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I-TASSER results for job id Rv3394c

[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
10.20 132 4f4xA NUC Rep, Mult 36,37,38,39,55,57,59,60,63,99,215,217,218,238,239,240,241,242,243,244,245,246,248,273,293,337,338,342
20.10 68 2alzA DCP Rep, Mult 12,13,14,15,16,41,42,45,48,54,102
30.06 48 3gijA NUC Rep, Mult 100,102,103,148,175,176,177,178,186,187,188,285,296,297,298,299,300,301,321,345
40.04 25 4jv0A NUC Rep, Mult 16,36,38,39,75,216,217,235,240,241,242,243,244,245,246,248,273,337,338,342
50.04 28 2au0B NUC Rep, Mult 41,42,54,55,102,103,176,178,186,188,191,218,294,295,296,297,298,299,301,345
60.03 23 2aslB NUC Rep, Mult 16,41,102,103,176,177,178,186,188,191,297,298,299,300,301
70.02 15 2w7oB CA Rep, Mult 12,13,14,102
80.01 5 3pvxA NUC Rep, Mult 16,73,75,216,217,235,240,241,242,243,244,245,273,295,342
90.01 10 3in5A MG Rep, Mult 172,174,177
100.01 5 3g6vA ATP Rep, Mult 13,14,15,16,36,41,42,45,48,54,55,102
110.01 8 1s0nA CA Rep, Mult 12,102,103,155
120.00 2 3khrA AF Rep, Mult 244,245,246,285,287,341,342
130.00 2 3gqcB NUC Rep, Mult 99,100,103,148,174,175,176,177,178,186,187,188,283,297,299
140.00 1 3khgB NUC Rep, Mult 176,178,187,188,294,296,297,298,299
150.00 1 3v6kJ CA Rep, Mult 91,92
160.00 1 3pw7A CA Rep, Mult 45,48,155
170.00 1 2ia6B BAP Rep, Mult 269,272,273
180.00 1 2w7oA CA Rep, Mult 12,151,152,155
190.00 1 3v6hA CA Rep, Mult 75,100,101
200.00 3 3ngdA NUC Rep, Mult 36,37,38,39,41,75,240,241,242,243,244,246,248,273,289

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
10.1483mr2A0.5653.190.1940.6362.7.7.742,49
20.0601h16A0.3327.810.0470.5542.3.1.54NA
30.0601kfyA0.2977.940.0340.5051.3.99.1158
40.0601mswD0.2807.500.0500.4542.7.7.6NA
50.0602r8jA0.5134.370.1440.6322.7.7.713,41,48,54
60.0601jnrA0.3198.080.0560.5451.8.99.2NA
70.0601cgtA0.2967.110.0240.4652.4.1.19NA
80.0602oh2B0.5982.150.1590.6322.7.7.770
90.0603bq1A0.4904.140.1160.5732.7.7.748,55
100.0602imwP0.5882.370.1300.6262.7.7.751,55
110.0601bxrA0.3167.380.0530.4996.3.5.5143
120.0601a47A0.2797.270.0330.4422.4.1.19483
130.0601lwdA0.3076.450.0390.4461.1.1.42190
140.0601t3nA0.5483.120.1650.6212.7.7.748
150.0601d7fA0.2966.870.0350.4542.4.1.19NA
160.0601s76D0.2697.690.0440.4542.7.7.6NA
170.0601n1hA0.2978.140.0390.5122.7.7.48NA
180.0609cgtA0.2986.860.0270.4542.4.1.1987,122,130
190.0603cirM0.2757.690.0400.4591.3.99.1NA
200.0601kf6A0.3147.890.0620.5291.3.99.1NA

(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
00.250.5822.070.140.614f4zA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
10.220.4413.170.130.483fdsA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
20.200.5663.330.190.644ecwA GO:0000731 GO:0003677 GO:0003684 GO:0003887 GO:0005634 GO:0005654 GO:0005737 GO:0006260 GO:0006281 GO:0006282 GO:0006290 GO:0006301 GO:0006974 GO:0010225 GO:0016740 GO:0016779 GO:0019985 GO:0046872 GO:0070987 GO:0071494 GO:0071897
30.190.6121.210.170.625c5jA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
40.180.5952.330.160.633pzpB GO:0003677 GO:0003684 GO:0003887 GO:0005634 GO:0005654 GO:0006260 GO:0006281 GO:0006283 GO:0006296 GO:0006297 GO:0006974 GO:0016740 GO:0016779 GO:0019985 GO:0033683 GO:0042276 GO:0043231 GO:0046872 GO:0071897
50.170.6071.110.170.624r8uB GO:0000287 GO:0000731 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0009432 GO:0016740 GO:0016779 GO:0019985 GO:0046872
60.160.5483.730.150.643ohaA GO:0003677 GO:0003684 GO:0003887 GO:0005634 GO:0005657 GO:0005739 GO:0006260 GO:0006281 GO:0006974 GO:0007059 GO:0007064 GO:0016740 GO:0016779 GO:0042276 GO:0046872 GO:0070987 GO:0071897
70.150.5483.120.170.621t3nA GO:0003677 GO:0003684 GO:0003887 GO:0005622 GO:0005634 GO:0005654 GO:0006260 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0019985 GO:0042276 GO:0043231 GO:0046872 GO:0071897
80.150.5662.920.150.633gqcB GO:0003677 GO:0003684 GO:0005634 GO:0005654 GO:0006260 GO:0006281 GO:0006974 GO:0009411 GO:0016740 GO:0016779 GO:0017125 GO:0019985 GO:0042276 GO:0046872 GO:0071897
90.150.5792.300.140.624f4wA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
100.100.4904.140.120.573bq1A GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
110.080.5423.650.100.632aq4A GO:0000790 GO:0003677 GO:0003684 GO:0003887 GO:0005634 GO:0005657 GO:0005739 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0017125 GO:0042276 GO:0046872 GO:0070987 GO:0071897
120.060.4212.960.130.451t94A GO:0003677 GO:0003684 GO:0003887 GO:0005634 GO:0005654 GO:0006260 GO:0006281 GO:0006283 GO:0006296 GO:0006297 GO:0006974 GO:0016740 GO:0016779 GO:0019985 GO:0033683 GO:0042276 GO:0043231 GO:0046872 GO:0071897
130.060.4022.010.220.424dezA GO:0000287 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0016740 GO:0016779 GO:0046872 GO:0071897
140.060.2437.720.050.402y51A GO:0000166 GO:0008152 GO:0016491 GO:0016620 GO:0055114
150.060.2537.690.020.421s48A GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004175 GO:0004197 GO:0004252 GO:0004386 GO:0005216 GO:0005524 GO:0006508 GO:0006810 GO:0006811 GO:0008026 GO:0008233 GO:0008234 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019062 GO:0019079 GO:0019082 GO:0030430 GO:0030683 GO:0033644 GO:0033650 GO:0033897 GO:0034220 GO:0039503 GO:0039520 GO:0039548 GO:0039654 GO:0039663 GO:0039694 GO:0039707 GO:0042025 GO:0044161 GO:0044177 GO:0044228 GO:0044385 GO:0046718 GO:0051259 GO:0055036 GO:0070008 GO:0075509 GO:0075512 GO:0090502
160.060.2448.090.030.422cjqA GO:0000166 GO:0001172 GO:0003723 GO:0003968 GO:0004175 GO:0004197 GO:0004252 GO:0004386 GO:0005216 GO:0005524 GO:0006508 GO:0006810 GO:0006811 GO:0008026 GO:0008233 GO:0008234 GO:0008236 GO:0016020 GO:0016021 GO:0016032 GO:0016740 GO:0016779 GO:0016787 GO:0016817 GO:0017111 GO:0019012 GO:0019062 GO:0019079 GO:0019082 GO:0030683 GO:0033644 GO:0033897 GO:0034220 GO:0039503 GO:0039520 GO:0039548 GO:0039654 GO:0039663 GO:0039694 GO:0039707 GO:0044228 GO:0044385 GO:0046718 GO:0051259 GO:0055036 GO:0070008 GO:0075509 GO:0075512 GO:0090502
170.060.1912.070.120.201unnD GO:0000287 GO:0000731 GO:0003677 GO:0003684 GO:0003887 GO:0005737 GO:0006260 GO:0006261 GO:0006281 GO:0006974 GO:0009432 GO:0016740 GO:0016779 GO:0019985 GO:0046872
180.060.1837.200.050.293l0gC GO:0003824 GO:0004514 GO:0009435 GO:0016740 GO:0016757 GO:0016763 GO:0019363


Consensus prediction of GO terms
 
Molecular Function GO:0003684 GO:0003887 GO:0000287
GO-Score 0.69 0.69 0.53
Biological Processes GO:0006261 GO:0010225 GO:0034644 GO:0051052 GO:2001020 GO:0033683 GO:0019985
GO-Score 0.53 0.41 0.41 0.41 0.41 0.35 0.35
Cellular Component GO:0005737 GO:0005654
GO-Score 0.62 0.35

(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.