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I-TASSER results for job id Rv3910

[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
10.06 3 5sv1F III Rep, Mult 146,149,156
20.04 2 4y282 CLA Rep, Mult 73,74
30.04 2 2bptA III Rep, Mult 105,108,109,112,113,181,184
40.04 2 4ogqB 2WM Rep, Mult 142,146
50.04 2 5a43B DMU Rep, Mult 149,157
60.04 2 3bz1Z CLA Rep, Mult 121,125
70.02 1 3prqX CLA Rep, Mult 112,119
80.02 1 3pyr4 MG Rep, Mult 67,68
90.02 1 1zoyC EPH Rep, Mult 39,42
100.02 1 2q5dB III Rep, Mult 86,89,164
110.02 1 1o6oA III Rep, Mult 67,70,71,75,137,140,143,144
120.02 1 4v1fA BQ1 Rep, Mult 80,81,84
130.02 1 1brrC ARC Rep, Mult 336,358,362
140.02 1 3ounB MN Rep, Mult 730,733
150.02 1 2bnwB NUC Rep, Mult 34,38
160.02 1 3fdoA MG Rep, Mult 137,157
170.02 1 4fe1L CLA Rep, Mult 84,107
180.02 1 2g3vB III Rep, Mult 119,127,130
190.02 1 1o6pB III Rep, Mult 104,108,177,180,181

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
10.0602rd0A0.2489.200.0470.3832.7.1.153NA
20.0602gtqA0.2718.350.0460.3893.4.11.232,157
30.0602dqmA0.2817.320.0570.3743.4.11.2NA
40.0601ea0A0.2599.800.0500.4141.4.1.13NA
50.0603b9jI0.0675.190.0940.0791.17.1.4,1.17.3.2NA
60.0603ebgA0.2817.730.0520.3843.4.11.-NA
70.0602x6fA0.2387.510.0450.3252.7.1.137,2.7.1.153,2.7.1.15441,48
80.0601fo4A0.2239.350.0300.3441.17.1.4NA
90.0602e1qA0.2269.710.0460.3581.17.3.2,1.17.1.4NA
100.0601t3tA0.2589.660.0510.4096.3.5.368
110.0602zxqA0.2609.140.0400.3963.2.1.9777
120.0602q1fA0.2517.730.0400.3454.2.2.21NA
130.0602vdcA0.2579.750.0310.4131.4.1.13NA
140.0603b9jJ0.1186.480.0510.1521.17.1.4,1.17.3.270
150.0602pdaA0.2409.390.0440.3681.2.7.113
160.0602eabA0.2477.670.0330.3343.2.1.63NA
170.0603ffzA0.2579.380.0330.3983.4.24.69129
180.0603b9jC0.1648.380.0390.2361.17.3.2,1.17.1.4NA
190.0602vkzG0.2899.670.0250.4572.3.1.38,3.1.2.14NA

(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
00.190.8703.360.090.935ijoJ GO:0005634 GO:0005635 GO:0005643 GO:0006405 GO:0006406 GO:0006409 GO:0006606 GO:0006810 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0044611 GO:0051028 GO:0075733 GO:1900034
10.070.6402.840.090.674kf7A GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
20.070.5017.400.070.685hb4B GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
30.070.4825.190.070.574knhB GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
40.060.4765.760.070.584knhA GO:0005634 GO:0005643 GO:0006810 GO:0015031 GO:0051028
50.060.4186.900.050.544ifqA GO:0000059 GO:0005634 GO:0005643 GO:0006810 GO:0006999 GO:0015031 GO:0017056 GO:0044611 GO:0046822 GO:0051028
60.060.3816.480.050.485ijnD GO:0000059 GO:0005634 GO:0005635 GO:0005643 GO:0005654 GO:0005737 GO:0006406 GO:0006409 GO:0006810 GO:0006913 GO:0007077 GO:0010827 GO:0015031 GO:0016020 GO:0016032 GO:0016925 GO:0017056 GO:0019083 GO:0031047 GO:0031965 GO:0034399 GO:0044611 GO:0051028 GO:0051292 GO:0075733 GO:1900034
70.060.1668.010.050.233qiaA GO:0000166 GO:0004518 GO:0004519 GO:0005524 GO:0006314 GO:0006754 GO:0006810 GO:0006811 GO:0015991 GO:0015992 GO:0016539 GO:0016787 GO:0016820 GO:0033178 GO:0046034 GO:0090305
80.060.1677.040.040.221k9xA GO:0004180 GO:0004181 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0050897
90.060.1647.860.040.234dozA GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
100.060.1496.120.070.194eqfA GO:0000268 GO:0005052 GO:0005737 GO:0005778 GO:0005829 GO:0016020 GO:0016560 GO:0030425 GO:0031267 GO:0042391 GO:0043235 GO:0043949 GO:0045185
110.060.1576.950.040.211bagA GO:0003824 GO:0004556 GO:0005576 GO:0005975 GO:0008152 GO:0016787 GO:0016798 GO:0043169 GO:0046872
120.060.1424.750.070.164f7rD GO:0019904
130.060.1297.090.020.172ptxA GO:0000015 GO:0000287 GO:0004634 GO:0006096 GO:0016829 GO:0046872
140.060.1317.140.040.174hs7A GO:0005363 GO:0015768
150.060.1126.270.050.144q0mA GO:0004067 GO:0006520
160.060.1186.920.040.161w62A GO:0005576 GO:0005737 GO:0007275 GO:0016020 GO:0016853 GO:0018112
170.060.1335.970.070.162pmzC GO:0003677 GO:0003899 GO:0006351 GO:0016740 GO:0016779
180.060.0986.900.040.134wa8A GO:0000287 GO:0003677 GO:0003824 GO:0004518 GO:0004519 GO:0004527 GO:0006260 GO:0006281 GO:0006974 GO:0008409 GO:0016787 GO:0016788 GO:0017108 GO:0043137 GO:0046872 GO:0090305


Consensus prediction of GO terms
 
Molecular Function GO:0005198
GO-Score 0.49
Biological Processes GO:0017038 GO:0044744 GO:0006405 GO:0071427 GO:1902593 GO:1902583 GO:0032446 GO:0019080 GO:0046794 GO:0051081 GO:0080135 GO:0051049 GO:0051031 GO:1903047 GO:0071431 GO:0032774 GO:0018205 GO:0015758 GO:0034605 GO:0016458 GO:0051028
GO-Score 0.49 0.49 0.49 0.49 0.49 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.34
Cellular Component GO:0043234 GO:0005643
GO-Score 0.49 0.39

(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.