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I-TASSER results for job id Rv2128

[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
10.23 211 3uoic HEM Rep, Mult 23,26,27,30,49,53,56,57,59,60
20.07 68 2ceiA ZN Rep, Mult 22,55,58
30.05 56 3wmm7 CRT Rep, Mult 53,57,60,61
40.05 58 1s5lH CLA Rep, Mult 44,48,51,52,54,55
50.05 52 2rlfB RIM Rep, Mult 60,61,64
60.05 50 3wqjA 22B Rep, Mult 27,30,33,34,45,48,49,52,53
70.04 49 1pssL BCL Rep, Mult 43,46,47,50,51
80.04 45 3arcI CLA Rep, Mult 50,51,53,54,57,61
90.03 33 5e1uA RIR Rep, Mult 34,37,42,45,46,49
100.03 31 3wu2h RRX Rep, Mult 48,51,52,54,55,58,61
110.00 1 1dmrA O Rep, Mult 13,44
120.00 5 4xtnB MPG Rep, Mult 32,36,41,44,48
130.00 1 2fkwF BCL Rep, Mult 25,26

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
10.1801urfA0.6302.000.0630.7912.7.11.1327
20.1601fyjA0.5921.280.0200.6876.1.1.15,6.1.1.1725,50,60
30.1421yvwC0.7142.490.0300.8953.6.1.31NA
40.1143eabA0.6103.060.0480.9253.6.4.3NA
50.1132a7wK0.7052.570.0620.8813.6.1.3130
60.0671yxbG0.6592.580.0940.8513.6.1.3130,34,56,62
70.0601syyA0.6652.850.0600.9401.17.4.1NA
80.0602zufA0.6663.140.0460.9706.1.1.19NA
90.0601wcrA0.6691.370.0880.7762.7.1.69NA
100.0603es3A0.7262.270.0600.8661.16.3.1NA
110.0602fenD0.6922.120.1360.9105.5.1.2NA
120.0602htnG0.7352.570.0600.9251.16.3.1NA
130.0601bg7A0.6511.630.0310.7911.16.3.1NA
140.0601biqB0.6702.810.1040.9701.17.4.1NA
150.0603c90A0.7162.780.0750.9103.6.1.3127,30
160.0601o9iA0.6912.740.0160.8951.11.1.6NA
170.0601h0nA0.6732.810.0300.9551.17.4.148
180.0603e6sF0.6912.200.0750.8511.16.3.119,33
190.0601xvgC0.6932.810.0750.9701.14.13.2557
200.0601mfrW0.7132.020.0750.8511.16.3.1NA
210.0601gaiA0.6882.880.1040.9853.2.1.3NA
220.0601krqA0.6961.900.0300.8361.16.3.161
230.0601cxzB0.6681.770.0360.8062.7.11.1336
240.0601r03A0.7241.920.0750.8511.16.3.119
250.0602uw1B0.7232.640.0750.9251.14.99.6NA

(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
00.270.7851.710.091.004x5mB GO:0005886 GO:0006810 GO:0008643 GO:0016020 GO:0016021
10.260.7491.780.110.994rngC GO:0016020 GO:0016021
20.210.7542.220.030.973uo2B GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0006457 GO:0006626 GO:0009060 GO:0016226 GO:0051087 GO:0051259
30.200.7441.840.110.994qncB GO:0005355 GO:0005886 GO:0006810 GO:0008643 GO:0015758 GO:0016020 GO:0016021 GO:0042803 GO:1904659
40.180.6591.420.040.731z0jB GO:0000011 GO:0005768 GO:0005829 GO:0005886 GO:0006810 GO:0006895 GO:0006896 GO:0006897 GO:0007596 GO:0008270 GO:0010008 GO:0010009 GO:0015031 GO:0016020 GO:0016197 GO:0017137 GO:0031901 GO:0034058 GO:0034498 GO:0043231 GO:0046872 GO:0070062 GO:0090160 GO:1903358
50.160.6821.350.030.784wheA GO:0005543 GO:0005737 GO:0005829 GO:0005886 GO:0009271 GO:0009408 GO:0016020 GO:0031234 GO:0042802 GO:0043433 GO:0060187
60.160.7752.080.100.994k1nA GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
70.150.6401.330.020.691z0kB GO:0000011 GO:0005768 GO:0005829 GO:0005886 GO:0006810 GO:0006895 GO:0006896 GO:0006897 GO:0007596 GO:0008270 GO:0010008 GO:0010009 GO:0015031 GO:0016020 GO:0016197 GO:0017137 GO:0031901 GO:0034058 GO:0034498 GO:0043231 GO:0046872 GO:0070062 GO:0090160 GO:1903358
80.140.7911.850.071.003nvoA GO:0005385 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006829 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085 GO:0071577 GO:0098655
90.140.7771.790.181.005ctgB GO:0005886 GO:0005887 GO:0006810 GO:0008643 GO:0016020 GO:0016021 GO:0034219 GO:0051119
100.140.7702.100.100.994iggB GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034332 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0051015 GO:0051149 GO:0051291 GO:0071681 GO:0090136 GO:0098641 GO:2000146 GO:2001045 GO:2001240 GO:2001241
110.120.6912.520.070.991st6A GO:0001725 GO:0002009 GO:0002162 GO:0003779 GO:0005198 GO:0005623 GO:0005737 GO:0005743 GO:0005856 GO:0005886 GO:0005903 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005916 GO:0005925 GO:0005927 GO:0007155 GO:0008013 GO:0015629 GO:0016020 GO:0017166 GO:0030018 GO:0030032 GO:0030054 GO:0030334 GO:0030486 GO:0031594 GO:0031625 GO:0034333 GO:0034394 GO:0042383 GO:0042803 GO:0043034 GO:0043234 GO:0043297 GO:0045121 GO:0045294 GO:0045296 GO:0048675 GO:0051015 GO:0051371 GO:0051393 GO:0070062 GO:0070527 GO:0090136 GO:0090636 GO:0090637 GO:0097110 GO:0098723 GO:1903561 GO:1990357
120.120.7512.370.030.993uo3A GO:0005739 GO:0005743 GO:0005758 GO:0005759 GO:0006457 GO:0006626 GO:0009060 GO:0016226 GO:0051087 GO:0051259
130.110.7192.620.040.993bvoA GO:0005634 GO:0005737 GO:0005739 GO:0006457 GO:0016226 GO:0046872 GO:0051087 GO:0051259
140.100.7961.600.091.004k6jB GO:0000775 GO:0000785 GO:0000795 GO:0000798 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005829 GO:0007049 GO:0007062 GO:0007064 GO:0007067 GO:0008156 GO:0008278 GO:0009636 GO:0015630 GO:0016032 GO:0035562 GO:0043231 GO:0045132 GO:0045875 GO:0048146 GO:0051301 GO:0051983 GO:0060623 GO:0071168 GO:0071922
150.100.7772.190.040.994it5B GO:0006457 GO:0016226 GO:0051087 GO:0051259
160.100.7032.430.080.963ck6E GO:0005886 GO:0016020 GO:0016021 GO:0030001 GO:0046873 GO:0055085
170.100.8031.570.091.004k6jA GO:0000775 GO:0000785 GO:0000795 GO:0000798 GO:0005634 GO:0005654 GO:0005694 GO:0005737 GO:0005829 GO:0007049 GO:0007062 GO:0007064 GO:0007067 GO:0008156 GO:0008278 GO:0009636 GO:0015630 GO:0016032 GO:0035562 GO:0043231 GO:0045132 GO:0045875 GO:0048146 GO:0051301 GO:0051983 GO:0060623 GO:0071168 GO:0071922
180.080.6672.100.040.813dyjA GO:0001726 GO:0003779 GO:0005178 GO:0005200 GO:0005737 GO:0005815 GO:0005856 GO:0005886 GO:0005925 GO:0007016 GO:0007044 GO:0007155 GO:0009986 GO:0016020 GO:0017166 GO:0030054 GO:0030274 GO:0030866 GO:0032403 GO:0032587 GO:0042995 GO:0051015 GO:0070062 GO:0070527
190.080.5592.600.040.841dowA GO:0001541 GO:0001669 GO:0005198 GO:0005737 GO:0005794 GO:0005829 GO:0005856 GO:0005886 GO:0005911 GO:0005912 GO:0005913 GO:0005915 GO:0005925 GO:0007015 GO:0007155 GO:0007163 GO:0007406 GO:0007568 GO:0008013 GO:0008584 GO:0014070 GO:0014704 GO:0015629 GO:0016020 GO:0016264 GO:0016342 GO:0016600 GO:0017166 GO:0030027 GO:0030054 GO:0031103 GO:0034613 GO:0042127 GO:0042475 GO:0043066 GO:0043231 GO:0043297 GO:0043627 GO:0044822 GO:0045295 GO:0045296 GO:0045880 GO:0046982 GO:0051015 GO:0051291 GO:0071681 GO:0090136 GO:2000146 GO:2001045 GO:2001240 GO:2001241
200.070.4912.610.080.612c2lA GO:0000151 GO:0000209 GO:0001664 GO:0004842 GO:0005634 GO:0005654 GO:0005737 GO:0005783 GO:0005886 GO:0006281 GO:0006457 GO:0006511 GO:0006515 GO:0006974 GO:0016567 GO:0016874 GO:0019899 GO:0019900 GO:0030018 GO:0030544 GO:0030579 GO:0030674 GO:0030911 GO:0030968 GO:0031072 GO:0031371 GO:0031398 GO:0031625 GO:0031647 GO:0031943 GO:0032091 GO:0032436 GO:0034450 GO:0036503 GO:0042405 GO:0042787 GO:0042803 GO:0043161 GO:0045111 GO:0046332 GO:0051443 GO:0051604 GO:0051787 GO:0051865 GO:0051879 GO:0061630 GO:0070062 GO:0070534 GO:0071218 GO:0090035 GO:1904264


Consensus prediction of GO terms
 
Molecular Function GO:0046983 GO:0042802 GO:0015149 GO:0017016 GO:0046914
GO-Score 0.41 0.41 0.41 0.36 0.36
Biological Processes GO:0051188 GO:0072655 GO:0006461 GO:0006839 GO:0031163 GO:0006605 GO:0006790 GO:0007005 GO:0045333 GO:0035428 GO:0007033 GO:0006896 GO:0048308 GO:0007041 GO:0007599 GO:0050817 GO:0042147 GO:0006906 GO:0042060 GO:0033043 GO:0007030
GO-Score 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.41 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36
Cellular Component GO:0016021 GO:0005886 GO:0031966 GO:0070013 GO:0019866 GO:0031970 GO:0005774 GO:0031988 GO:1903561 GO:0005769 GO:0044440 GO:0098562
GO-Score 0.57 0.52 0.43 0.43 0.43 0.43 0.36 0.36 0.36 0.36 0.36 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.