0.3457.560.0510.4933.4.11.2NA
60.0603b9jJ0.1506.840.0620.2051.17.1.4,1.17.3.2NA
70.0603b9jI0.0895.460.0290.1101.17.1.4,1.17.3.2NA
80.0602eabA0.3158.190.0490.4723.2.1.63NA
90.0602dqmA0.3497.550.0420.4953.4.11.2NA
100.0602j5wA0.3058.780.0370.4861.16.3.1NA
110.0602pdaA0.2928.290.0340.4461.2.7.159
120.0601ea0A0.3718.970.0480.6021.4.1.13NA
130.0601w3bB0.2946.170.0890.3822.4.1.-116,141,169
140.0601fa9A0.2968.290.0500.4552.4.1.1NA
150.0602vuaA0.1577.320.0310.2263.4.24.69124,134
160.0602cqsA0.2928.590.0500.4602.4.1.20NA
170.0601n1hA0.2928.960.0440.4692.7.7.48NA
180.0602vdcF0.3718.630.0390.5791.4.1.13107
190.0602vdcA0.3758.460.0280.5791.4.1.13NA

(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
00.170.8223.830.080.903w3uA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
10.070.5926.380.070.781qgkA GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
20.070.5626.420.070.744xriA GO:0005622 GO:0006886 GO:0008536
30.070.5515.200.060.663w3zA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0006406 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0007088 GO:0008139 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0060188
40.070.5436.470.070.722q5dB GO:0000059 GO:0000060 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006309 GO:0006606 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0007079 GO:0007080 GO:0008139 GO:0008270 GO:0008536 GO:0008565 GO:0015031 GO:0016020 GO:0016032 GO:0019054 GO:0019899 GO:0019904 GO:0030953 GO:0031291 GO:0031965 GO:0034399 GO:0040001 GO:0043234 GO:0044822 GO:0045184 GO:0051879 GO:0070062 GO:0071782 GO:0075733 GO:0090307
50.070.5166.970.070.714jlqA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
60.070.5557.020.060.773nd2A GO:0000059 GO:0000060 GO:0000176 GO:0005087 GO:0005634 GO:0005643 GO:0005737 GO:0006606 GO:0006607 GO:0006610 GO:0006612 GO:0006656 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965 GO:0034399 GO:0043547 GO:0051028 GO:0051292 GO:0060188
70.070.4917.800.070.721qbkB GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
80.060.4417.380.070.624a0cA GO:0000151 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0010265 GO:0016020 GO:0016567 GO:0017025 GO:0030154 GO:0031461 GO:0043086 GO:0045893 GO:0045899 GO:0070062
90.060.3876.710.060.515dlqA GO:0005049 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0046827
100.060.3455.550.060.431b3uA GO:0000086 GO:0000159 GO:0000184 GO:0000188 GO:0000775 GO:0003823 GO:0004722 GO:0005634 GO:0005694 GO:0005737 GO:0005739 GO:0005829 GO:0006275 GO:0006355 GO:0006461 GO:0006470 GO:0006672 GO:0006915 GO:0007059 GO:0007084 GO:0007143 GO:0008380 GO:0008601 GO:0010033 GO:0015630 GO:0016020 GO:0019932 GO:0030111 GO:0030155 GO:0030308 GO:0034047 GO:0040008 GO:0042518 GO:0045595 GO:0046982 GO:0051232 GO:0051306 GO:0051754 GO:0070062 GO:0070262 GO:1903538 GO:2001241
110.060.2885.950.070.371ialA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0042826 GO:0044822
120.060.2885.280.070.354uadA GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0016020 GO:0045944 GO:0060135
130.060.2825.650.050.354rxhB GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0008565 GO:0015031
140.060.2755.570.050.341wa5B GO:0000176 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0005829 GO:0006606 GO:0006607 GO:0006612 GO:0006810 GO:0008139 GO:0008565 GO:0015031 GO:0031144 GO:0048471
150.060.2538.330.050.391tllA GO:0001666 GO:0001917 GO:0004517 GO:0005506 GO:0005516 GO:0005634 GO:0005737 GO:0005739 GO:0005741 GO:0005829 GO:0005886 GO:0006527 GO:0006809 GO:0007263 GO:0007565 GO:0007568 GO:0008016 GO:0008285 GO:0009408 GO:0010181 GO:0010243 GO:0010288 GO:0012506 GO:0014069 GO:0014070 GO:0014823 GO:0016020 GO:0016491 GO:0016597 GO:0017080 GO:0018119 GO:0019899 GO:0020037 GO:0030425 GO:0031284 GO:0031667 GO:0031965 GO:0032496 GO:0033137 GO:0033197 GO:0035094 GO:0042383 GO:0042582 GO:0042803 GO:0042995 GO:0043066 GO:0043197 GO:0043234 GO:0043434 GO:0043627 GO:0044325 GO:0045202 GO:0045471 GO:0045776 GO:0045822 GO:0045906 GO:0045909 GO:0046676 GO:0046870 GO:0046872 GO:0048148 GO:0048471 GO:0050660 GO:0050661 GO:0051117 GO:0051481 GO:0051930 GO:0055114 GO:0071260 GO:0071731 GO:0071872 GO:0097110 GO:1900273 GO:1901216 GO:1902307
160.060.2274.350.070.261oyzA GO:0006974 GO:0046677
170.060.2027.390.050.293f3fH GO:0000055 GO:0005634 GO:0005643 GO:0006406 GO:0006606 GO:0006810 GO:0015031 GO:0016020 GO:0017056 GO:0031080 GO:0031081 GO:0031965 GO:0045893 GO:0051028
180.060.1583.660.070.183ltjA


Consensus prediction of GO terms
 
Molecular Function GO:0017016 GO:0008565 GO:0008139
GO-Score 0.37 0.32 0.32
Biological Processes GO:0016926 GO:1903320 GO:0007067 GO:0006405 GO:0051783 GO:0007346 GO:0051028 GO:0010467 GO:0071427 GO:0010564 GO:0030162 GO:0000060 GO:0000059 GO:0006607 GO:0006610
GO-Score 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.32 0.32 0.32 0.32
Cellular Component GO:0034399 GO:0005737 GO:0031965
GO-Score 0.32 0.32 0.32

(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.