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I-TASSER results for job id Rv0612

[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 6 1f59B III Rep, Mult 125,126,129,130,169,170,171,172,175,176
20.06 2 4a8yA ATP Rep, Mult 116,118,166
30.03 1 1izcA MG Rep, Mult 139,168
40.03 1 3a68A CA Rep, Mult 63,66
50.03 1 5jreH ADE Rep, Mult 46,47,99
60.03 1 3mqyA NUC Rep, Mult 118,119
70.03 1 3dhdA POP Rep, Mult 56,140
80.03 1 2ia5A SO4 Rep, Mult 18,19,22,23,27,28,116
90.03 1 3rl3A MN Rep, Mult 160,162
100.03 1 1q9xA CA Rep, Mult 140,146
110.03 1 3ihiB SO4 Rep, Mult 151,165

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
10.0661ujkB0.4713.690.0530.6523.4.23.4649,93
20.0602eabA0.5595.070.0630.8763.2.1.63NA
30.0601rw9A0.5214.620.0530.7964.2.2.5NA
40.0601w6jA0.5164.890.0700.8215.4.99.7NA
50.0601fo2A0.5095.000.0580.8063.2.1.113127,175
60.0602d0tB0.5003.990.0610.6871.13.11.52109,156
70.0601ug9A0.5114.930.1030.7913.2.1.7066
80.0601f1sA0.5354.700.0620.8314.2.2.1NA
90.0602q1fA0.5464.640.0510.8064.2.2.21NA
100.0602noxB0.5223.570.0720.6871.13.11.11NA
110.0601nxcA0.5245.010.0610.8413.2.1.11345
120.0602jg0A0.5175.010.0530.8063.2.1.28150,159
130.0603dsxA0.5154.210.0510.7562.5.1.60NA
140.0602qnoA0.5065.090.0660.8013.2.1.421
150.0601gaiA0.5145.380.0670.8563.2.1.3NA
160.0603ebgA0.5334.280.0360.7663.4.11.-NA
170.0602vn7A0.5124.920.0990.7963.2.1.3141,150
180.0603e08A0.5163.570.0720.6771.13.11.1150
190.0603evhA0.5583.700.0450.7564.2.2.3NA
200.0601hcuB0.4994.950.0530.7963.2.1.113NA

(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
00.140.5984.510.060.894bsmA GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005215 GO:0005487 GO:0005634 GO:0005635 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0007062 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0016032 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0043488 GO:0046825 GO:0051028 GO:0075733
10.140.6244.270.070.914uvkA GO:0000755 GO:0003682 GO:0005634 GO:0005829 GO:0006473 GO:0007064 GO:0009847 GO:0031505 GO:0031618 GO:0031934 GO:0034990 GO:1990707
20.110.6653.870.090.913gb8A GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005215 GO:0005487 GO:0005634 GO:0005635 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0007062 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0016032 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0043488 GO:0046825 GO:0051028 GO:0075733
30.110.6833.570.070.915difC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
40.100.6813.560.070.913wyfC GO:0000055 GO:0000776 GO:0005634 GO:0005737 GO:0005816 GO:0006406 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0034501 GO:0048471
50.090.6663.730.060.905dlqB GO:0005049 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0046827
60.080.6743.800.100.943a6pA GO:0000049 GO:0003723 GO:0003729 GO:0005634 GO:0005654 GO:0005737 GO:0005829 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0015031 GO:0031047 GO:0035281 GO:0042565 GO:0044822 GO:0070883 GO:0090631 GO:1900370
70.070.6563.810.050.925dlqA GO:0005049 GO:0005634 GO:0005643 GO:0005654 GO:0005737 GO:0006611 GO:0006810 GO:0008536 GO:0015031 GO:0046827
80.070.6154.420.060.913zjyE GO:0005634 GO:0005737 GO:0006606 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0031965
90.070.5604.070.070.804jlqA GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
100.070.6103.600.070.821qbkB GO:0000059 GO:0000060 GO:0005634 GO:0005737 GO:0005829 GO:0006607 GO:0006610 GO:0006810 GO:0006886 GO:0008139 GO:0008536 GO:0008565 GO:0015031 GO:0016032 GO:0031965 GO:0034399 GO:0043488 GO:0044822 GO:0070062 GO:0072372
110.070.6623.990.060.953gjxA GO:0000055 GO:0000056 GO:0000122 GO:0000776 GO:0003723 GO:0005487 GO:0005634 GO:0005642 GO:0005654 GO:0005730 GO:0005737 GO:0006611 GO:0006810 GO:0006886 GO:0008536 GO:0008565 GO:0010824 GO:0015030 GO:0015031 GO:0016020 GO:0019904 GO:0030529 GO:0031965 GO:0034504 GO:0042176 GO:0042493 GO:0043231 GO:0046825 GO:0051028
120.070.4575.210.060.733l0oA GO:0000166 GO:0003676 GO:0003723 GO:0004386 GO:0005524 GO:0006351 GO:0006353 GO:0006355 GO:0008186 GO:0016787
130.060.4264.230.080.622y4uA GO:0004860 GO:0005737 GO:0005783 GO:0005788 GO:0005790 GO:0005829 GO:0006417 GO:0006986 GO:0016020 GO:0019901 GO:0031205 GO:0036494 GO:0036498 GO:0043066 GO:0051087 GO:0051603 GO:0051607 GO:0051787 GO:0070062 GO:0070417 GO:1903561 GO:1903912 GO:1904030
140.060.4375.260.050.723renA GO:0003824 GO:0004553 GO:0005975 GO:0016020 GO:0016021 GO:0016787
150.060.3725.630.080.654upkA GO:0003824 GO:0006793 GO:0008152 GO:0008484 GO:0016787 GO:0042578
160.060.3375.600.070.594p7kA GO:0000287 GO:0005737 GO:0005739 GO:0005829 GO:0005886 GO:0006584 GO:0007565 GO:0007612 GO:0007614 GO:0008168 GO:0008171 GO:0008210 GO:0009712 GO:0014070 GO:0016020 GO:0016021 GO:0016036 GO:0016206 GO:0016740 GO:0030424 GO:0030425 GO:0032259 GO:0032496 GO:0032502 GO:0035814 GO:0042135 GO:0042417 GO:0042420 GO:0042493 GO:0043197 GO:0044297 GO:0045211 GO:0045963 GO:0046498 GO:0046500 GO:0046872 GO:0048265 GO:0048609 GO:0048662 GO:0050668 GO:0051930 GO:0070062
170.060.3844.180.130.541n0rA
180.060.3546.080.060.672j42A GO:0005576 GO:0009405 GO:0051260


Consensus prediction of GO terms
 
Molecular Function GO:0003676 GO:0008536 GO:0008565
GO-Score 0.46 0.38 0.38
Biological Processes GO:0006357 GO:0046822 GO:0051298 GO:0009894 GO:0030163 GO:0042221 GO:0000819 GO:0019058 GO:0046605 GO:1902583 GO:0051246 GO:0033157 GO:0046794 GO:0043487 GO:0045892 GO:0071427 GO:0071459 GO:0006405 GO:0006611 GO:0000055
GO-Score 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.39 0.39 0.39 0.38 0.38
Cellular Component GO:0042175 GO:0005635 GO:0031090 GO:1990904 GO:0098589 GO:0016604 GO:0000922 GO:0005815 GO:0000776 GO:0005829
GO-Score 0.46 0.46 0.46 0.46 0.46 0.46 0.39 0.39 0.38 0.34

(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.