[Home] [Server] [About] [Statistics] [Annotation]

I-TASSER results for job id Rv1637c

[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
10.64 183 5lmcA FEO Rep, Mult 119,121,123,124,178,202,243
20.41 119 2p18A ZN Rep, Mult 119,121,178,202
30.04 22 5ewaA 9BZ Rep, Mult 2,74,121,123,178,202,205,211,243
40.03 12 2bmiB NA Rep, Mult 76,77,93,123,199
50.02 11 1qh5A GTT Rep, Mult 123,178,202,205,209,210,211,214,243
60.01 5 2fu8A MCO Rep, Mult 41,47,119,123,124,178,205,207,242
70.01 6 1jt1A MCO Rep, Mult 178,203,210,245,258
80.00 2 2hb9A L13 Rep, Mult 132,133,135
90.00 1 4awyB MG Rep, Mult 96,97,98,99,127,130
100.00 2 2bfkB AZI Rep, Mult 178,205,213,214
110.00 2 2fhxA AZI Rep, Mult 93,118,119,199,201,202
120.00 2 1m2xA MCO Rep, Mult 121,122,123,150,178,202,214,243
130.00 1 1qh3A CAC Rep, Mult 223,224,228
140.00 1 2fu7B PHN Rep, Mult 63,83,86
150.00 1 3m8tA ZN Rep, Mult 102,130,134
160.00 1 3m8tA ZN Rep, Mult 52,107
170.00 2 1jjeA ZN Rep, Mult 77,245
180.00 2 2fu7A PHN Rep, Mult 66,83,166,167,168,187
190.00 1 2gmnA ZN Rep, Mult 159,173,228

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
10.4792p18A0.7042.360.2080.7843.1.2.6123
20.3901m2xA0.6362.950.1300.7503.5.2.6123
30.3891l9yA0.6463.220.1270.7733.5.2.6123
40.3243dhaA0.5703.050.1890.6703.1.1.-123
50.3021ko2A0.6443.160.1390.7733.5.2.6123
60.2791jjeB0.6443.130.1530.7613.5.2.6123
70.2741a8tA0.6542.990.1500.7613.5.2.6123
80.2492gmnA0.6453.240.1700.7733.5.2.6123
90.2311x8hA0.6342.940.1260.7463.5.2.6123
100.1812q42A0.6682.000.2680.7203.1.2.675,205
110.1351qh3A0.6841.780.2280.7313.1.2.6123
120.0601xm8A0.6701.960.2680.7203.1.2.6123,211
130.0602i7tA0.5154.670.1520.7123.1.27.-NA
140.0602ohhA0.6413.030.1900.7501.-.-.-123
150.0601smlA0.6453.520.2080.7883.5.2.6123
160.0602eo5A0.4216.170.0720.7272.6.1.19NA
170.0601p9eA0.6283.230.1380.7503.1.8.1209
180.0602a0mA0.4404.930.0920.6513.5.3.8258
190.0601ycfA0.6322.990.2030.7421.7.99.7NA
200.0602fk6A0.4315.730.0590.6863.1.26.1176
210.0602qedA0.6561.790.2040.7053.1.2.6NA
220.0601bvtA0.6442.850.1230.7463.5.2.6123
230.0602qnoA0.4175.490.0590.6703.2.1.4120
240.0602cbnA0.5164.580.1130.6933.1.26.1176,121,123
250.0603hnnA0.6163.510.0890.7651.-.-.-NA
260.0601znbB0.6563.010.1590.7613.5.2.6243
270.0603maxA0.4585.670.1130.7243.5.1.98NA
280.0602zo4A0.6382.630.1960.7273.-.-.-123
290.0601qh5A0.6841.760.2280.7313.1.2.6183,205

(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
00.550.6841.780.230.731qh3A GO:0004416 GO:0005737 GO:0005739 GO:0005759 GO:0005829 GO:0005975 GO:0006090 GO:0006749 GO:0006750 GO:0016787 GO:0019243 GO:0046872 GO:0070062
10.530.6802.510.220.763r2uA
20.510.7101.110.310.732xf4A GO:0016787
30.500.6761.640.310.722zwrB GO:0046872
40.490.6922.180.210.752gcuA GO:0005739 GO:0009651 GO:0009793 GO:0009960 GO:0016491 GO:0016788 GO:0046872 GO:0047951 GO:0048316 GO:0050313 GO:0051213 GO:0055114
50.480.6052.850.170.703adrA GO:0008270 GO:0046872
60.460.6382.630.200.732zo4A GO:0046872
70.450.6492.860.170.752q0jA GO:0044550
80.450.7042.360.210.782p18A GO:0004416 GO:0016787 GO:0046872
90.420.6283.230.140.751p9eA GO:0016787 GO:0046872
100.410.5703.050.190.673dhaA GO:0016787 GO:0046872 GO:0102007
110.400.6561.790.200.702qedA GO:0004416 GO:0016787 GO:0019243 GO:0046872
120.350.5472.960.130.651ztcA
130.340.6262.490.190.712p97A GO:0046872
140.280.6473.510.210.795evdA GO:0008270 GO:0008800 GO:0016787 GO:0017001 GO:0042597 GO:0046677 GO:0046872
150.270.6682.000.270.722q42A GO:0004416 GO:0005506 GO:0005739 GO:0008270 GO:0016787 GO:0019243 GO:0046872
160.270.6702.570.200.764ad9A GO:0004521 GO:0005739 GO:0005759 GO:0008270 GO:0016787 GO:0046872 GO:0090502
170.230.6852.310.210.754chlB GO:0005506 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005759 GO:0006749 GO:0016491 GO:0046872 GO:0050313 GO:0051213 GO:0055114 GO:0070221 GO:0070813
180.230.6183.230.180.744xukA GO:0016787
190.200.6463.220.130.771l9yA GO:0008800 GO:0016787 GO:0046872
200.190.6283.360.180.765axoA GO:0046872
210.190.6373.390.200.774awyB GO:0046872
220.160.5663.420.150.694le6A GO:0004063 GO:0016311 GO:0016787 GO:0046872
230.110.6972.490.230.774efzA GO:0016787 GO:0046872
240.110.6543.440.170.793lvzB GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0004416 GO:0047951 GO:0050313
GO-Score 0.88 0.55 0.49 0.49
Biological Processes GO:0006090 GO:0006750 GO:0005975 GO:0019243 GO:0009960 GO:0009793 GO:0009651 GO:0055114
GO-Score 0.55 0.55 0.55 0.55 0.49 0.49 0.49 0.49
Cellular Component GO:0005759 GO:0005829 GO:0070062
GO-Score 0.55 0.55 0.55

(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.