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I-TASSER results for job id Rv0742

[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
10.13 5 3potB UUU Rep, Mult 55,62
20.08 3 5kc1J III Rep, Mult 48,51,52,55,62,63
30.03 1 3ar2A NA Rep, Mult 87,89,91
40.03 1 2xqtE CVM Rep, Mult 62,65
50.03 1 2w6dA GDP Rep, Mult 75,76,78,79,120
60.03 1 2eauA PTY Rep, Mult 84,86,113,117,121
70.03 1 3ojaB MAN Rep, Mult 48,51
80.03 1 3qmkB SGN Rep, Mult 73,124
90.03 1 1p3uA NO Rep, Mult 23,26,27
100.03 1 1pprM PID Rep, Mult 80,84
110.03 1 2w6dB CPL Rep, Mult 88,89,112,113,115
120.03 1 2dqsA PTY Rep, Mult 40,44,51,154
130.03 1 3ar3A PTY Rep, Mult 25,28,32,36,169

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
10.0601mo7A0.1825.270.0280.2913.6.3.975,116
20.0602pdaA0.4074.400.0870.6061.2.7.1NA
30.0603i9wA0.5483.530.0490.7662.7.13.382,89,120
40.0602cseA0.3994.640.0710.6172.7.7.50NA
50.0601mc0A0.3144.130.0220.4573.1.4.17NA
60.0602b5uA0.4494.040.0860.6173.1.-.-NA
70.0601b8fA0.3994.400.0860.5894.3.1.3NA
80.0603ixzA0.5244.510.0730.7893.6.3.10NA
90.0601z0hB0.2345.020.0190.3713.4.24.6975
100.0603a1cB0.2504.870.0280.4113.6.3.-88
110.0602hkjA0.3224.940.0130.5095.99.1.3123
120.0603b8cA0.4804.130.0360.6573.6.3.6NA
130.0603iydD0.4105.590.0290.7492.7.7.6NA
140.0603b8cB0.4804.130.0360.6573.6.3.684,115
150.0601y2mB0.4075.160.0520.7094.3.1.24NA
160.0603b8eC0.5224.620.0720.8063.6.3.995,110
170.0601u7lA0.4005.410.0300.6973.6.3.14NA
180.0601ynnJ0.2266.170.0490.4512.7.7.695,97
190.0602iw5A0.4994.610.0360.7431.-.-.-NA

(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
00.170.6523.800.060.894gnkE GO:0003073 GO:0004435 GO:0004629 GO:0004871 GO:0005509 GO:0005516 GO:0005654 GO:0005829 GO:0005913 GO:0006629 GO:0006892 GO:0007165 GO:0007186 GO:0007223 GO:0007268 GO:0008081 GO:0016020 GO:0016042 GO:0016787 GO:0035556 GO:0042383 GO:0043234 GO:0043647 GO:0098609 GO:0098641
10.140.7722.770.020.941jadA GO:0004435 GO:0004629 GO:0004871 GO:0005509 GO:0005829 GO:0006629 GO:0007165 GO:0008081 GO:0016042 GO:0016787 GO:0035556
20.110.6863.220.100.874aurA GO:0005525
30.080.6433.680.050.884wicA GO:0042025 GO:0050792
40.070.5453.940.020.763q0kD GO:0005215 GO:0005654 GO:0005737 GO:0005768 GO:0005769 GO:0005829 GO:0005856 GO:0005886 GO:0005901 GO:0005911 GO:0005913 GO:0005925 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0019898 GO:0030036 GO:0030100 GO:0030659 GO:0031410 GO:0032587 GO:0036010 GO:0042802 GO:0042995 GO:0043231 GO:0045806 GO:0048858 GO:0055038 GO:0070062 GO:0070300 GO:0070836 GO:0072584 GO:0097320 GO:0098609 GO:0098641
50.070.5373.820.040.743qniA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
60.070.5273.760.030.713haiA GO:0005543 GO:0005737 GO:0005768 GO:0005829 GO:0005886 GO:0006897 GO:0007015 GO:0008092 GO:0008289 GO:0016020 GO:0030054 GO:0030100 GO:0030137 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0043005 GO:0043209 GO:0043679 GO:0045202 GO:0045806 GO:0048471 GO:0048488 GO:0048666 GO:0048812 GO:0072657 GO:0090002 GO:0097320 GO:1900006
70.060.4233.460.020.572lemA GO:0001523 GO:0001540 GO:0001932 GO:0001935 GO:0002740 GO:0005319 GO:0005543 GO:0005548 GO:0005576 GO:0005615 GO:0005634 GO:0005829 GO:0006629 GO:0006644 GO:0006656 GO:0006695 GO:0006810 GO:0006869 GO:0006898 GO:0007186 GO:0007229 GO:0007584 GO:0008035 GO:0008104 GO:0008202 GO:0008203 GO:0008211 GO:0008289 GO:0009986 GO:0010804 GO:0010873 GO:0010898 GO:0010903 GO:0015485 GO:0015914 GO:0017127 GO:0018158 GO:0018206 GO:0019433 GO:0019899 GO:0019915 GO:0030139 GO:0030300 GO:0030301 GO:0030325 GO:0031100 GO:0031103 GO:0031210 GO:0031410 GO:0032489 GO:0033344 GO:0033700 GO:0034115 GO:0034190 GO:0034191 GO:0034361 GO:0034364 GO:0034365 GO:0034366 GO:0034372 GO:0034375 GO:0034380 GO:0035025 GO:0042157 GO:0042158 GO:0042493 GO:0042627 GO:0042632 GO:0042802 GO:0043534 GO:0043627 GO:0043691 GO:0045499 GO:0045723 GO:0046470 GO:0050713 GO:0050728 GO:0050821 GO:0050919 GO:0051006 GO:0051180 GO:0051345 GO:0051346 GO:0051496 GO:0055091 GO:0055102 GO:0060192 GO:0060228 GO:0060354 GO:0060761 GO:0070062 GO:0070328 GO:0070508 GO:0070653 GO:0071813 GO:0072562 GO:1900026 GO:1903561
80.060.5583.680.030.764bneA GO:0005737 GO:0005768 GO:0005769 GO:0005802 GO:0005829 GO:0005856 GO:0005886 GO:0005901 GO:0005925 GO:0006897 GO:0008092 GO:0008289 GO:0016020 GO:0030036 GO:0030054 GO:0030100 GO:0030659 GO:0031410 GO:0032587 GO:0042995 GO:0045806 GO:0055038 GO:0070300 GO:0070836 GO:0097320
90.060.5014.060.020.712j68A GO:0000166 GO:0003924 GO:0005525 GO:0005886 GO:0008289 GO:0016020 GO:0016021 GO:0016787
100.060.3205.470.060.575i0nA GO:0000166 GO:0000287 GO:0002561 GO:0003796 GO:0003824 GO:0004430 GO:0005524 GO:0005739 GO:0005765 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006661 GO:0008152 GO:0009253 GO:0016020 GO:0016023 GO:0016301 GO:0016310 GO:0016740 GO:0016787 GO:0016798 GO:0016998 GO:0019835 GO:0030054 GO:0030425 GO:0030672 GO:0031083 GO:0031224 GO:0031410 GO:0031901 GO:0032403 GO:0035651 GO:0035838 GO:0042734 GO:0042742 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043234 GO:0044231 GO:0045121 GO:0045202 GO:0046854 GO:0070382 GO:0098779
110.060.3454.750.020.541xzpA GO:0000166 GO:0002098 GO:0003924 GO:0005525 GO:0005622 GO:0005737 GO:0006400 GO:0008033 GO:0016787 GO:0030488 GO:0046872
120.060.2754.800.020.434dcsA GO:0000027 GO:0000166 GO:0003924 GO:0005525 GO:0005737 GO:0042254 GO:0043022
130.060.3003.360.060.383kwoA GO:0005737 GO:0006879 GO:0006950 GO:0008199 GO:0016491 GO:0042262 GO:0046872 GO:0055114
140.060.2904.050.010.392wm9A GO:0005085 GO:0005829 GO:0005913 GO:0007264 GO:0007596 GO:0012505 GO:0016020 GO:0043547 GO:0098609 GO:0098641
150.060.2424.320.040.354hndA GO:0000166 GO:0000287 GO:0002561 GO:0004430 GO:0005524 GO:0005739 GO:0005765 GO:0005768 GO:0005794 GO:0005829 GO:0005886 GO:0005887 GO:0006661 GO:0016020 GO:0016023 GO:0016301 GO:0016310 GO:0016740 GO:0030054 GO:0030425 GO:0030672 GO:0031083 GO:0031224 GO:0031410 GO:0031901 GO:0032403 GO:0035651 GO:0035838 GO:0042734 GO:0042995 GO:0043005 GO:0043025 GO:0043204 GO:0043231 GO:0043234 GO:0044231 GO:0045121 GO:0045202 GO:0046854 GO:0070382 GO:0098779
160.060.2515.950.040.493gb8A 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
170.060.2444.550.040.364g59B GO:0001913 GO:0003823 GO:0005886 GO:0006955 GO:0009897 GO:0016020 GO:0019882 GO:0031225 GO:0042267 GO:0042742 GO:0046658 GO:0046703 GO:0071222 GO:0071360
180.060.2504.520.020.393n6sA GO:0003677 GO:0003690 GO:0005739 GO:0005759 GO:0006351 GO:0006353 GO:0006355 GO:0006393 GO:0007005 GO:0032392 GO:0042645 GO:0044822


Consensus prediction of GO terms
 
Molecular Function GO:0004629 GO:0046872 GO:0045296 GO:0098632
GO-Score 0.57 0.57 0.44 0.44
Biological Processes GO:1901575 GO:0044712 GO:0044238 GO:0007155 GO:0098916 GO:0035567 GO:0019637 GO:0006796 GO:0008217 GO:0048193 GO:0019751
GO-Score 0.57 0.57 0.49 0.44 0.33 0.33 0.33 0.33 0.33 0.33 0.33
Cellular Component GO:0031981 GO:0005912 GO:0005911 GO:0005829 GO:0032991 GO:0005886
GO-Score 0.44 0.44 0.44 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.