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I-TASSER results for job id Rv0401

[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
10.08 4 1u6hA III Rep, Mult 42,45,47,48,49,51,82,95,99,102,110,113
20.08 4 5c65A 37X Rep, Mult 70,104
30.04 2 3v2d2 MG Rep, Mult 106,110
40.04 2 1y7iA SAL Rep, Mult 54,83,84
50.04 2 2ljcA RIM Rep, Mult 95,98,99
60.04 2 2uxhB QUE Rep, Mult 7,10,11,28,50,73,74,77,78,81
70.04 2 4ryrA MPG Rep, Mult 77,78,85,94,97,98,101
80.02 1 1m56G CA Rep, Mult 13,16,44,46
90.02 1 1g42A CA Rep, Mult 66,69
100.02 1 3uoiW HEM Rep, Mult 72,79,106,110
110.02 1 3k7tB GP7 Rep, Mult 34,36,39
120.02 1 2wsc2 CLA Rep, Mult 47,54
130.02 1 2gsmA CA Rep, Mult 86,91,93,96,97
140.02 1 3ae5C EPH Rep, Mult 14,82,85

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
10.1673dwwA0.6063.480.0930.8705.3.99.350,77
20.0601yqwR0.6103.760.0750.9191.12.2.174
30.0602occN0.5993.150.0750.8131.9.3.1NA
40.0601fgjA0.5883.920.0660.8621.7.3.4NA
50.0601z8lA0.5674.370.0430.9353.4.17.21NA
60.0602pnoL0.6413.230.1280.8864.4.1.2073,106
70.0601b8fA0.5723.820.0600.8544.3.1.3NA
80.0602ix6E0.5943.970.0750.8941.3.3.6NA
90.0601cc1L0.6013.920.0490.9111.12.99.6106
100.0602jifA0.5543.770.0650.8131.3.99.-NA
110.0603gzhA0.5574.280.0670.8624.3.2.2NA
120.0602ebaA0.5614.070.0820.8701.3.99.7NA
130.0603djlA0.5564.360.0670.9511.3.99.-NA
140.0602uxwA0.5973.810.0870.8781.3.99.-NA
150.0603b8eC0.5234.310.0460.8293.6.3.941
160.0603fedA0.5753.940.0430.9113.4.17.21NA
170.0602pmzQ0.4664.190.0700.7562.7.7.695
180.0602v8tA0.5564.500.1230.9111.11.1.6NA
190.0601m56A0.6223.860.0820.9681.9.3.144
200.0603ii9C0.5794.030.0710.8861.3.99.7NA

(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
00.170.6563.190.120.945duoA GO:0005886 GO:0006810 GO:0008289 GO:0016020 GO:0016021 GO:0033013 GO:0046906
10.160.6553.340.120.951r0dA GO:0003779 GO:0005543 GO:0005737 GO:0005856 GO:0005905 GO:0006897 GO:0006898 GO:0006915 GO:0012505 GO:0016020 GO:0030136 GO:0030276 GO:0030665 GO:0031410 GO:0035091 GO:0043231 GO:0048471 GO:0072583
20.110.6963.320.110.982jswA 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
30.110.5123.440.060.764onsC GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
40.100.7142.830.080.924rymA GO:0005886 GO:0006810 GO:0016020 GO:0016021 GO:0033013 GO:0046906
50.090.6792.730.100.851st6A 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
60.080.6413.710.070.964av6A GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
70.070.5713.950.090.922mgyA GO:0005497 GO:0005737 GO:0005739 GO:0005741 GO:0006694 GO:0006810 GO:0006811 GO:0006821 GO:0006869 GO:0007268 GO:0007568 GO:0008347 GO:0008503 GO:0010042 GO:0010266 GO:0010823 GO:0010940 GO:0014012 GO:0016020 GO:0016021 GO:0030325 GO:0031397 GO:0031965 GO:0031966 GO:0032570 GO:0032720 GO:0033574 GO:0042493 GO:0043065 GO:0043231 GO:0044325 GO:0045019 GO:0048265 GO:0048266 GO:0048678 GO:0050810 GO:0051901 GO:0051928 GO:0060242 GO:0060252 GO:0060253 GO:0070062 GO:0071222 GO:0071294 GO:0071476 GO:0072655 GO:0072656 GO:0098794 GO:0099565 GO:1903147 GO:1903579 GO:2000379
80.070.6093.190.090.834iggB 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
90.070.6643.170.070.954a01A GO:0004427 GO:0005773 GO:0005774 GO:0006810 GO:0006811 GO:0009678 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0046872 GO:0055085
100.070.5173.510.050.774p9tA GO:0005198 GO:0005634 GO:0005737 GO:0005856 GO:0005886 GO:0005912 GO:0005913 GO:0007155 GO:0007275 GO:0007409 GO:0015629 GO:0016020 GO:0016323 GO:0016337 GO:0021942 GO:0030027 GO:0030054 GO:0030154 GO:0030424 GO:0042995 GO:0045296 GO:0048813 GO:0048854 GO:0051015 GO:0051823 GO:0060134 GO:0097481
110.070.5613.910.080.875ic0A 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
120.070.5732.730.020.731sj8A 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
130.070.5063.270.080.751dowA 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
140.070.4694.280.050.784wnlC GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0005789 GO:0005934 GO:0006810 GO:0007533 GO:0008289 GO:0008298 GO:0051028
150.070.5462.760.050.714k1nA 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
160.070.6613.160.070.944av3B GO:0000287 GO:0004427 GO:0005509 GO:0005886 GO:0005887 GO:0006810 GO:0006811 GO:0006814 GO:0009678 GO:0015081 GO:0015992 GO:0016020 GO:0016021 GO:0016787 GO:0030955 GO:0035725 GO:0042803 GO:0046872
170.070.4754.050.070.743mdsA GO:0004784 GO:0006801 GO:0016491 GO:0019430 GO:0046872 GO:0055114
180.070.4683.970.050.721rccA GO:0005623 GO:0006826 GO:0006879 GO:0008199 GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0008092 GO:1901363 GO:0097159 GO:0032403
GO-Score 0.51 0.48 0.48 0.41
Biological Processes GO:1901564 GO:0046483 GO:0006725 GO:1901360 GO:0022610 GO:0012501 GO:0006897
GO-Score 0.51 0.51 0.51 0.51 0.41 0.33 0.33
Cellular Component GO:0005886 GO:0031224 GO:0005856 GO:0098589 GO:0030662 GO:0012505
GO-Score 0.41 0.40 0.33 0.33 0.33 0.33

(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.