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I-TASSER results for job id Rv0259c

[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
10.09 5 2xvyA CO Rep, Mult 8,40,70
20.07 4 2xvzA HEM Rep, Mult 67,72,75,91,127,128,130
30.07 4 2xwqA SIR Rep, Mult 123,124,125,126,156,157,187,188,191,192,193
40.05 3 2xwpA SIR Rep, Mult 8,40,41,64,65,66,68,70,123,124,125,187,188,189,196
50.04 2 2qd1D PP9 Rep, Mult 21,22,25,209
60.04 2 2xvxA HEM Rep, Mult 67,73,76,77,80,129
70.02 1 2z0aD GLY Rep, Mult 225,229
80.02 1 2jh3B SF4 Rep, Mult 103,106,184,208,211,212,215
90.02 1 4nxaA XE Rep, Mult 93,99,103,209,215
100.02 1 4f8eA MG Rep, Mult 1,3,227
110.02 1 3p52A NO3 Rep, Mult 5,6,62,219
120.02 1 2fkaA CXS Rep, Mult 30,220,224
130.02 1 3eteD H3P Rep, Mult 140,141,143
140.02 1 2e85B CA Rep, Mult 106,109

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
10.2532c8jA0.7632.860.1020.9154.99.1.18
20.1951lbqA0.7752.900.0850.9354.99.1.18
30.1931qgoA0.7253.050.1600.8874.99.1.310,188
40.0601b3bE0.5405.180.0750.8541.4.1.398,219
50.0603etdA0.5735.030.0820.8781.4.1.3NA
60.0603k92A0.5595.260.0400.8701.4.1.2NA
70.0602j6iA0.5455.130.0640.8341.2.1.2NA
80.0601u9yC0.5743.820.1230.7572.7.6.1NA
90.0602fssA0.5485.150.0600.8341.2.1.2NA
100.0603k2qA0.5444.790.0720.8022.7.1.909
110.0601hrkA0.7763.030.0930.9434.99.1.1NA
120.0603h9uC0.5495.250.0690.8463.3.1.1NA
130.0603d64B0.5514.960.0710.8223.3.1.1NA
140.0601bgvA0.5525.260.0930.8751.4.1.2NA
150.0601dozA0.7612.810.1240.9114.99.1.18
160.0601dkrB0.5914.600.0770.8382.7.6.1NA
170.0601x15A0.5554.710.0980.8101.6.1.2NA
180.0602f48B0.5484.850.0820.8222.7.1.9011
190.0601bw9A0.5644.720.1060.8141.4.1.20NA
200.0601v8bC0.5495.260.0600.8463.3.1.1209
210.0601hrdA0.5185.520.0760.8541.4.1.220
220.0603hnoA0.5494.640.0990.7982.7.1.9011

(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
00.250.7753.040.090.943aqiA GO:0004325 GO:0005739 GO:0005743 GO:0005759 GO:0006091 GO:0006779 GO:0006783 GO:0008198 GO:0009416 GO:0010038 GO:0010288 GO:0016020 GO:0016829 GO:0017085 GO:0042493 GO:0045471 GO:0046501 GO:0046685 GO:0046872 GO:0051536 GO:0051537 GO:0051597 GO:0070541 GO:0071549
10.220.7482.880.180.902xvzA GO:0016829 GO:0016852 GO:0019251 GO:0020037 GO:0042597 GO:0046872 GO:0050897 GO:0051262 GO:0051266
20.220.7582.860.120.912ac2A GO:0004325 GO:0005737 GO:0006779 GO:0006783 GO:0016829 GO:0046872
30.210.7253.050.160.891qgoA GO:0006779 GO:0009236 GO:0016829 GO:0016852 GO:0019251 GO:0046872 GO:0046906 GO:0050897
40.170.3882.770.220.452dj5A GO:0009236 GO:0016829 GO:0016852 GO:0019251 GO:0046872 GO:0046906 GO:0050897
50.140.7632.860.100.922c8jA GO:0004325 GO:0005737 GO:0006779 GO:0006783 GO:0016829 GO:0046872
60.140.7752.900.090.941lbqA GO:0004325 GO:0005739 GO:0005743 GO:0006779 GO:0006783 GO:0016020 GO:0016829
70.120.3962.460.200.463lyhB GO:0009236 GO:0016852
80.070.4465.340.080.702iv7A GO:0008919 GO:0009103 GO:0009244 GO:0016740 GO:0016757
90.070.3005.690.060.494x6uA GO:0004806 GO:0016787 GO:0046872
100.060.4085.210.060.623ct4A GO:0004371 GO:0006071 GO:0016301 GO:0016310 GO:0016740 GO:0019563
110.060.4334.940.060.641c47A GO:0000287 GO:0004614 GO:0005737 GO:0005975 GO:0006006 GO:0016529 GO:0016853 GO:0016868 GO:0046872 GO:0071704
120.060.4085.320.040.624qlaA GO:0003824 GO:0005783 GO:0005789 GO:0016020 GO:0016021 GO:0016787 GO:0019439 GO:0031090 GO:0033961 GO:0043231
130.060.3665.190.040.553tbfC GO:0004360 GO:0005737 GO:0005975 GO:0006541 GO:0008483 GO:0016740 GO:0030246 GO:1901137
140.060.3936.150.060.682vr2A GO:0002058 GO:0002059 GO:0004157 GO:0005737 GO:0005829 GO:0006208 GO:0006210 GO:0006212 GO:0008270 GO:0016597 GO:0016787 GO:0016810 GO:0019482 GO:0019860 GO:0046135 GO:0046872 GO:0051219 GO:0051260 GO:0051289 GO:0070062
150.060.3435.560.040.574uhmA GO:0003824 GO:0008483 GO:0016740 GO:0030170
160.060.3635.150.070.553gemC GO:0016491 GO:0055114
170.060.2576.060.070.461fpsA GO:0004161 GO:0004337 GO:0005737 GO:0006629 GO:0006694 GO:0006695 GO:0008202 GO:0008203 GO:0008299 GO:0016126 GO:0016740 GO:0033384 GO:0045337 GO:0046872
180.060.3035.850.070.511gynA GO:0003824 GO:0004332 GO:0005618 GO:0005829 GO:0005886 GO:0005975 GO:0006094 GO:0006096 GO:0008270 GO:0016829 GO:0016832 GO:0046872
190.060.3375.110.050.511oquC GO:0004748 GO:0005971 GO:0006260 GO:0009186 GO:0009263 GO:0016491 GO:0046872 GO:0055114
200.060.2915.130.060.464m85A GO:0008080


Consensus prediction of GO terms
 
Molecular Function GO:0051536 GO:0005506 GO:0016852 GO:0050897 GO:0004325 GO:0046906
GO-Score 0.50 0.50 0.50 0.50 0.41 0.35
Biological Processes GO:1990267 GO:0009314 GO:0010035 GO:0009636 GO:0097305 GO:1901655 GO:0071548 GO:0071385 GO:0019251 GO:0051259 GO:0006783
GO-Score 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.45 0.41
Cellular Component GO:0031966 GO:0070013 GO:0019866
GO-Score 0.50 0.50 0.50

(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.