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I-TASSER results for job id Rv2012

[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 4 5lczB GSH Rep, Mult 30,54
20.04 2 3rszB GLC Rep, Mult 18,19
30.02 1 3wmoS BCL Rep, Mult 25,36
40.02 1 2h2sB SEK Rep, Mult 56,57,58
50.02 1 1gsaA MG Rep, Mult 132,150
60.02 1 2a68C MG Rep, Mult 112,150
70.02 1 3wmn1 CRT Rep, Mult 25,29
80.02 1 3jskD AHZ Rep, Mult 94,96
90.02 1 2j8rA AZI Rep, Mult 53,133
100.02 1 2no5A CNR Rep, Mult 10,13
110.02 1 3k0aA MG Rep, Mult 20,150
120.02 1 4h0dA MN Rep, Mult 150,151
130.02 1 1aiiA ETA Rep, Mult 110,112
140.02 1 2h2sA SEK Rep, Mult 49,52,71
150.02 1 1cq1A CA Rep, Mult 58,76,77
160.02 1 1jgwH CDL Rep, Mult 125,129
170.02 1 1r9jA TPP Rep, Mult 96,97,126
180.02 1 1bjyA CTC Rep, Mult 100,104
190.02 1 2obeC 2HP Rep, Mult 139,140

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
10.0602e6kA0.4305.600.0980.8172.2.1.1NA
20.0602noxB0.4284.850.0630.6581.13.11.1148,68
30.0601of6C0.4344.750.0460.6892.5.1.54NA
40.0602qtcB0.4395.770.0720.8421.2.4.1NA
50.0603dwcB0.4344.560.0790.6773.4.17.19NA
60.0602tysB0.4394.860.0880.7264.2.1.20NA
70.0601j38A0.4894.530.0630.7743.4.15.126,29
80.0603hhsA0.4265.030.0500.7441.14.18.1NA
90.0601g5aA0.4275.170.0630.7442.4.1.4NA
100.0601l5jA0.4255.450.0660.7384.2.1.3NA
110.0602gi3A0.4465.250.0400.7626.3.5.-121
120.0603a2pA0.4405.160.0920.7563.5.2.12NA
130.0602g25A0.4365.440.0410.8111.2.4.1NA
140.0601r9jB0.4515.570.0680.8542.2.1.1NA
150.0601j36A0.4854.720.0680.7933.4.15.190
160.0601v8zB0.4374.950.0680.7384.2.1.20NA
170.0601s46A0.3995.650.0770.7682.4.1.4NA
180.0602jgdA0.4265.910.0730.8601.2.4.2NA
190.0602o36A0.4435.020.0620.7383.4.24.15134

(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
00.070.4655.200.050.804f4fA GO:0004795 GO:0006520 GO:0016829 GO:0030170
10.060.3924.260.050.574aa1A GO:0004180 GO:0005576 GO:0005615 GO:0006508 GO:0007289 GO:0007291 GO:0007552 GO:0008233 GO:0008237 GO:0008241 GO:0008270 GO:0009609 GO:0016020 GO:0016787 GO:0046872
20.060.4255.040.070.743wkyA GO:0008152 GO:0016491 GO:0046872 GO:0055114
30.060.4604.770.060.763bkkA GO:0001822 GO:0001974 GO:0002003 GO:0002005 GO:0002019 GO:0002446 GO:0002474 GO:0003081 GO:0003779 GO:0004175 GO:0004180 GO:0005576 GO:0005615 GO:0005737 GO:0005764 GO:0005768 GO:0005886 GO:0006508 GO:0007283 GO:0008144 GO:0008217 GO:0008233 GO:0008237 GO:0008238 GO:0008240 GO:0008241 GO:0008270 GO:0009897 GO:0014910 GO:0016020 GO:0016021 GO:0016787 GO:0019229 GO:0031404 GO:0031434 GO:0031711 GO:0032943 GO:0042312 GO:0042447 GO:0043171 GO:0046872 GO:0050435 GO:0050482 GO:0051019 GO:0060047 GO:0060177 GO:0060218 GO:0061098 GO:0070062 GO:0070573 GO:0071838 GO:1900086 GO:1902033 GO:1903597 GO:2000170
40.060.3275.430.030.585am8D GO:0001822 GO:0001974 GO:0002003 GO:0002005 GO:0002019 GO:0002446 GO:0002474 GO:0003081 GO:0003779 GO:0004175 GO:0004180 GO:0005576 GO:0005615 GO:0005737 GO:0005764 GO:0005768 GO:0005886 GO:0006508 GO:0007283 GO:0008144 GO:0008217 GO:0008233 GO:0008237 GO:0008238 GO:0008240 GO:0008241 GO:0008270 GO:0009897 GO:0014910 GO:0016020 GO:0016021 GO:0016787 GO:0019229 GO:0031404 GO:0031434 GO:0031711 GO:0032943 GO:0042312 GO:0042447 GO:0043171 GO:0046872 GO:0050435 GO:0050482 GO:0051019 GO:0060047 GO:0060177 GO:0060218 GO:0061098 GO:0070062 GO:0070573 GO:0071838 GO:1900086 GO:1902033 GO:1903597 GO:2000170
50.060.3315.520.010.611m98A GO:0005622 GO:0006810 GO:0007165 GO:0009579 GO:0009881 GO:0016020 GO:0016037 GO:0018298 GO:0030089 GO:0031404 GO:0042651 GO:0050896
60.060.4344.560.080.683dwcB GO:0004180 GO:0004181 GO:0006508 GO:0016787
70.060.3384.700.020.512ajfA GO:0001618 GO:0001817 GO:0001948 GO:0002003 GO:0002005 GO:0003051 GO:0003081 GO:0004175 GO:0004180 GO:0004181 GO:0005576 GO:0005615 GO:0005737 GO:0005886 GO:0006508 GO:0008233 GO:0008237 GO:0008241 GO:0008270 GO:0009986 GO:0015827 GO:0016020 GO:0016021 GO:0016032 GO:0016787 GO:0019229 GO:0032800 GO:0042127 GO:0042312 GO:0045121 GO:0046718 GO:0046813 GO:0046872 GO:0050727 GO:0060452 GO:0070062 GO:1903598 GO:1903779 GO:2000379
80.060.4764.940.060.791kl7A GO:0004795 GO:0006520 GO:0008652 GO:0009088 GO:0016829 GO:0030170
90.060.3235.760.050.633i58A GO:0008168 GO:0008171 GO:0016740 GO:0017000 GO:0032259
100.060.3175.260.040.573oekA GO:0004872 GO:0004970 GO:0004972 GO:0005216 GO:0005234 GO:0005261 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0016020 GO:0016021 GO:0016595 GO:0017146 GO:0022843 GO:0030054 GO:0034220 GO:0034765 GO:0035235 GO:0035249 GO:0042165 GO:0045202 GO:0045211 GO:0098655
110.060.2885.930.050.572rjqA GO:0004222 GO:0005178 GO:0005576 GO:0005578 GO:0005615 GO:0005788 GO:0006508 GO:0008201 GO:0008233 GO:0008237 GO:0008270 GO:0016787 GO:0022617 GO:0031012 GO:0036066 GO:0042742 GO:0046872 GO:0050840
120.060.3015.150.050.514pacA GO:0000160 GO:0004871 GO:0005634 GO:0005737 GO:0005829 GO:0009736 GO:0009927 GO:0016310 GO:0043424
130.060.3175.650.020.593hwcA GO:0004497 GO:0008152 GO:0016491 GO:0016627 GO:0016712 GO:0019439 GO:0051289 GO:0055114
140.060.3075.420.040.563oenA GO:0004872 GO:0004970 GO:0004972 GO:0005216 GO:0005234 GO:0005261 GO:0005886 GO:0006810 GO:0006811 GO:0008328 GO:0016020 GO:0016021 GO:0016595 GO:0017146 GO:0022843 GO:0030054 GO:0034220 GO:0034765 GO:0035235 GO:0035249 GO:0042165 GO:0045202 GO:0045211 GO:0098655
150.060.2984.710.060.485ijhB GO:0000822 GO:0001618 GO:0004872 GO:0004888 GO:0004930 GO:0005794 GO:0005886 GO:0007186 GO:0009615 GO:0015114 GO:0015562 GO:0016020 GO:0016021 GO:0030643 GO:0031226 GO:0035435 GO:0046718
160.060.2885.760.050.543dtnA GO:0046872
170.060.3025.970.050.624hhzD GO:0000122 GO:0000715 GO:0000717 GO:0000724 GO:0000784 GO:0003677 GO:0003910 GO:0003950 GO:0005634 GO:0005635 GO:0005654 GO:0005667 GO:0005730 GO:0005739 GO:0006273 GO:0006281 GO:0006293 GO:0006294 GO:0006295 GO:0006296 GO:0006302 GO:0006351 GO:0006355 GO:0006366 GO:0006471 GO:0006974 GO:0007005 GO:0007179 GO:0008134 GO:0008270 GO:0010613 GO:0016020 GO:0016540 GO:0016740 GO:0016757 GO:0016925 GO:0019899 GO:0019901 GO:0023019 GO:0030225 GO:0032042 GO:0032869 GO:0033683 GO:0034599 GO:0036211 GO:0042769 GO:0042802 GO:0042826 GO:0043234 GO:0043504 GO:0044822 GO:0045944 GO:0046872 GO:0047485 GO:0051103 GO:0051287 GO:0060391 GO:0070212 GO:0070412 GO:0070911 GO:1903827 GO:1904357 GO:2000679
180.060.3565.930.020.713kv4A GO:0000082 GO:0003682 GO:0005506 GO:0005634 GO:0005654 GO:0005730 GO:0006351 GO:0006355 GO:0007049 GO:0007420 GO:0008270 GO:0016491 GO:0016568 GO:0016706 GO:0031965 GO:0032452 GO:0032454 GO:0033169 GO:0035064 GO:0035574 GO:0035575 GO:0045893 GO:0045943 GO:0046872 GO:0051213 GO:0051864 GO:0055114 GO:0061188 GO:0070544 GO:0071557 GO:0071558


Consensus prediction of GO terms
 
Molecular Function GO:0046914 GO:0008238
GO-Score 0.36 0.36
Biological Processes GO:0019538
GO-Score 0.36
Cellular Component GO:0044421
GO-Score 0.36

(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.