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I-TASSER results for job id Rv1780

[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
10.04 2 1bp1A PC1 Rep, Mult 9,12,63,65,76,78,101,107,109,118,121,159,163,167,170,171,175
20.04 2 2dysN DCW Rep, Mult 127,156
30.04 2 2ckjD FES Rep, Mult 12,13,17,62,63,64
40.04 2 2hbkA MN Rep, Mult 41,148
50.04 2 2b51A MN Rep, Mult 70,87
60.02 1 1wrkB TFP Rep, Mult 11,12
70.02 1 4ep7B MG Rep, Mult 70,83
80.02 1 1smyF MG Rep, Mult 54,151
90.02 1 3mouB XE Rep, Mult 21,78,167
100.02 1 1usu1 III Rep, Mult 62,76,78,125,127,129,131,142,148
110.02 1 2obdA UUU Rep, Mult 122,123,124,160,161
120.02 1 2wl3A CA Rep, Mult 42,91
130.02 1 3ke6B MN Rep, Mult 32,33,35
140.02 1 1yklG DHB Rep, Mult 46,47
150.02 1 3a0bd CLA Rep, Mult 147,151
160.02 1 1k9zA ZN Rep, Mult 32,162
170.02 1 3ehbB HEA Rep, Mult 80,163
180.02 1 2ckjD PO4 Rep, Mult 78,107,118,120
190.02 1 1h9jA MOO Rep, Mult 106,109
200.02 1 4gfjA ZN Rep, Mult 11,179

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
10.0601fo4A0.4305.380.0620.7381.17.1.4NA
20.0603d35A0.4524.000.0930.6312.3.1.48NA
30.0601sojL0.4454.370.0420.6523.1.4.1714,66
40.0601z45A0.4484.470.0480.6635.1.3.2,5.1.3.3NA
50.0603b9jC0.4974.970.0560.7911.17.3.2,1.17.1.4NA
60.0601wqlA0.4354.840.0560.6741.14.12.-32
70.0602x4mA0.4744.990.0340.7753.4.23.4858,81,128
80.0603hkzJ0.4555.170.0960.7272.7.7.6129
90.0603b8eC0.4434.960.0200.7273.6.3.929,33
100.0601jroB0.4994.800.0520.7811.1.1.204178
110.0601eulA0.4254.820.0520.6793.6.3.8NA
120.0602qykB0.4354.280.0500.6263.1.4.1720,62
130.0601zklA0.4334.490.0440.6313.1.4.17NA
140.0601mo7A0.2844.760.0310.4333.6.3.920,163
150.0601rm6A0.4904.630.0520.7491.3.99.20NA
160.0601e3pA0.4504.350.0640.6632.7.7.8127
170.0601b65A0.4345.260.0910.7273.4.11.956,81,99
180.0603msuA0.4565.100.0480.7592.3.3.163
190.0601ndoA0.4344.830.0470.6631.14.12.1218,26,170

(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
00.290.8272.570.100.975i7kB GO:0002376 GO:0005576 GO:0005615 GO:0008289 GO:0019731 GO:0042742 GO:0045087 GO:0050828 GO:0050891 GO:1900229 GO:1902305
10.220.7083.250.090.913zpmA GO:0001659 GO:0005576 GO:0008289 GO:0050828
20.160.6433.200.040.833uv1A GO:0005576
30.120.6313.740.070.854kegA GO:0002376 GO:0005215 GO:0005363 GO:0005576 GO:0005615 GO:0006810 GO:0006974 GO:0008289 GO:0008643 GO:0015768 GO:0019731 GO:0030288 GO:0034289 GO:0042597 GO:0042742 GO:0042956 GO:0043190 GO:0045087 GO:0050828 GO:0050891 GO:0055052 GO:0060326 GO:1900229 GO:1901982 GO:1902305 GO:1990060
40.100.6493.220.050.843h4zA GO:0005215 GO:0005363 GO:0005576 GO:0006810 GO:0006974 GO:0008643 GO:0015768 GO:0030288 GO:0034289 GO:0042597 GO:0042956 GO:0043190 GO:0055052 GO:0060326 GO:1901982 GO:1990060
50.090.6153.920.040.874m4dA GO:0001530 GO:0001889 GO:0002232 GO:0002281 GO:0002376 GO:0005102 GO:0005576 GO:0005615 GO:0006810 GO:0006869 GO:0006953 GO:0008228 GO:0008289 GO:0009986 GO:0015920 GO:0016020 GO:0031663 GO:0032490 GO:0032496 GO:0032720 GO:0032722 GO:0032755 GO:0032757 GO:0032760 GO:0034145 GO:0042535 GO:0042742 GO:0043032 GO:0044130 GO:0045087 GO:0050829 GO:0050830 GO:0060100 GO:0060265 GO:0070062 GO:0070891 GO:0071222 GO:0071223 GO:0090023 GO:0090559
60.090.6563.690.030.891bp1A GO:0001530 GO:0005576 GO:0005615 GO:0005737 GO:0005887 GO:0006955 GO:0008289 GO:0016020 GO:0032715 GO:0032717 GO:0032720 GO:0042742 GO:0043031 GO:0050829 GO:0070062
70.070.6053.710.060.834ewsA GO:0005319 GO:0005548 GO:0005576 GO:0005615 GO:0006629 GO:0006641 GO:0006810 GO:0006869 GO:0006898 GO:0008202 GO:0008203 GO:0008289 GO:0010745 GO:0010874 GO:0015485 GO:0015914 GO:0017127 GO:0017129 GO:0030301 GO:0031210 GO:0031982 GO:0034197 GO:0034364 GO:0034372 GO:0034374 GO:0034375 GO:0042157 GO:0042632 GO:0043691 GO:0046470 GO:0055088 GO:0055091 GO:0070062 GO:0070328
80.070.5313.600.040.721usvF GO:0001671 GO:0005737 GO:0006457 GO:0006950 GO:0032781 GO:0034605 GO:0051087
90.060.3705.370.040.653d8uB GO:0003677 GO:0003700 GO:0006351 GO:0006355
100.060.3754.590.030.574uwhA GO:0000045 GO:0000166 GO:0000910 GO:0004672 GO:0005524 GO:0005768 GO:0005770 GO:0005776 GO:0005829 GO:0005930 GO:0005942 GO:0006468 GO:0006661 GO:0006914 GO:0007032 GO:0007049 GO:0016020 GO:0016236 GO:0016301 GO:0016303 GO:0016310 GO:0016485 GO:0016740 GO:0030496 GO:0030670 GO:0031410 GO:0032465 GO:0034162 GO:0035004 GO:0035032 GO:0036092 GO:0042149 GO:0043201 GO:0045022 GO:0045335 GO:0046854 GO:0048015 GO:0050708 GO:0051301
110.060.3385.250.040.563ihyC GO:0000045 GO:0000166 GO:0000910 GO:0004672 GO:0005524 GO:0005768 GO:0005770 GO:0005776 GO:0005829 GO:0005930 GO:0005942 GO:0006468 GO:0006661 GO:0006914 GO:0007032 GO:0007049 GO:0016020 GO:0016236 GO:0016301 GO:0016303 GO:0016310 GO:0016485 GO:0016740 GO:0030496 GO:0030670 GO:0031410 GO:0032465 GO:0034162 GO:0035004 GO:0035032 GO:0036092 GO:0042149 GO:0043201 GO:0045022 GO:0045335 GO:0046854 GO:0048015 GO:0050708 GO:0051301
120.060.3305.800.070.593r9rA GO:0000166 GO:0004639 GO:0005524 GO:0006164 GO:0006189 GO:0016874
130.060.2516.430.020.524kp1A GO:0003861 GO:0008152 GO:0008652 GO:0009082 GO:0009097 GO:0009098 GO:0016829 GO:0016836 GO:0046872 GO:0047508 GO:0050075 GO:0051536 GO:0051539
140.060.2585.310.070.431l0qA GO:0016020 GO:0016021
150.060.2995.500.020.514yplC GO:0000166 GO:0004176 GO:0004252 GO:0005524 GO:0005737 GO:0006508 GO:0006515 GO:0008233 GO:0008236 GO:0016787 GO:0016887 GO:0030163 GO:0033554 GO:0043565
160.060.3374.950.070.554ds4D GO:0000166 GO:0003676 GO:0003677 GO:0003824 GO:0003887 GO:0004518 GO:0006139 GO:0006260 GO:0006261 GO:0008408 GO:0016740 GO:0016779 GO:0016787 GO:0046872 GO:0071897 GO:0090305
170.060.3525.080.030.571lrwA GO:0005509 GO:0015945 GO:0016020 GO:0016491 GO:0016614 GO:0030288 GO:0042597 GO:0046872 GO:0052930 GO:0052931 GO:0052932 GO:0052933 GO:0055114
180.060.2874.900.060.461j6xB GO:0003824 GO:0005506 GO:0009372 GO:0016829 GO:0043768 GO:0046872
190.060.2855.980.050.523k13C GO:0005829 GO:0008168 GO:0008270 GO:0008705 GO:0008898 GO:0009086 GO:0016740 GO:0031419 GO:0032259 GO:0042558 GO:0044237 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0008289 GO:0015154 GO:0048030
GO-Score 0.51 0.42 0.42
Biological Processes GO:0050828 GO:0034286 GO:0034288 GO:0070887 GO:0015774 GO:0033554 GO:0006935 GO:0016477 GO:0015766 GO:1902305 GO:0045087 GO:1900229 GO:0050891 GO:0019731
GO-Score 0.51 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.37 0.37 0.37 0.37 0.37
Cellular Component GO:0098533 GO:0005887 GO:0030313 GO:0098797 GO:0005615
GO-Score 0.42 0.42 0.42 0.42 0.37

(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.