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I-TASSER results for job id Rv1950c

[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
10.11 125 4bpmA LVJ Rep, Mult 15,16,19,20,22,23,24
20.09 102 1i94T MG Rep, Mult 11,12,13,14,15,16
30.07 80 3mnnG MML Rep, Mult 28,31,32
40.07 84 2q7rA 3CS Rep, Mult 19,20,22,23,24,26
50.06 73 4f4sL EFO Rep, Mult 19,22,23,26,27,30
60.06 72 4i7zF OZ2 Rep, Mult 15,16,19,20
70.05 61 1dgcA NUC Rep, Mult 2,5,6,9,10,13
80.05 60 2dyrB TGL Rep, Mult 30,33,34,37,38
90.05 57 3wmoE BCL Rep, Mult 22,23,26,27,30,31,58
100.02 30 3eymB EYK Rep, Mult 14,17,18
110.00 1 1h6gA CA Rep, Mult 32,52
120.00 1 2w6dB CPL Rep, Mult 41,53,54,57
130.00 3 2xcrS RXV Rep, Mult 38,42,45,52
140.00 1 2yl4A 14Y Rep, Mult 37,40,41,44,50
150.00 2 3d6aA MG Rep, Mult 4,5
160.00 1 1e1cB DCA Rep, Mult 37,40

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
10.3593brtA0.5251.290.0510.6192.7.11.1016,20,24
20.2841wt6B0.6521.380.0750.7462.7.11.114,16,27
30.2262h8nA0.6541.640.0190.7463.5.1.9836
40.2253e7kH0.6511.720.0190.7622.7.11.122,29
50.2173brvC0.5071.960.0480.6032.7.11.1019
60.1722jwaA0.4902.020.0500.5712.7.10.16
70.1571xtcC0.5211.770.0450.6352.4.2.3626
80.1161k1fA0.5622.060.0850.6512.7.11.158
90.1031qleD0.5220.940.0540.5711.9.3.1NA
100.0841ybzA0.6122.680.0190.8095.4.99.5NA
110.0661cxzB0.6612.410.0480.8732.7.11.1345
120.0602fenD0.6992.480.0810.9685.5.1.236
130.0601c3cA0.7232.200.0650.9364.3.2.2NA
140.0601no3A0.7182.070.0650.9841.13.11.12NA
150.0601bucB0.6742.410.0500.9521.3.99.238,60
160.0602zr3B0.6992.360.0500.9526.1.1.11NA
170.0602uz5A0.3983.010.0710.6195.2.1.850,53
180.0601dcnB0.6852.560.0630.9684.3.2.1NA
190.0601q5nA0.6822.800.0790.9845.5.1.2NA
200.0601y2mB0.6852.550.1000.9524.3.1.24NA
210.0603d3lA0.7082.180.0160.9521.13.11.31NA
220.0601yisA0.7132.620.0950.9684.3.2.2NA
230.0602inrA0.6912.540.0320.9525.99.1.-NA
240.0601bucA0.6772.810.0480.9841.3.99.2NA
250.0602iukA0.7311.980.0480.9841.13.11.12NA
260.0601w27A0.7432.030.0660.9684.3.1.24NA
270.0602b5uA0.7512.460.0631.0003.1.-.-NA
280.0601jqiA0.6862.720.0320.9841.3.99.2NA
290.0603dy5A0.7112.380.0000.9841.13.11.40,4.2.1.92NA
300.0601rx0A0.6992.290.0330.9521.3.99.-57

(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
00.180.7732.000.131.001uruA GO:0005543 GO:0005737 GO:0005829 GO:0005886 GO:0006887 GO:0006897 GO:0006937 GO:0007269 GO:0008104 GO:0032154 GO:0042052 GO:0045202 GO:0045313 GO:0048488 GO:0098793
10.170.8141.540.030.954om3D GO:0000122 GO:0001106 GO:0005634 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006351 GO:0006355 GO:0007165 GO:0007275 GO:0008134 GO:0009887 GO:0010628 GO:0016055 GO:0030178 GO:0042802 GO:0043124 GO:0045892 GO:1904837 GO:2000811
20.160.7652.230.101.004atmA GO:0005086 GO:0005543 GO:0005737 GO:0005802 GO:0005856 GO:0006897 GO:0007268 GO:0008021 GO:0015629 GO:0016020 GO:0030054 GO:0030672 GO:0031256 GO:0031410 GO:0043547 GO:0045202
30.150.7952.110.050.981cz7D GO:0000022 GO:0000166 GO:0000212 GO:0001578 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005872 GO:0005874 GO:0007018 GO:0007049 GO:0007051 GO:0007052 GO:0007056 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008569 GO:0016887 GO:0030981 GO:0031534 GO:0032837 GO:0032888 GO:0042803 GO:0048471 GO:0051028 GO:0051297 GO:0051298 GO:0051301 GO:0051321 GO:0072687 GO:0090306 GO:0090307 GO:1901673 GO:1990498
40.140.8081.700.050.971f5nA GO:0000139 GO:0000166 GO:0002376 GO:0003779 GO:0003924 GO:0005525 GO:0005576 GO:0005737 GO:0005794 GO:0005829 GO:0005886 GO:0016020 GO:0016787 GO:0019899 GO:0019955 GO:0030507 GO:0042802 GO:0050848 GO:0050860 GO:0051607 GO:0051879 GO:0060333 GO:0070373 GO:1900025 GO:1900041 GO:1903076 GO:1903077
50.120.7702.040.081.004avmA GO:0001891 GO:0002102 GO:0005543 GO:0005737 GO:0005886 GO:0005938 GO:0006911 GO:0016020 GO:0030054 GO:0042995 GO:0060326 GO:0071800 GO:0097320
60.120.7342.380.070.943u06B GO:0000022 GO:0000166 GO:0000212 GO:0001578 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005813 GO:0005819 GO:0005829 GO:0005856 GO:0005871 GO:0005872 GO:0005874 GO:0007018 GO:0007049 GO:0007051 GO:0007052 GO:0007056 GO:0007059 GO:0007067 GO:0007100 GO:0008017 GO:0008569 GO:0016887 GO:0030981 GO:0031534 GO:0032837 GO:0032888 GO:0042803 GO:0048471 GO:0051028 GO:0051297 GO:0051298 GO:0051301 GO:0051321 GO:0072687 GO:0090306 GO:0090307 GO:1901673 GO:1990498
70.110.6722.620.080.985ca9A GO:0000166 GO:0003924 GO:0005525 GO:0005783 GO:0005789 GO:0007029 GO:0008645 GO:0009405 GO:0016020 GO:0016021 GO:0016787 GO:0035690
80.100.7992.080.051.001dg3A GO:0000139 GO:0000166 GO:0002376 GO:0003779 GO:0003924 GO:0005525 GO:0005576 GO:0005737 GO:0005794 GO:0005829 GO:0005886 GO:0016020 GO:0016787 GO:0019899 GO:0019955 GO:0030507 GO:0042802 GO:0050848 GO:0050860 GO:0051607 GO:0051879 GO:0060333 GO:0070373 GO:1900025 GO:1900041 GO:1903076 GO:1903077
90.100.6012.100.100.781jq0A GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
100.090.7702.060.101.002ficB GO:0005634 GO:0005737 GO:0006897 GO:0006997 GO:0007275 GO:0008283 GO:0015629 GO:0016020 GO:0016032 GO:0030018 GO:0030100 GO:0030154 GO:0030315 GO:0030424 GO:0031674 GO:0033268 GO:0042692 GO:0042802 GO:0043065 GO:0043194 GO:0045664 GO:0048156 GO:0048711 GO:0051015 GO:0060987 GO:0060988 GO:0070063 GO:0071156
110.080.6392.830.020.954etpA GO:0000166 GO:0000741 GO:0000742 GO:0000743 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005816 GO:0005856 GO:0005874 GO:0005881 GO:0007018 GO:0007049 GO:0007064 GO:0007067 GO:0007126 GO:0008017 GO:0008569 GO:0046982 GO:0051301 GO:0060236
120.070.6710.730.090.713k9aA
130.070.7022.380.050.902i1jA GO:0003779 GO:0005737 GO:0005856 GO:0008092 GO:0019898
140.070.7302.060.100.943wfvA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
150.070.5543.600.050.924idnB GO:0000137 GO:0000139 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0005783 GO:0005789 GO:0005794 GO:0007029 GO:0007409 GO:0016020 GO:0016021 GO:0016787 GO:0030424 GO:0042802 GO:0042995 GO:0051260
160.070.7152.110.040.861qbzA GO:0005198 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0020002 GO:0033644 GO:0039663 GO:0044174 GO:0044175 GO:0046718 GO:0055036
170.070.7222.120.050.981envA GO:0000122 GO:0000790 GO:0000978 GO:0000981 GO:0001080 GO:0001084 GO:0001135 GO:0001190 GO:0001191 GO:0002223 GO:0003677 GO:0003682 GO:0003700 GO:0005198 GO:0005634 GO:0005667 GO:0006351 GO:0006355 GO:0006366 GO:0008652 GO:0010691 GO:0016020 GO:0016021 GO:0016032 GO:0019012 GO:0019031 GO:0019062 GO:0019064 GO:0019082 GO:0020002 GO:0030683 GO:0033644 GO:0039654 GO:0039663 GO:0042802 GO:0043565 GO:0044174 GO:0044175 GO:0045899 GO:0046718 GO:0055036 GO:0060261 GO:0075509 GO:0075512 GO:1903833
180.070.4982.590.080.634ozqB GO:0000166 GO:0001558 GO:0003777 GO:0005524 GO:0005634 GO:0005737 GO:0005819 GO:0005856 GO:0005874 GO:0005886 GO:0007018 GO:0007019 GO:0007080 GO:0008017 GO:0008284 GO:0008574 GO:0010389 GO:0015631 GO:0016020 GO:0016887 GO:0019901 GO:0021685 GO:0021693 GO:0021695 GO:0021766 GO:0021772 GO:0021846 GO:0021987 GO:0030155 GO:0030165 GO:0030334 GO:0030496 GO:0031146 GO:0031641 GO:0032147 GO:0032467 GO:0032487 GO:0033624 GO:0034446 GO:0043066 GO:0043161 GO:0043523 GO:0043524 GO:0045184 GO:0051233 GO:0051301 GO:1902519 GO:1903047 GO:1903429 GO:2000045
190.070.4922.210.020.653b6vA GO:0000166 GO:0003774 GO:0003777 GO:0005524 GO:0005737 GO:0005829 GO:0005856 GO:0005871 GO:0005874 GO:0006890 GO:0007018 GO:0008017 GO:0016887 GO:0019886 GO:0072372 GO:0072384 GO:0097542
200.070.4143.000.040.604b2th GO:0000166 GO:0005524 GO:0005737 GO:0005832 GO:0006457 GO:0051082
210.070.4893.210.050.712owmA GO:0000166 GO:0003777 GO:0005524 GO:0005874 GO:0007018 GO:0008017 GO:0072383
220.070.4792.740.040.683cnzA GO:0000166 GO:0003777 GO:0003824 GO:0005524 GO:0005856 GO:0007018 GO:0008017 GO:0016491 GO:0055114
230.070.5082.060.020.673dcbA GO:0000166 GO:0003777 GO:0005524 GO:0005737 GO:0005856 GO:0005871 GO:0005874 GO:0007018 GO:0007052 GO:0007057 GO:0007143 GO:0008017 GO:0016887 GO:0031116 GO:0032837 GO:0045132 GO:0051010 GO:0051296


Consensus prediction of GO terms
 
Molecular Function GO:0005515 GO:1901265 GO:0036094 GO:0001191 GO:0003714 GO:0001104 GO:0005085 GO:0005543
GO-Score 0.58 0.54 0.54 0.35 0.35 0.35 0.31 0.31
Biological Processes GO:0099643 GO:0036465 GO:0006936 GO:0042052 GO:0072583 GO:0001505 GO:0090257 GO:0099531 GO:0044091 GO:0033036 GO:0006836 GO:0043122 GO:0006357 GO:0010604 GO:0045892 GO:0006461 GO:0043066 GO:0030111 GO:2000209 GO:1902532 GO:0051345 GO:0043087
GO-Score 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.31 0.31
Cellular Component GO:0043232 GO:0005829 GO:0097610 GO:0032155 GO:0031981 GO:0099501 GO:0044459 GO:0098791 GO:0008021 GO:0031252
GO-Score 0.56 0.51 0.36 0.36 0.35 0.31 0.31 0.31 0.31 0.31

(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.