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I-TASSER results for job id Rv3699

[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
10.65 50 4necA SAH Rep, Mult 8,12,24,50,51,52,71,72,73,97,98,99,119,120,121,125
20.04 4 4er6A AW2 Rep, Mult 36,48,50,51,52,56,71,72,73,97,98,99,117,119,125,148,149,226
30.03 3 4necD III Rep, Mult 7,8,17,18,23,24,123,124,152,156,166,168

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
10.2943lccA0.7082.610.1940.8162.1.1.-8,50,93,95
20.2062pxxA0.6622.800.2120.7553.4.24.71NA
30.2033bgdA0.6963.210.1330.8332.1.1.6754,99
40.1572iftA0.5513.010.1360.6612.1.1.52NA
50.1433e05D0.5983.020.1070.7172.1.1.132NA
60.0843e05B0.5973.050.1120.7172.1.1.132NA
70.0823hnrA0.5993.100.1450.7082.1.1.-123
80.0751f38A0.5883.070.1370.7122.1.1.-NA
90.0673grzB0.5732.810.1140.6692.1.1.-NA
100.0672cl5A0.6023.510.0820.7602.1.1.6NA
110.0673gdhA0.5923.240.1450.7302.1.1.-NA
120.0673bwmA0.6013.510.0870.7602.1.1.6NA
130.0671nt2A0.5853.010.1020.7042.1.1.-NA
140.0601uirB0.6213.560.1240.7942.5.1.1671,98,121,134
150.0601kpiA0.7013.770.1230.8842.1.1.79NA
160.0601kpgA0.6953.800.1120.8752.1.1.79NA
170.0602h11B0.7013.230.1180.8412.1.1.6754,99
180.0602opbB0.6903.490.1320.8712.1.1.2850,52,71
190.0602vdwG0.7003.550.0960.8802.7.7.5036
200.0601tpyA0.7093.870.1370.8972.1.1.79NA
210.0601xcjA0.6413.930.1270.8542.1.1.2118
220.0601wznA0.6863.390.2040.8242.1.1.-NA
230.0601jq3A0.6253.590.1130.7942.5.1.16119
240.0603c6mD0.6253.860.0870.8072.5.1.22NA
250.0601l1eA0.6783.940.1080.8672.1.1.79NA
260.0601fp1D0.6273.380.1070.7552.1.1.-123
270.0602ip2A0.6573.140.1340.7852.1.1.-NA
280.0602a14A0.6903.480.1170.8542.1.1.4950,52
290.0601sqfA0.6203.600.0880.7772.1.1.-NA
300.0602ytzA0.6193.540.1110.7682.1.1.3271,118,122,124
310.0602ex4A0.6693.040.1050.8162.1.1.-NA
320.0601ri1A0.6723.540.1640.8332.1.1.5650,71

(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
00.480.8691.020.350.894necB GO:0008168 GO:0016740 GO:0032259
10.350.6723.060.130.804kifB GO:0008168 GO:0016740 GO:0017000 GO:0032259
20.320.7082.610.190.823lccA GO:0005886 GO:0006952 GO:0008168 GO:0008757 GO:0016740 GO:0018708 GO:0019762 GO:0032259
30.310.6692.370.250.753sm3A GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
40.290.7293.290.130.883ggdA
50.290.6313.240.170.753ccfB GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
60.290.6903.620.230.843busA GO:0008152 GO:0008168 GO:0016740 GO:0032259
70.280.6353.160.180.773g5lA
80.280.5922.210.180.665cm2Z GO:0000049 GO:0002098 GO:0005634 GO:0005737 GO:0005829 GO:0008152 GO:0008168 GO:0008198 GO:0016300 GO:0016706 GO:0030488 GO:0032259 GO:0055114
90.270.6863.390.200.821wznA
100.270.6543.520.180.803mggB GO:0008168 GO:0016740 GO:0032259
110.270.6033.240.180.713cggA GO:0008168 GO:0016740 GO:0032259
120.270.7463.290.180.884pneB GO:0008152 GO:0008168 GO:0016740 GO:0032259
130.260.6672.980.170.773g2pA GO:0046872 GO:0051536 GO:0051539
140.260.5923.240.140.733gdhA GO:0000387 GO:0001510 GO:0005615 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0008168 GO:0008173 GO:0009452 GO:0015030 GO:0016740 GO:0022613 GO:0030532 GO:0032259 GO:0036261 GO:0044255 GO:0071164 GO:0071167
150.260.5993.050.150.711dusA GO:0008168 GO:0016740 GO:0032259
160.260.5983.690.150.762xvaA GO:0005737 GO:0005829 GO:0008168 GO:0008757 GO:0009636 GO:0016740 GO:0032259 GO:0046677 GO:0046690
170.250.7003.170.140.841bhjA GO:0001887 GO:0005542 GO:0005634 GO:0005737 GO:0005829 GO:0006544 GO:0008168 GO:0008757 GO:0016594 GO:0016740 GO:0017174 GO:0032259 GO:0046498 GO:0046500 GO:0046655 GO:0051262 GO:0051289 GO:0098603 GO:1901052
180.250.6792.490.170.773h2bB GO:0008168 GO:0016740 GO:0032259
190.240.6633.420.130.794htfB GO:0008033 GO:0008168 GO:0016740 GO:0032259
200.240.6413.020.140.753l8dA GO:0008152 GO:0008168 GO:0016740 GO:0032259
210.240.6733.980.130.873f4kA GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
220.230.6593.070.140.795bszA GO:0008168 GO:0016740 GO:0032259
230.230.6843.820.100.883kkzA GO:0046872 GO:0051536 GO:0051539
240.230.6933.400.160.845je1A GO:0008168 GO:0016740 GO:0032259
250.220.6473.370.170.782gluA GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
260.220.5893.800.190.754hg2B GO:0008152 GO:0008168 GO:0016740 GO:0032259
270.220.6653.010.200.794oqdC GO:0008168 GO:0008757 GO:0016740 GO:0017000 GO:0032259 GO:0042803
280.220.6713.060.180.793ou7A GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
290.210.6882.660.170.791ve3B GO:0046872 GO:0051536 GO:0051539
300.210.5883.070.140.711f38A GO:0006479 GO:0008168 GO:0008276 GO:0009236 GO:0016740 GO:0032259 GO:0046140
310.200.6573.850.160.852yqzA GO:0008152 GO:0008168 GO:0032259 GO:0046872 GO:0051536 GO:0051539
320.200.5643.620.150.722kw5A GO:0005737 GO:0008757 GO:0032259
330.200.5693.980.170.741pjzA GO:0005737 GO:0008119 GO:0008168 GO:0008757 GO:0010038 GO:0016740 GO:0032259 GO:0046690
340.200.6783.290.150.803d2lC GO:0008168 GO:0016740 GO:0032259
350.200.6923.340.150.832avnA GO:0008152 GO:0008168 GO:0016740 GO:0032259
360.200.5793.600.150.732i6gB GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690
370.200.6383.420.180.771vl5A GO:0008152 GO:0008168 GO:0016740 GO:0032259
380.190.6903.020.170.824qdkA GO:0005737 GO:0008168 GO:0008757 GO:0015979 GO:0015995 GO:0016740 GO:0032259 GO:0036068 GO:0046406
390.190.5604.100.130.752pkwA GO:0005737 GO:0006364 GO:0008168 GO:0008990 GO:0016740 GO:0031167 GO:0032259
400.180.5872.940.170.693cc8A
410.170.5533.490.110.703mtiB GO:0008168 GO:0016740 GO:0032259
420.110.6143.350.140.754rsrA GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
430.100.6573.630.190.814kdcA GO:0005829 GO:0006744 GO:0008168 GO:0008425 GO:0008689 GO:0008757 GO:0016740 GO:0032259 GO:0043431 GO:0061542 GO:0102004
440.090.6683.210.180.815bp9A GO:0008168 GO:0016740 GO:0032259
450.080.6633.530.120.811y8cA GO:0008168 GO:0016740 GO:0032259
460.070.6103.310.160.763m70A GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690
470.070.5833.150.130.701sg9A GO:0003676 GO:0006479 GO:0008168 GO:0008276 GO:0016740 GO:0018364 GO:0032259 GO:0036009


Consensus prediction of GO terms
 
Molecular Function GO:0018708 GO:0046872
GO-Score 0.32 0.31
Biological Processes GO:0032259 GO:0017000 GO:0019762 GO:0006952
GO-Score 0.84 0.35 0.32 0.32
Cellular Component GO:0005886
GO-Score 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.