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I-TASSER results for job id Rv1972

[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
10.17 9 3ov4B EQU Rep, Mult 80,86,113,152,154,156,167,171,187,191
20.06 3 1jn5B III Rep, Mult 141,142,143,145,146,147,175,176,177,182
30.04 2 3fkaC UNL Rep, Mult 80,84,152,169,171,187
40.04 2 1a2k0 III Rep, Mult 134,136,138,139,140,141,142,143,147,149,151,152,153,168,170,172,174,176,185,186,187,188,190
50.04 2 4fcmA III Rep, Mult 71,72,75,76,79,100,102,180,181,182,183
60.04 2 2fhyA A37 Rep, Mult 104,105
70.02 1 1bt0A ZN Rep, Mult 171,186
80.02 1 1nr5B CO Rep, Mult 98,105
90.02 1 3oa0B HP7 Rep, Mult 137,138
100.02 1 2vn9A GVD Rep, Mult 136,137,138,150,170,172,190
110.02 1 2wlzA PEG Rep, Mult 86,87,89,187
120.02 1 1nh2C NUC Rep, Mult 181,183

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
10.1121hkxA0.5043.110.0660.6392.7.11.1779
20.0662ux0A0.4963.390.0890.6442.7.11.17NA
30.0604stdA0.4873.060.0760.6234.2.1.9488
40.0601yiqA0.4364.900.0560.6651.1.99.-NA
50.0601jrpB0.4444.780.0400.7231.17.1.4116
60.0603e99A0.4593.320.1040.5921.14.12.1088
70.0601rsrB0.4585.140.0300.7541.17.4.1NA
80.0601e3vB0.4473.100.0660.5505.3.3.1NA
90.0601jroB0.4515.080.0400.7491.1.1.204NA
100.0608choA0.4462.800.1070.5395.3.3.1103,183
110.0601biqB0.4615.250.0300.7591.17.4.1118
120.0601kb0A0.4384.250.0480.6281.1.99.-NA
130.0601nu3B0.4333.470.0680.5653.3.2.8148
140.0601lrwC0.4384.420.0570.6491.1.99.888,157
150.0602vuxB0.3765.080.0620.6281.17.4.1NA
160.0603czoB0.4135.500.0540.7174.3.1.3111
170.0603b9jI0.3155.480.0530.5391.17.1.4,1.17.3.2145
180.0601t3qB0.4545.060.0630.7641.3.99.17NA
190.0601h0nA0.4394.930.0560.7071.17.4.1NA
200.0603b9jJ0.4764.490.0300.7021.17.1.4,1.17.3.2131,133
210.0601buqA0.4412.700.0980.5345.3.3.1111

(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
00.170.5612.120.110.634o3vB GO:0016020 GO:0016021
10.130.5252.740.180.634jf8A GO:0016020 GO:0016021 GO:0030255
20.120.5322.690.170.634akzA GO:0005886 GO:0009405 GO:0016020 GO:0016021 GO:0030255 GO:0042802
30.110.5292.260.140.614meiA GO:0016020 GO:0030255
40.100.5612.270.160.643wz4G GO:0016020 GO:0016021
50.090.5322.660.130.634lsoA GO:0005886 GO:0006810 GO:0009405 GO:0016020 GO:0016021 GO:0030255
60.090.5592.300.070.642cc3A GO:0005886 GO:0016020 GO:0016021 GO:0030255 GO:0042802 GO:0043684
70.090.5262.630.140.634nhfA GO:0016020 GO:0016021 GO:0030255
80.080.4963.390.090.642ux0A GO:0000082 GO:0000165 GO:0000166 GO:0004672 GO:0004674 GO:0004683 GO:0004723 GO:0005088 GO:0005516 GO:0005524 GO:0005654 GO:0005829 GO:0005886 GO:0006468 GO:0006470 GO:0006816 GO:0007275 GO:0007399 GO:0014733 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0030073 GO:0030154 GO:0030666 GO:0033017 GO:0042803 GO:0043547 GO:0046777 GO:0051259 GO:0051924 GO:0060333 GO:0097481 GO:1900034 GO:1901897
90.070.5623.650.060.774xzzA GO:0016740
100.070.4783.050.080.612w2cH GO:0000082 GO:0000165 GO:0000166 GO:0001558 GO:0001666 GO:0002026 GO:0002028 GO:0003254 GO:0004672 GO:0004674 GO:0004683 GO:0005088 GO:0005516 GO:0005524 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0005886 GO:0006357 GO:0006468 GO:0006816 GO:0008016 GO:0010389 GO:0010613 GO:0010649 GO:0010666 GO:0010880 GO:0010881 GO:0014704 GO:0014911 GO:0016020 GO:0016301 GO:0016310 GO:0016529 GO:0016740 GO:0018105 GO:0018107 GO:0019871 GO:0030007 GO:0030315 GO:0030666 GO:0031432 GO:0031594 GO:0032469 GO:0033017 GO:0034704 GO:0035022 GO:0042383 GO:0042803 GO:0043025 GO:0043194 GO:0043234 GO:0043547 GO:0044325 GO:0046777 GO:0048471 GO:0048661 GO:0050998 GO:0051259 GO:0055119 GO:0060048 GO:0060314 GO:0060333 GO:0060341 GO:0061049 GO:0070374 GO:0071277 GO:0086003 GO:0086091 GO:0098901 GO:0098909 GO:1900034 GO:1901725 GO:1901844 GO:1901897 GO:1902306 GO:1902514 GO:2000650
110.060.4422.910.070.553b7cA GO:0004067 GO:0016787
120.060.2705.990.070.494xhrA GO:0005739 GO:0005743 GO:0005758 GO:0006810 GO:0006869 GO:0008289 GO:0015914 GO:0016020 GO:0031314 GO:0032048 GO:1990050 GO:2001247
130.060.2945.010.060.462ws2A GO:0016740
140.060.3215.000.050.521x9qA
150.060.2155.890.040.403cxdH
160.060.2355.470.080.411ck0H
170.060.2435.740.080.451lo0H GO:0001788 GO:0001798 GO:0001812 GO:0002455 GO:0003823 GO:0005771 GO:0005829 GO:0005886 GO:0006910 GO:0006911 GO:0006958 GO:0008333 GO:0009897 GO:0016020 GO:0016021 GO:0016064 GO:0019882 GO:0030162 GO:0034987 GO:0042571 GO:0042742 GO:0045022 GO:0045087 GO:0045807 GO:0050766 GO:0050778 GO:0050853 GO:0050871 GO:0072562
180.060.2445.390.020.412ojzH


Consensus prediction of GO terms
 
Molecular Function GO:0042802
GO-Score 0.12
Biological Processes GO:0030255
GO-Score 0.31
Cellular Component GO:0016021
GO-Score 0.43

(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.