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I-TASSER results for job id Rv1268c

[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
10.23 24 2fraA CRV Rep, Mult 50,54,55,56,57,98,110,111,159,182,184,227
20.19 16 1ppdA BME Rep, Mult 50,54,56,182,183
30.02 2 8pchA III Rep, Mult 56,110,111,137,138,159,182,184,227,228
40.02 2 2fkwD BCL Rep, Mult 153,156
50.01 1 2wvkA ZN Rep, Mult 183,193
60.01 1 2aznB MA5 Rep, Mult 199,200
70.01 1 1z2nX MG Rep, Mult 191,201
80.01 1 3mpeA N2A Rep, Mult 115,116,117,137,183,184,227
90.01 1 2x8fA CA Rep, Mult 41,183
100.01 1 2wl3A CA Rep, Mult 91,132
110.01 1 3fcsC IMD Rep, Mult 173,224

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
10.4281iwdA0.5703.200.1320.7033.4.22.-50,56,183,200
20.4182pnsA0.5643.200.1210.6943.4.22.-50,56,183,200
30.4171cqdA0.5713.350.1140.7073.4.22.6750,56,183,200
40.4131o0eA0.5653.250.1160.6943.4.22.-50,56,183,200
50.3711bp4A0.5663.310.1620.7033.4.22.250,56,183
60.3422efmA0.5753.090.1450.7033.4.22.5150,56,183
70.3411s4vB0.5763.300.1300.7163.4.22.-50,56,183
80.3382fo5A0.5803.260.1240.7163.4.22.-50,56,183
90.3202bdzA0.5653.140.1520.6903.4.22.-50,56,183
100.3161cv8A0.5493.240.0700.6683.4.22.4850,56,183
110.2443f75A0.5863.570.1360.7463.4.22.1556,183
120.1171cqdC0.5713.350.1140.7073.4.22.6750,56,183,203
130.1073bpmA0.5924.010.1100.7723.4.22.-50,56,183,200
140.0939papA0.5673.150.1580.6943.4.22.256,107
150.0881jqpA0.5783.840.1000.7463.4.14.150,56,183,200
160.0842ghuA0.5943.780.1150.7673.4.22.-50,56,183,200
170.0703d6sA0.6033.250.1120.7503.4.22.6550,56,183,200
180.0671m6dA0.5743.460.1290.7243.4.22.41NA
190.0671nb3A0.5933.390.0980.7373.4.22.16189
200.0672frqA0.5733.360.1120.7163.4.22.27NA
210.0602c0yA0.5943.480.0890.7503.4.22.2750,183
220.0601fh0A0.5783.440.1160.7243.4.22.4356,182
230.0602o6xA0.6013.840.1030.7803.4.22.1550,200
240.0607pckD0.5723.430.1030.7203.4.22.3850,56,183
250.0607pckA0.5983.670.1020.7673.4.22.38220
260.0601csbE0.4503.350.0900.5563.4.22.1113
270.0602nqdB0.5723.420.1340.7203.4.22.15109,158,183,202
280.0601itoA0.5893.310.0870.7243.4.22.151,56
290.0601megA0.5723.190.1380.7033.4.22.3056,184,203
300.0601gecE0.5743.280.1320.7073.4.22.2556,183,200
310.0602oz2C0.5743.090.1450.7033.4.22.5151,56,107,183,204
320.0601aecA0.5753.220.1420.7113.4.22.1450,56,183
330.0601pbhA0.6143.620.0970.7803.4.22.1NA
340.0602djfC0.1803.530.1210.2283.4.14.1184,202
350.0608pchA0.5933.240.1030.7333.4.22.16NA

(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
00.250.5122.260.180.583k8uA GO:0000166 GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016887 GO:0022885 GO:0042626 GO:0043213 GO:0055085
10.220.5863.570.140.753f75A GO:0006508 GO:0008233 GO:0008234 GO:0016020 GO:0016021 GO:0016787
20.220.5493.240.070.671cv8A GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0009405 GO:0016787
30.210.6183.540.070.781mirA GO:0004175 GO:0004197 GO:0005576 GO:0005615 GO:0005737 GO:0005739 GO:0005764 GO:0005901 GO:0006508 GO:0006914 GO:0007283 GO:0007519 GO:0008233 GO:0008234 GO:0009611 GO:0009612 GO:0009749 GO:0009897 GO:0009986 GO:0014070 GO:0014075 GO:0016324 GO:0016787 GO:0030984 GO:0032403 GO:0034097 GO:0042277 GO:0042383 GO:0042470 GO:0043434 GO:0043621 GO:0045471 GO:0048471 GO:0050790 GO:0051603 GO:0060548 GO:0070670 GO:0071260
40.210.7541.280.160.793ervA GO:0016020 GO:0016021
50.200.5743.280.130.711gecE GO:0006508 GO:0008233 GO:0008234 GO:0016787
60.150.4622.310.130.533b79A GO:0000166 GO:0005524 GO:0006508 GO:0006810 GO:0008233 GO:0016020 GO:0016021 GO:0016887 GO:0042626 GO:0055085
70.140.4632.440.080.533zuaA GO:0000166 GO:0005524 GO:0005886 GO:0006508 GO:0006810 GO:0008233 GO:0008565 GO:0016020 GO:0016021 GO:0016787 GO:0016887 GO:0030253 GO:0030256 GO:0042626 GO:0055085
80.140.6143.630.090.781pbhA GO:0002224 GO:0004175 GO:0004197 GO:0004252 GO:0005518 GO:0005576 GO:0005615 GO:0005622 GO:0005730 GO:0005737 GO:0005739 GO:0005764 GO:0005901 GO:0006508 GO:0006914 GO:0007283 GO:0007519 GO:0008233 GO:0008234 GO:0009611 GO:0009612 GO:0009749 GO:0009897 GO:0009986 GO:0014070 GO:0014075 GO:0016324 GO:0016787 GO:0030574 GO:0030855 GO:0030984 GO:0032403 GO:0034097 GO:0036021 GO:0042277 GO:0042383 GO:0042470 GO:0042981 GO:0043231 GO:0043394 GO:0043434 GO:0043621 GO:0045471 GO:0046697 GO:0046718 GO:0048471 GO:0050790 GO:0051603 GO:0060548 GO:0070062 GO:0070670 GO:0071260 GO:0097067
90.070.6273.370.140.783oisA GO:0000166 GO:0006508 GO:0008233 GO:0008234
100.070.6143.660.090.784i04B GO:0004197 GO:0005615 GO:0005764 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0050790 GO:0051603
110.070.6103.810.150.803qj3A GO:0006508 GO:0008233 GO:0008234 GO:0016787
120.070.5823.400.120.732b1nA GO:0006508 GO:0008234
130.070.6033.250.110.753d6sA GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0016787
140.070.6093.760.090.785egwA GO:0006508 GO:0008233 GO:0008234 GO:0016787
150.070.5913.840.120.781cs8A GO:0001968 GO:0002224 GO:0002250 GO:0004197 GO:0004252 GO:0005518 GO:0005576 GO:0005615 GO:0005634 GO:0005764 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0019882 GO:0019886 GO:0022617 GO:0030574 GO:0036021 GO:0042393 GO:0043202 GO:0043394 GO:0051603 GO:0070062 GO:0071888 GO:0097067 GO:0097655
160.070.5983.800.100.771a6rA GO:0000122 GO:0000978 GO:0003677 GO:0003690 GO:0003697 GO:0003729 GO:0004197 GO:0005737 GO:0005739 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0043418 GO:0046677
170.070.6043.270.110.751xkgA GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0016787
180.070.6163.400.110.774ci7A GO:0006508 GO:0008233 GO:0008234 GO:0046872
190.070.6013.840.100.782o6xA GO:0004175 GO:0004197 GO:0005576 GO:0006508 GO:0008233 GO:0008234 GO:0016787
200.070.6173.590.100.784n4zA GO:0004197 GO:0005615 GO:0005764 GO:0006508 GO:0008234 GO:0016787 GO:0051603
210.070.5903.290.090.722dc6A GO:0004197 GO:0005518 GO:0005576 GO:0005615 GO:0005730 GO:0005739 GO:0005764 GO:0006508 GO:0008233 GO:0008234 GO:0016787 GO:0030574 GO:0030855 GO:0042470 GO:0043231 GO:0043394 GO:0046697 GO:0046718 GO:0048471 GO:0050790 GO:0051603 GO:0070062 GO:0097067
220.070.5793.400.100.723n4cB GO:0001968 GO:0002224 GO:0002250 GO:0004197 GO:0004252 GO:0005518 GO:0005576 GO:0005615 GO:0005764 GO:0006508 GO:0006955 GO:0008233 GO:0008234 GO:0010447 GO:0016485 GO:0016787 GO:0019882 GO:0019886 GO:0022617 GO:0030574 GO:0034769 GO:0036021 GO:0043202 GO:0043231 GO:0043236 GO:0043394 GO:0048002 GO:0051603 GO:0097067 GO:2001259


Consensus prediction of GO terms
 
Molecular Function GO:0008234 GO:0032559 GO:1904680 GO:0032550 GO:0043492 GO:0015450 GO:0035639 GO:0016820 GO:0005515 GO:0033218 GO:0044877
GO-Score 0.64 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.42 0.42 0.42
Biological Processes GO:0006508 GO:0044765 GO:0015833 GO:0048232 GO:0009725 GO:0010941 GO:0014706 GO:0071496 GO:0065009 GO:0044257 GO:0006950 GO:0071214 GO:0060538 GO:0097305 GO:0009746 GO:0048523 GO:1901652
GO-Score 0.64 0.51 0.51 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42
Cellular Component GO:0016021 GO:0048770 GO:0009986 GO:0045177 GO:0044853 GO:0044421 GO:0098552 GO:0000323
GO-Score 0.54 0.42 0.42 0.42 0.42 0.42 0.42 0.42

(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.