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I-TASSER results for job id Rv0817c

[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
10.12 4 1qiyF III Rep, Mult 62,63
20.09 3 1fo4A FES Rep, Mult 94,95,96,125,126,127,165
30.06 2 2e7fA CA Rep, Mult 26,28
40.04 1 4dlqA III Rep, Mult 24,135,138,142,145,146,147,148,149,157,158,159,161,162,164,165,166,167,168,182,184,186,188,193,194,195,197,198,200,201,202,213,253,255,258
50.03 1 3ee6A ZN Rep, Mult 73,96
60.03 1 2ckjD PO4 Rep, Mult 32,72,125,262
70.03 1 2vl1B III Rep, Mult 190,191
80.03 1 3ddrA HEM Rep, Mult 70,72,152,153
90.03 1 2hdqB C21 Rep, Mult 234,236
100.03 1 1fiqA FAD Rep, Mult 36,39,40,76

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
10.0601zyzA0.3866.420.0720.6891.17.4.1NA
20.0602ewbA0.3856.160.0500.6593.4.11.1,3.4.11.5121
30.0602e1qA0.4505.690.0760.7191.17.3.2,1.17.1.4108
40.0601hdhA0.3855.870.0310.6193.1.6.132,74
50.0603b9jI0.2465.590.0610.3891.17.1.4,1.17.3.259
60.0602ckjA0.4655.570.0720.7301.17.1.4,1.17.3.2108
70.0601t3qB0.4606.070.0620.7631.3.99.17NA
80.0601ffuB0.4575.930.0790.7481.2.99.2NA
90.0601bglA0.3346.300.0470.5823.2.1.2371
100.0602qvrA0.3855.740.0390.6263.1.3.11254
110.0601jroB0.4565.960.0570.7331.1.1.204NA
120.0601bdgA0.3926.140.0700.6632.7.1.150
130.0601ig8A0.3986.140.0500.6702.7.1.1NA
140.0601spiA0.3405.920.0570.5743.1.3.11156
150.0603b9jJ0.2926.130.0300.4961.17.1.4,1.17.3.220,22,72,126
160.0601gytJ0.3916.390.0470.6813.4.11.1188
170.0602hb6B0.3876.150.0400.6563.4.11.171
180.0601gytA0.3856.360.0530.6813.4.11.1131
190.0602pflA0.3486.890.0690.6522.3.1.5453

(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
00.180.7072.350.120.774dlqA GO:0004871 GO:0004888 GO:0004930 GO:0005622 GO:0005829 GO:0005886 GO:0007157 GO:0007165 GO:0007166 GO:0007186 GO:0007420 GO:0014069 GO:0015643 GO:0016020 GO:0016021 GO:0016079 GO:0016524 GO:0030054 GO:0030246 GO:0030424 GO:0030426 GO:0035584 GO:0042734 GO:0042995 GO:0043005 GO:0045202 GO:0050839 GO:0090129
10.070.5923.480.080.714dloA GO:0004871 GO:0004888 GO:0004930 GO:0005096 GO:0005886 GO:0007165 GO:0007166 GO:0007186 GO:0007520 GO:0016020 GO:0016021 GO:0016525 GO:0043547 GO:0048814 GO:0051965
20.060.4606.070.060.761t3qB GO:0016491 GO:0055114
30.060.4565.930.090.733ax7A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
40.060.3546.310.040.614ikvA GO:0005215 GO:0006810 GO:0006857 GO:0015197 GO:0015833 GO:0016020 GO:0016021
50.060.4655.570.070.732ckjA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
60.060.3176.460.050.562qdeA GO:0003824 GO:0008152 GO:0009063
70.060.3556.090.030.602yk0A GO:0004872 GO:0009405 GO:0016020 GO:0016021 GO:0046872
80.060.4705.510.070.731fo4A GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0009055 GO:0009115 GO:0016491 GO:0016614 GO:0016903 GO:0043546 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0055114
90.060.3315.960.070.551ffuC GO:0003824 GO:0016491 GO:0016614 GO:0018492 GO:0050660 GO:0055114
100.060.3215.960.070.541t3qC GO:0000166 GO:0003824 GO:0016491 GO:0016614 GO:0050660 GO:0055114
110.060.4576.040.070.751rm6A GO:0016491 GO:0018525 GO:0055114
120.060.4366.070.060.714zohA GO:0016491 GO:0055114
130.060.2886.270.050.503hrdG GO:0003824 GO:0016491 GO:0016614 GO:0050138 GO:0050660 GO:0051187 GO:0055114
140.060.3736.230.050.643fahA GO:0009055 GO:0016491 GO:0033727 GO:0046872 GO:0051536 GO:0051537 GO:0055114
150.060.3186.900.050.613o04A GO:0003824 GO:0006633 GO:0008152 GO:0016740 GO:0016746 GO:0016747 GO:0033817
160.060.3686.300.050.641dgjA GO:0009055 GO:0016491 GO:0046872 GO:0051536 GO:0051537 GO:0055114
170.060.4505.690.080.722e1qA GO:0001933 GO:0001937 GO:0003824 GO:0004854 GO:0004855 GO:0005506 GO:0005576 GO:0005615 GO:0005737 GO:0005777 GO:0005829 GO:0006195 GO:0006919 GO:0007595 GO:0009055 GO:0009115 GO:0010629 GO:0016491 GO:0016529 GO:0016614 GO:0016903 GO:0030856 GO:0042803 GO:0043546 GO:0045602 GO:0046872 GO:0050660 GO:0051536 GO:0051537 GO:0051898 GO:0055114 GO:1900745 GO:1900747 GO:2000379 GO:2001213
180.060.3066.660.020.573wqoA GO:0003677 GO:0006281 GO:0008270


Consensus prediction of GO terms
 
Molecular Function GO:0004888 GO:0005515
GO-Score 0.48 0.37
Biological Processes GO:0019722 GO:0007417 GO:0060322 GO:0048513 GO:0048489 GO:0051962 GO:0099504 GO:0051130 GO:0099003 GO:0090128 GO:0017156 GO:0007269 GO:0098742
GO-Score 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0044444 GO:0031224 GO:0098793 GO:0099572 GO:0060076 GO:0097060 GO:0030427 GO:0043005 GO:0044463
GO-Score 0.47 0.46 0.37 0.37 0.37 0.37 0.37 0.37 0.37

(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.