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I-TASSER results for job id Rv0807

[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
10.08 4 3r1bC TB2 Rep, Mult 39,43
20.06 3 4jgxA PLM Rep, Mult 47,58,93,94,100,121
30.06 3 2ps1A PRP Rep, Mult 85,86,90,92,95,96,98,99
40.04 2 4ujwE MG Rep, Mult 41,42,45
50.04 2 1iktA OXN Rep, Mult 58,90,93,94,100,101,104,116,117,120,122
60.04 2 2c11A CU Rep, Mult 57,74
70.04 2 1uthB SCN Rep, Mult 48,51,52,56
80.04 2 3wqtD MG Rep, Mult 32,34
90.02 1 3l26B MG Rep, Mult 79,80
100.02 1 1lh0A ORO Rep, Mult 49,57,58,120
110.02 1 3bpxA SAL Rep, Mult 37,41
120.02 1 3ku4B SO4 Rep, Mult 113,114,115
130.02 1 3gyyB ZN Rep, Mult 86,89
140.02 1 1zkjA ZN Rep, Mult 34,74

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
10.0661c44A0.5613.250.1220.7292.3.1.176109
20.0601qcdA0.4764.680.0730.8302.4.2.748,85
30.0601f2dA0.4684.900.0500.8683.5.99.785,118
40.0603i58A0.5094.960.0960.9152.1.1.-NA
50.0601jlrA0.4744.080.0880.7602.4.2.9NA
60.0601o5oD0.4914.070.0850.7752.4.2.948,50,117
70.0601v9sB0.4704.250.0870.7602.4.2.967
80.0602qyoA0.4314.800.0240.7522.1.1.46NA
90.0603ezoA0.4684.140.0570.7362.3.1.39NA
100.0602ps1A0.5213.880.0530.8142.4.2.10NA
110.0601i5eB0.4963.940.0730.7442.4.2.948,117,123
120.0601kywC0.4784.640.0700.8612.1.1.68NA
130.0602p1zB0.5074.180.1390.8142.4.2.10NA
140.0601g2qA0.4853.920.1000.7602.4.2.7NA
150.0602e55A0.5014.190.0770.7752.4.2.9NA
160.0601xtvG0.4984.180.0970.7752.4.2.945,85
170.0601nt4A0.4713.950.0610.7053.1.3.1013,38,43
180.0602cuyA0.4784.110.0570.7362.3.1.39NA
190.0601lh0A0.5074.170.1180.8062.4.2.10NA
200.0602ehjA0.4874.200.0630.7602.4.2.995,103

(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
00.250.6243.580.120.903ssmB GO:0000287 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259 GO:0046872 GO:0051289 GO:0102302
10.230.6193.710.120.913ssoB GO:0000287 GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259 GO:0046872 GO:0051289 GO:0102302
20.120.5353.200.130.691iktA GO:0000038 GO:0001649 GO:0003857 GO:0005102 GO:0005739 GO:0005777 GO:0005778 GO:0005782 GO:0006629 GO:0006631 GO:0006635 GO:0006699 GO:0008209 GO:0008210 GO:0016020 GO:0016491 GO:0016508 GO:0016616 GO:0016829 GO:0016853 GO:0033540 GO:0033989 GO:0036109 GO:0036111 GO:0036112 GO:0042803 GO:0043231 GO:0044594 GO:0055114 GO:0060009
30.070.5954.180.080.902i00C GO:0008080 GO:0016740
40.070.5864.170.100.882hv2B GO:0008080
50.070.5774.410.100.893n7zB GO:0008080 GO:0016740
60.070.5704.300.090.885ebvA GO:0008080 GO:0016740 GO:0030649 GO:0034069 GO:0044119 GO:0044121 GO:0052035 GO:0052040 GO:0052164 GO:0052167
70.070.5634.450.080.902ozgA GO:0008080 GO:0016740
80.070.5444.330.090.874my0C GO:0008080 GO:0016740
90.070.5574.220.110.874qb9A GO:0008080
100.070.5613.250.120.731c44A GO:0003824 GO:0005737 GO:0005739 GO:0005777 GO:0006810 GO:0006869 GO:0008152 GO:0008289 GO:0016740 GO:0016746 GO:0016747 GO:0033814
110.070.5413.480.100.721pz4A
120.060.3904.930.050.664yzeA GO:0000976 GO:0003677 GO:0003700 GO:0005829 GO:0006351 GO:0006355 GO:0045892
130.060.3084.970.030.571tz9A GO:0006064 GO:0008927 GO:0016829
140.060.3155.540.030.663mjfA GO:0000166 GO:0000287 GO:0003824 GO:0004637 GO:0005524 GO:0006164 GO:0006189 GO:0009113 GO:0016874 GO:0030145 GO:0046872
150.060.3635.020.040.663ezsA GO:0003824 GO:0009058 GO:0030170
160.060.3404.970.030.634qusB GO:0004596 GO:0006474 GO:0008080 GO:0016740 GO:0016746 GO:0016747 GO:0031248
170.060.3394.890.050.602cy2A GO:0008080 GO:0016740
180.060.3464.740.030.604yr9A GO:0003824 GO:0005739 GO:0006567 GO:0008743 GO:0016491 GO:0019518 GO:0050662 GO:0055114
190.060.3535.000.130.673ec4A GO:0008080 GO:0016740 GO:0016747
200.060.3374.550.080.563a5zC GO:0000166 GO:0004812 GO:0004824 GO:0005524 GO:0005737 GO:0005829 GO:0006418 GO:0006430 GO:0016874 GO:0016880 GO:0043687 GO:0052868 GO:0071915 GO:0072581
210.060.3185.070.040.592ge3A GO:0008080 GO:0016740


Consensus prediction of GO terms
 
Molecular Function GO:0008171 GO:0000287 GO:0102302
GO-Score 0.42 0.42 0.42
Biological Processes GO:0051289 GO:0017000 GO:0032259
GO-Score 0.42 0.42 0.42
Cellular Component GO:0005739 GO:0005782 GO:0005778
GO-Score 0.12 0.12 0.12

(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.