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I-TASSER results for job id Rv0326

[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
10.37 18 3lhdD SAH Rep, Mult 5,6,7,10,33,35,36,50,52,53,85,113
20.04 2 3zkrG B4M Rep, Mult 80,81,82,147
30.02 1 3wmnA MQ8 Rep, Mult 70,74
40.02 1 1d2hC SAH Rep, Mult 5,6,7,10,32,33
50.02 1 4qjsU MG Rep, Mult 68,72
60.02 1 1yz30 III Rep, Mult 86,115,116,119,130,131

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
10.0671wznA0.7572.440.1160.8872.1.1.-NA
20.0673eppB0.7653.100.1730.9932.1.1.5630
30.0673bgdA0.7102.680.0830.8812.1.1.6757
40.0662fcaA0.6402.850.1130.8212.1.1.33NA
50.0662iftA0.6162.360.1070.7422.1.1.5269,75
60.0663e05D0.6152.750.1110.7752.1.1.13227
70.0661pjzA0.6073.310.1020.8282.1.1.672,10
80.0663ckkA0.5982.990.0950.7552.1.1.33NA
90.0661yzhB0.6193.030.1240.7882.1.1.33NA
100.0601ri5A0.7513.140.1610.9802.1.1.5633
110.0601xxlA0.7822.460.1510.9202.1.1.-NA
120.0601sqfA0.6642.780.0980.8152.1.1.-31
130.0602ex4A0.7252.400.1280.8812.1.1.-NA
140.0601l1eA0.7402.670.0940.9072.1.1.79NA
150.0603i58A0.6743.050.1570.8872.1.1.-NA
160.0601nt2A0.6452.810.0820.7812.1.1.-NA
170.0602h11B0.7132.590.0830.8742.1.1.67NA
180.0603dxxA0.6462.990.1290.8152.1.1.3363
190.0603g07A0.6492.930.1400.8152.1.1.-NA
200.0603ccfB0.7322.160.1460.8612.1.1.1445,50
210.0603hnrA0.6913.030.1180.8612.1.1.-NA
220.0601tw2B0.6913.180.1860.9272.1.1.-54
230.0602ip2A0.6572.890.1380.8612.1.1.-NA
240.0602opbB0.7472.720.1520.9142.1.1.285,38,50
250.0602frxA0.6712.830.1530.8152.1.1.-NA
260.0601tpyA0.7462.460.1080.9012.1.1.79NA
270.0603lccA0.7002.600.1280.8812.1.1.-NA
280.0601ri1A0.7533.220.1610.9872.1.1.565

(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
00.410.9290.970.160.972p8jB GO:0008152 GO:0008168 GO:0016740 GO:0032259
10.250.7872.320.110.921y8cA GO:0008168 GO:0016740 GO:0032259
20.230.7812.540.120.941bhjA 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
30.230.7421.750.170.835cm2Z 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
40.220.7852.430.170.921vl5A GO:0008152 GO:0008168 GO:0016740 GO:0032259
50.170.8462.310.150.973sm3A GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872
60.170.7832.320.150.912gluA GO:0005737 GO:0008152 GO:0008168 GO:0008757 GO:0016740 GO:0032259
70.170.7812.440.190.913busA GO:0008152 GO:0008168 GO:0016740 GO:0032259
80.160.7982.360.120.933d2lC GO:0008168 GO:0016740 GO:0032259
90.160.7712.340.200.904pneB GO:0008152 GO:0008168 GO:0016740 GO:0032259
100.150.7762.490.090.914iv8A GO:0000234 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
110.150.7692.390.200.911ve3B GO:0046872 GO:0051536 GO:0051539
120.150.7572.290.210.894htfB GO:0008033 GO:0008168 GO:0016740 GO:0032259
130.150.7752.360.170.914ineA GO:0000773 GO:0005737 GO:0006656 GO:0008152 GO:0008168 GO:0016740 GO:0032259 GO:0080101
140.150.7712.720.160.955je1A GO:0008168 GO:0016740 GO:0032259
150.140.7452.150.150.873ccfB GO:0008152 GO:0008168 GO:0016740 GO:0030798 GO:0032259
160.140.7742.390.110.903uj7A GO:0008168 GO:0016740 GO:0032259 GO:0046872 GO:0051536 GO:0051539
170.140.7572.440.120.891wznA
180.140.7272.270.080.854qdkA GO:0005737 GO:0008168 GO:0008757 GO:0015979 GO:0015995 GO:0016740 GO:0032259 GO:0036068 GO:0046406
190.140.7342.990.130.913kkzA GO:0046872 GO:0051536 GO:0051539
200.080.7042.520.190.852i6gB GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690
210.070.7252.470.170.872xvaA GO:0005737 GO:0005829 GO:0008168 GO:0008757 GO:0009636 GO:0016740 GO:0032259 GO:0046677 GO:0046690
220.070.7362.780.120.903e7pA GO:0046872 GO:0051536 GO:0051539
230.070.7302.440.090.873m70A GO:0005737 GO:0008168 GO:0008757 GO:0016740 GO:0032259 GO:0046690


Consensus prediction of GO terms
 
Molecular Function GO:0003723 GO:0008170 GO:0016597 GO:0051213 GO:0019842 GO:0008175 GO:0043177 GO:0005506 GO:0016705 GO:0072341 GO:0033218
GO-Score 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45
Biological Processes GO:0051260 GO:0051262 GO:0043603 GO:0006760 GO:0001510 GO:0009069 GO:0002097 GO:0006767 GO:0006520 GO:0006790 GO:0046128
GO-Score 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45
Cellular Component GO:0005829 GO:0005634
GO-Score 0.40 0.40

(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.