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I-TASSER results for job id Rv2078

[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 2 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
10.10 30 3qb9A HEM Rep, Mult 16,19,20,23,64,68,71,72,75
20.07 20 2h7hB NUC Rep, Mult 52,53,56,57,59,60,63,64
30.07 20 2e42B NUC Rep, Mult 48,49,52,53,55,56,57,59
40.05 14 3m4cB HEM Rep, Mult 23,26,30,57,60,64,67,71
50.05 14 4jolB III Rep, Mult 73,76,77,80,81
60.04 11 4s1xA III Rep, Mult 57,60,61,63,64,67,68,71,74,75,78
70.04 11 3a5tB NUC Rep, Mult 55,56,59,60,63,67,70,71
80.04 11 2e50P TRE Rep, Mult 70,73,74,77
90.03 9 3eymB EYK Rep, Mult 69,72,73
100.02 7 1w5cB CLA Rep, Mult 8,77,80,83,84,87
110.02 5 4xtlA NA Rep, Mult 5,81,84,87
120.01 2 2ie7A CA Rep, Mult 40,41
130.01 2 1vsgA UUU Rep, Mult 11,14,15,18,21,70
140.01 2 2onjB ANP Rep, Mult 33,34,53,54
150.01 2 3dylB MG Rep, Mult 4,21
160.01 2 1yo7A ZN Rep, Mult 23,27
170.01 2 2ck3G III Rep, Mult 36,40,45,46,49
180.00 1 2ohjA FE Rep, Mult 8,9
190.00 1 2q6qA CO Rep, Mult 72,76
200.00 1 2gciB MRR Rep, Mult 35,39

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
10.2293e7kH0.4751.700.0710.5382.7.11.173
20.1821urfA0.5182.690.0670.6922.7.11.1368,72
30.1241cxzB0.5092.550.1030.6442.7.11.1326
40.0661wu0A0.4613.020.0710.6633.6.3.14NA
50.0603errA0.6033.010.0400.7696.1.1.1115
60.0601syyA0.5622.740.0840.7121.17.4.1NA
70.0601serB0.5413.590.0690.7606.1.1.1161
80.0601mo7A0.3174.440.0760.5673.6.3.911
90.0602iw5A0.6782.570.0620.8271.-.-.-NA
100.0602wl2B0.5783.690.0910.8465.99.1.3NA
110.0602fonB0.5833.170.1240.7881.3.3.6NA
120.0601w27A0.5953.190.0440.8464.3.1.24NA
130.0602vuaA0.3384.690.0520.6353.4.24.69NA
140.0603b8eC0.5783.460.0600.8943.6.3.9NA
150.0602b5uA0.6862.630.0380.8853.1.-.-NA
160.0601biqB0.5713.380.0390.8271.17.4.184
170.0601u7lA0.6373.150.0580.9043.6.3.14NA
180.0601rsrB0.5713.360.0390.8271.17.4.182
190.0601sc7A0.5672.860.0790.7125.99.1.2NA
200.0602np0A0.5763.870.0290.8943.4.24.69NA
210.0601a31A0.4323.400.0600.6735.99.1.2NA
220.0601x75B0.4372.710.0650.5965.99.1.3NA
230.0601is2A0.5792.750.0710.7311.3.3.624

(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
00.350.7542.300.070.883ajwA GO:0003774 GO:0005886 GO:0006810 GO:0006935 GO:0009288 GO:0015031 GO:0016020 GO:0044781 GO:0071973
10.320.6663.040.070.903ofnY GO:0005739 GO:0005743 GO:0005756 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0045261 GO:0046933 GO:0046961
20.310.7682.410.040.943oehY GO:0005739 GO:0005743 GO:0005756 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0045261 GO:0046933 GO:0046961
30.290.4651.660.070.542x7rC GO:0002223 GO:0005198 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:0044174 GO:0044175 GO:0046718 GO:0055036 GO:0075509 GO:0075512
40.250.6223.470.060.942jj1G GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
50.220.6782.310.080.801ohhG GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
60.220.5791.910.060.673k9aA
70.190.5951.950.060.683p30A
80.170.6382.770.020.862f43G GO:0000275 GO:0005739 GO:0005740 GO:0005743 GO:0005753 GO:0006119 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0045261 GO:0046034 GO:0046933 GO:0046961
90.150.5873.240.050.872w6gG GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
100.140.7342.360.060.904xd7G GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0042777 GO:0045261 GO:0046933 GO:0046961
110.130.5412.410.080.663cp1A GO:0005198 GO:0019031
120.130.7332.410.040.904e68A GO:0000790 GO:0000978 GO:0000981 GO:0001077 GO:0001103 GO:0001228 GO:0001659 GO:0001754 GO:0003677 GO:0003700 GO:0004871 GO:0004879 GO:0005634 GO:0005654 GO:0005737 GO:0005739 GO:0005743 GO:0005829 GO:0005886 GO:0006351 GO:0006355 GO:0006366 GO:0006606 GO:0006953 GO:0007165 GO:0007259 GO:0007568 GO:0008134 GO:0008283 GO:0008285 GO:0010033 GO:0010628 GO:0010730 GO:0014070 GO:0016310 GO:0019221 GO:0019827 GO:0019901 GO:0019903 GO:0019953 GO:0030522 GO:0031490 GO:0031730 GO:0032355 GO:0032870 GO:0033210 GO:0034097 GO:0035259 GO:0035278 GO:0040014 GO:0042493 GO:0042517 GO:0042593 GO:0042755 GO:0042802 GO:0043066 GO:0043434 GO:0043565 GO:0044212 GO:0044320 GO:0044321 GO:0045471 GO:0045747 GO:0045820 GO:0045893 GO:0045944 GO:0046902 GO:0046983 GO:0048708 GO:0051726 GO:0060019 GO:0060259 GO:0060396 GO:0060397 GO:0060548 GO:0070102 GO:0071345 GO:0071407 GO:0090575 GO:0097009 GO:1901215 GO:1902728 GO:1902895 GO:1904685 GO:2000637 GO:2000737 GO:2001171 GO:2001223
130.120.5822.650.020.753wfvA 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
140.120.6083.680.070.983oehP GO:0005739 GO:0005743 GO:0005756 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0045261 GO:0046933 GO:0046961
150.120.7192.860.050.954b2qG GO:0005739 GO:0005743 GO:0005756 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0045261 GO:0046933 GO:0046961
160.110.6083.370.030.924yxwG GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
170.110.6283.380.070.932jizG GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
180.100.7012.930.040.965araG GO:0005739 GO:0005743 GO:0005753 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0016887 GO:0043209 GO:0044822 GO:0045261 GO:0046933 GO:0046961 GO:0070062
190.090.7442.500.080.901i49A GO:0001726 GO:0005525 GO:0005737 GO:0005829 GO:0005886 GO:0005913 GO:0005938 GO:0006928 GO:0007264 GO:0019904 GO:0030032 GO:0030036 GO:0030742 GO:0031529 GO:0032588 GO:0034315 GO:0048365 GO:0070273 GO:0098609 GO:0098641
200.070.5993.690.070.943oaaG GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0042777 GO:0045261 GO:0046933 GO:0046961
210.070.6173.040.070.885dn6G GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0042777 GO:0045261 GO:0046933 GO:0046961
220.070.5673.110.080.842qe7G GO:0005524 GO:0005886 GO:0006754 GO:0006810 GO:0006811 GO:0015986 GO:0015992 GO:0016020 GO:0042777 GO:0045261 GO:0046933 GO:0046961
230.070.5054.150.040.814w9uB GO:0003995 GO:0004361 GO:0008152 GO:0016491 GO:0016627 GO:0050660 GO:0055114


Consensus prediction of GO terms
 
Molecular Function GO:0046933 GO:0046961 GO:0003723 GO:0003774
GO-Score 0.65 0.65 0.50 0.35
Biological Processes GO:0015986 GO:0020012 GO:0072583 GO:0019080 GO:0050687 GO:0019065 GO:0044650 GO:0044800 GO:0019049 GO:0016485 GO:0050690 GO:0002220 GO:0015031 GO:0071973 GO:0044781 GO:0006935
GO-Score 0.65 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.35 0.35 0.35 0.35
Cellular Component GO:0036338 GO:0044174 GO:0044218 GO:0005756 GO:1903561 GO:0031988 GO:0031224 GO:0005886 GO:0009288
GO-Score 0.59 0.59 0.59 0.53 0.50 0.50 0.47 0.35 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.